+/******************************COPYRIGHT NOTICE*******************************/
+/* (c) Centro de Regulacio Genomica */
+/* and */
+/* Cedric Notredame */
+/* 12 Aug 2014 - 22:07. */
+/*All rights reserved. */
+/*This file is part of T-COFFEE. */
+/* */
+/* T-COFFEE is free software; you can redistribute it and/or modify */
+/* it under the terms of the GNU General Public License as published by */
+/* the Free Software Foundation; either version 2 of the License, or */
+/* (at your option) any later version. */
+/* */
+/* T-COFFEE is distributed in the hope that it will be useful, */
+/* but WITHOUT ANY WARRANTY; without even the implied warranty of */
+/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the */
+/* GNU General Public License for more details. */
+/* */
+/* You should have received a copy of the GNU General Public License */
+/* along with Foobar; if not, write to the Free Software */
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */
+/*............................................... */
+/* If you need some more information */
+/* cedric.notredame@europe.com */
+/*............................................... */
+/******************************COPYRIGHT NOTICE*******************************/
char *PerlScriptName[]={"rec_sum.pl","count.pl","p\
rocess_list.pl","make_license.pl","CCsed.script","\
msa2bootstrap.pl","t_coffee_dpa","t_coffee_dpa2","\
-tc_generic_method.pl","generic_method.tc_method","\
-clustalw_method.tc_method","extract_from_pdb","ins\
-tall.pl","clean_cache.pl","nature_protocol.pl","mo\
-cca","dalilite.pl","wublast.pl","blastpgp.pl","ncb\
-iblast_lwp.pl","wublast_lwp.pl","RNAplfold2tclib.p\
-l","fasta_seq2RNAplfold_templatefile.pl","fasta_se\
-q2hmmtop_fasta.pl","fasta_seq2consan_aln.pl","clus\
-talw_aln2fasta_aln.pl","msf_aln2fasta_aln.pl","bla\
-st_aln2fasta_aln.pl","blast_xml2fasta_aln.pl","fas\
-ta_aln2fasta_aln_unique_name.pl","newick2name_list\
-.pl","excel2fasta.pl","any_file2unix_file.pl","End\
-List"};char *PerlScriptFile[]={"use File::Copy;\nu\
-se Env qw(HOST);\nuse Env qw(HOME);\nuse Env qw(US\
-ER);\n$x_field=0;\n$y_field=1;\n$interval=0;\n$fil\
-e=\"stdin\";\n$print_avg=1;\n$print_sd=0;\n$print_\
+tc_generic_method.pl","rnapdb2protpdb.pl","generic\
+_method.tc_method","clustalw_method.tc_method","ex\
+tract_from_pdb","install.pl","clean_cache.pl","nat\
+ure_protocol.pl","mocca","dalilite.pl","wublast.pl\
+","blastpgp.pl","ncbiblast_lwp.pl","wublast_lwp.pl\
+","RNAplfold2tclib.pl","fasta_seq2RNAplfold_templa\
+tefile.pl","fasta_seq2hmmtop_fasta.pl","fasta_seq2\
+consan_aln.pl","clustalw_aln2fasta_aln.pl","msf_al\
+n2fasta_aln.pl","blast_aln2fasta_aln.pl","blast_xm\
+l2fasta_aln.pl","fasta_aln2fasta_aln_unique_name.p\
+l","newick2name_list.pl","excel2fasta.pl","any_fil\
+e2unix_file.pl","EndList"};char *PerlScriptFile[]=\
+{"use File::Copy;\nuse Env qw(HOST);\nuse Env qw(H\
+OME);\nuse Env qw(USER);\n$x_field=0;\n$y_field=1;\
+\n$y_field_set=1;\n$nyf=1;\n\n$interval=0;\n$file=\
+\"stdin\";\n\n$print_avg=1;\n$print_sd=0;\n$print_\
sum=0;\n$print_n=0;\nforeach $value ( @ARGV)\n \
{\n if ($value ne $ARGV[$np]) \n {\n ;\n \
}\n elsif($value eq \"-print_all\")\n {\n \
ax= $ARGV[++$np];\n $np++;\n }\n \n el\
sif ($value eq \"-x\")\n {\n $x_field= $AR\
GV[++$np]-1;\n $np++;\n }\n elsif ($va\
-lue eq \"-y\")\n {\n \n while ($ARGV\
-[$np+1] && !($ARGV[$np+1]=~/\\-/))\n {\n $y\
-_field[$nyf++]=$ARGV[++$np]-1;\n $y_field_set=1;\\
-n }\n\n $np++;\n }\n elsif ($val\
-ue eq \"-file\")\n {\n $file= $ARGV[++$np]\
-;\n $file_set=1;\n $np++;\n } \
- \n elsif ( $value eq \"h\" || $value eq \"-h\" \
-|| $value eq \"-H\" || $value eq \"-help\" || $val\
-ue eq \"help\")\n {\n print STDOUT \"data_an\
-alyse: Analyse and discretization of data\\n\";\n \
- print STDOUT \" -file: <file containi\
-ng the data to analyze>,.<def=STDIN>\\n\";\n p\
-rint STDOUT \" -x: <field containing the X>,\
-...............<Def=0>\\n\";\n print STDOUT \"\
- -y: <field containing the Y>,..............\
-.<Def=1>\\n\";\n print STDOUT \" -i:<Int\
-erval size on the X>,...............<Def=0>\\n\";\\
-n print STDOUT \" -i:<0:only one interva\
-l>\\n\";\n print STDOUT \" -r:<Range of \
-the X>\\n\";\n print STDOUT \" -sd: prin\
-t standard deviation on the Y\";\n print STDOU\
-T \" -h : print column header \\n\";\n \
-exit (0);\n }\n elsif ($value=~/-/)\n {\n \
-print \"$value is not a valid FLAG[FATAL]\\n\";\n \
- exit (0);\n } \n elsif ($list eq \"\") \n \
- {\n $file=$ARGV[$np];\n $np++;\n }\\
-n \n \n }\n\n\n\n\n\nif ($file eq \"stdin\")\\
-n {\n $remove_file=1;\n $file=\"tmp$$\";\n open (F\
-, \">$file\");\n while (<STDIN>)\n {\n print F $\
-_;\n }\n close (F);\n \n ;}\n\n\nopen(F,$file);\\
-n\nif ($interval)\n {\n $interval_size=($max-$\
-min)/$interval;\n }\nwhile (<F>)\n {\n $line=\
-$_;\n if (!/\\S/){next;}\n @list=($line=~/(\\
-\S+)/g);\n \n if ($interval==0){$bin=0;}\n \
- else{$bin=int (($list[$x_field]-$min)/($interval\
-_size));}\n\n \n if ($bin && $bin==$interval\
-){$bin--;}\n for ( $a=0; $a<$nyf; $a++)\n \
-{\n $sum{$a}{$bin}+=$list[$y_field[$a]];\n $sum2{$\
-a}{$bin}+=$list[$y_field[$a]]*$list[$y_field[$a]];\
-\n $n{$a}{$bin}++;\n }\n }\n\nif (!$interval\
-){$interval=1;}\nfor ( $a=0; $a<$interval; $a++)\n\
- {\n printf ( \"%3d %3d \", $interval_size*$a,\
- $interval_size*($a+1));\n for ( $b=0; $b<$nyf;\
- $b++) \n {\n $i=$interval*$a;\n if ( $n{$b}{\
-$a}==0)\n {\n $avg=0;\n $sd=0;\n }\n e\
-lse\n {\n $avg=$sum{$b}{$a}/$n{$b}{$a};\n \
- $sd=sqrt($sum2{$b}{$a}*$n{$b}{$a}-$sum{$b}{$a}*$\
-sum{$b}{$a})/($n{$b}{$a}*$n{$b}{$a});\n }\n if (\
-$print_n) {printf \"%10.4f \", $n{$b}{$a};}\n if (\
-$print_sum){printf \"%10.4f \", $sum{$b}{$a};}\n i\
-f ($print_avg){printf \"%10.4f \", $avg}\n if ($pr\
-int_sd) {printf \"%10.4f \", $sd;}\n }\n p\
-rintf (\"\\n\");\n }\n\n\nif ( $remove_file){unli\
-nk $file;}\n","use File::Copy;\nuse Env qw(HOST);\\
-nuse Env qw(HOME);\nuse Env qw(USER);\n\nforeach $\
-v (@ARGV){$cl.=$v;}\n\n\nif ( $cl=~/-k(\\d+)/){$k=\
-$1;}\nelse {$k=1;}\nif ( $cl=~/-w(\\d+)/){$w=$1;}\\
-nelse {$w=-1;}\nif ( $cl=~/-p(\\d+)/){$p=$1;}\nels\
-e {$p=-1;}\n\nwhile (<STDIN>)\n {\n @l=($_=~/(\
-\\S+)/g);\n $v=$l[$k-1];\n if ( !$h{$v}){@ll\
-=($v, @ll);}\n \n if ( $w==-1)\n {$h{$v\
-}++;}\n else\n {$h{$v}+=$l[$w-1];}\n\n \
-if ($p!=-1){$print{$v}=$l[$p-1];}\n\n }\nforeach \
-$v (@ll)\n {\n print \"$v $print{$v} $h{$v}\\n\
-\";\n }\n","\nuse Env qw(HOST);\nuse Env qw(HOME)\
-;\nuse Env qw(USER);\n$random_tag=int (rand 10000)\
-+1;\n$unique_prefix=\"$$.$HOST.$random_tag\";\n$qu\
-eue=\"distillery.and.mid\";\n$monitor=0;\n$stderr_\
-file=\"/dev/null\";\n$stdio_file=\"/dev/null\";\n$\
-log_file=\"/dev/null\";\n$pause_time=0;\n$max_sub_\
-jobs=60;\n$min_sub_jobs=30;\n$output_all=0;\n$var=\
-'\\$';\n\nforeach $value ( @ARGV)\n {\n if ($va\
-lue ne $ARGV[$np]) \n {\n ;\n }\n elsi\
-f ($value eq \"-max_sub_jobs\")\n {\n $max\
-_sub_jobs= $ARGV[++$np];\n $np++;\n } \
-\n elsif ($value eq \"-min_sub_jobs\" )\n {\n \
- $min_sub_jobs= $ARGV[++$np];\n $np++;\n \
- }\n elsif ($value eq \"-para\")\n {\n \
- $para=1;\n $monitor=1;\n $np++;\n \
- }\n elsif ($value eq \"-monitor\") \n {\n \
- $monitor=1;\n $np++;\n }\n elsif ($value\
- eq \"-no_monitor\") \n {\n $monitor=0;\n \
- $np++;\n }\n elsif ($value eq \"-queue\")\\
-n {\n $queue=$ARGV[++$np];\n $np++;\n \
- } \n elsif ($value eq \"-stderr_file\")\n \
-{\n $stderr_file=$ARGV[++$np];\n $np++;\n \
- }\n elsif ($value eq \"-stdio_file\")\n {\\
-n $stdio_file=$ARGV[++$np];\n $np++;\n \
- }\n elsif ($value eq \"-output_all\")\n {\n \
- $output_all=1;\n $np++;\n }\n elsif ($v\
-alue eq \"-pause\") \n {\n $pause_time=$AR\
+lue eq \"-y\")\n {\n $nyf=0; \n while\
+ ($ARGV[$np+1] && !($ARGV[$np+1]=~/\\-/))\n \
+{\n $y_field[$nyf++]=$ARGV[++$np]-1;\n $y_field_\
+set=1;\n }\n\n $np++;\n }\n elsi\
+f ($value eq \"-file\")\n {\n $file= $ARGV\
+[++$np];\n $file_set=1;\n $np++;\n \
+ } \n elsif ( $value eq \"h\" || $value eq \
+\"-h\" || $value eq \"-H\" || $value eq \"-help\" \
+|| $value eq \"help\")\n {\n print STDOUT \"\
+data_analyse: Analyse and discretization of data\\\
+n\";\n print STDOUT \" -file: <file c\
+ontaining the data to analyze>,.<def=STDIN>\\n\";\\
+n print STDOUT \" -x: <field containing \
+the X>,...............<Def=0>\\n\";\n print ST\
+DOUT \" -y: <field containing the Y>,.......\
+........<Def=1>\\n\";\n print STDOUT \" \
+-i:<Interval size on the X>,...............<Def=0>\
+\\n\";\n print STDOUT \" -i:<0:only one \
+interval>\\n\";\n print STDOUT \" -r:<Ra\
+nge of the X>\\n\";\n print STDOUT \" -s\
+d: print standard deviation on the Y\";\n prin\
+t STDOUT \" -h : print column header \\n\";\
+\n exit (0);\n }\n elsif ($value=~/-/)\n {\
+\n print \"$value is not a valid FLAG[FATAL]\\\
+n\";\n exit (0);\n } \n elsif ($list eq \"\\
+") \n {\n $file=$ARGV[$np];\n $np++;\n\
+ }\n \n \n }\n\n\n\n\n\nif ($file eq \"st\
+din\")\n {\n $remove_file=1;\n $file=\"tmp$$\";\n \
+open (F, \">$file\");\n while (<STDIN>)\n {\n pr\
+int F $_;\n }\n close (F);\n \n ;}\n\n\n\n\nif (\
+$interval && $max)\n {\n $interval_size=($max-\
+$min)/$interval;\n }\nelsif ($interval)\n {\n \
+ open(F,$file); \n my $set_max=0;\n my $set\
+_min=0;\n while (<F>)\n {\n my $v=$_;\n ch\
+omp($v);\n print \"--$v--\";\n \n if ($v<$min ||!$\
+set_min){$set_min=1;$min=$v;}\n if ($v>$max ||!$se\
+t_max){$set_max=1;$max=$v;}\n }\n close (F\
+);\n print \"$min $max uuuu\";\n $interval_s\
+ize=($max-$min)/$interval;\n }\nopen(F,$file); \\
+nwhile (<F>)\n {\n $line=$_;\n if (!/\\S/){\
+next;}\n @list=($line=~/(\\S+)/g);\n \n i\
+f ($interval==0){$bin=0;}\n else{$bin=int (($li\
+st[$x_field]-$min)/($interval_size));}\n\n \n \
+ if ($bin && $bin==$interval){$bin--;}\n for (\
+ $a=0; $a<$nyf; $a++)\n {\n $sum{$a}{$bin}+=$\
+list[$y_field[$a]];\n $sum2{$a}{$bin}+=$list[$y_fi\
+eld[$a]]*$list[$y_field[$a]];\n $n{$a}{$bin}++;\n \
+ }\n }\n\nif (!$interval){$interval=1;}\nfor \
+( $a=0; $a<$interval; $a++)\n {\n printf ( \"%\
+4d %4d \", $interval_size*$a, $interval_size*($a+1\
+));\n for ( $b=0; $b<$nyf; $b++) \n {\n $i\
+=$interval*$a;\n if ( $n{$b}{$a}==0)\n {\n $\
+avg=0;\n $sd=0;\n }\n else\n {\n $avg=\
+$sum{$b}{$a}/$n{$b}{$a};\n $sd=sqrt($sum2{$b}{\
+$a}*$n{$b}{$a}-$sum{$b}{$a}*$sum{$b}{$a})/($n{$b}{\
+$a}*$n{$b}{$a});\n }\n if ($print_n) {printf \"%\
+15.4f \", $n{$b}{$a};}\n if ($print_sum){printf \"\
+%15.4f \", $sum{$b}{$a};}\n if ($print_avg){printf\
+ \"%15.4f \", $avg}\n if ($print_sd) {printf \"%15\
+.4f \", $sd;}\n }\n printf (\"\\n\");\n }\
+\n\n\nif ( $remove_file){unlink $file;}\n","use Fi\
+le::Copy;\nuse Env qw(HOST);\nuse Env qw(HOME);\nu\
+se Env qw(USER);\n\nforeach $v (@ARGV){$cl.=$v;}\n\
+\n\nif ( $cl=~/-k(\\d+)/){$k=$1;}\nelse {$k=1;}\ni\
+f ( $cl=~/-w(\\d+)/){$w=$1;}\nelse {$w=-1;}\nif ( \
+$cl=~/-p(\\d+)/){$p=$1;}\nelse {$p=-1;}\n\nwhile (\
+<STDIN>)\n {\n @l=($_=~/(\\S+)/g);\n $v=$l[\
+$k-1];\n if ( !$h{$v}){@ll=($v, @ll);}\n \n \
+ if ( $w==-1)\n {$h{$v}++;}\n else\n \
+ {$h{$v}+=$l[$w-1];}\n\n if ($p!=-1){$print{$v\
+}=$l[$p-1];}\n\n }\nforeach $v (@ll)\n {\n pr\
+int \"$v $print{$v} $h{$v}\\n\";\n }\n","\nuse En\
+v qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER);\\
+n$random_tag=int (rand 10000)+1;\n$unique_prefix=\\
+"$$.$HOST.$random_tag\";\n$queue=\"distillery.and.\
+mid\";\n$monitor=0;\n$stderr_file=\"/dev/null\";\n\
+$stdio_file=\"/dev/null\";\n$log_file=\"/dev/null\\
+";\n$pause_time=0;\n$max_sub_jobs=60;\n$min_sub_jo\
+bs=30;\n$output_all=0;\n$var='\\$';\n\nforeach $va\
+lue ( @ARGV)\n {\n if ($value ne $ARGV[$np]) \n\
+ {\n ;\n }\n elsif ($value eq \"-max_s\
+ub_jobs\")\n {\n $max_sub_jobs= $ARGV[++$n\
+p];\n $np++;\n } \n elsif ($value eq \\
+"-min_sub_jobs\" )\n {\n $min_sub_jobs= $A\
+RGV[++$np];\n $np++;\n }\n elsif ($val\
+ue eq \"-para\")\n {\n $para=1;\n $mon\
+itor=1;\n $np++;\n }\n elsif ($value e\
+q \"-monitor\") \n {\n $monitor=1;\n $\
+np++;\n }\n elsif ($value eq \"-no_monitor\") \
+\n {\n $monitor=0;\n $np++;\n }\n \
+elsif ($value eq \"-queue\")\n {\n $queue=\
+$ARGV[++$np];\n $np++;\n } \n elsif ($valu\
+e eq \"-stderr_file\")\n {\n $stderr_file=\
+$ARGV[++$np];\n $np++;\n }\n elsif ($value\
+ eq \"-stdio_file\")\n {\n $stdio_file=$AR\
GV[++$np];\n $np++;\n }\n elsif ($value eq\
- \"-log\")\n {\n $log=1;\n \n \
- if ($ARGV[$np+1]=~/\\-\\S+/) \n {\
-\n $log_file=\"stderr\";\n }\n \
- else \n {\n $log_file=$ARGV[++$np]; \
-\n ++$np;\n \n }\n }\n elsif \
-( $value eq \"-com\")\n {\n \n if (!$ARGV[$n\
-p+1]=~/^\\'/) { $com=$ARGV[++$np];}\n else {$com=\
-$ARGV[++$np];}\n\n $np++;\n }\n elsif ( $\
-value eq \"-check\")\n {\n \n if (!$ARGV\
-[$np+1]=~/^\\'/) { $check=$ARGV[++$np];}\n els\
-e {$check=$ARGV[++$np];}\n $np++;\n }\n elsi\
-f ($com eq \"\") \n {\n $com_set=1;\n \
-$com=$ARGV[$np];\n \n $np++;\n }\n els\
-if ($list eq \"\") \n {\n $list_set=1;\n \
- $list=$ARGV[$np];\n $np++;\n }\n elsif \
-( $var_set eq \"\")\n {\n $var_set=1;\n \
- $var=$ARGV[$np];\n $np++;\n }\n }\n\n\n\\
-n\nif ( $com eq \"\"){print \"You Need to Provide \
-a Command [FATAL]\\n\";\n die;\n }\n\n\\
-n\nif ($list_set==0) \n {\n $x= int (rand 10\
-0000)+1;\n $tmp_file_name=\"tmp_file_$x\";\n \
- open ( TMP, \">$tmp_file_name\");\n while (<ST\
-DIN>)\n {\n print TMP $_;\n }\n close\
- (TMP);\n open (F, $tmp_file_name);\n }\nels\
-e \n {\n open (F, $list);\n }\n\nif ($par\
-a==0) \n {\n\n @tc_list= <F>;\n close (\
-F); \n \n foreach $val(@tc_list) \n {\\
-n \n \n \n $loc_com=$com;\\
-n if ($check){$loc_check=$check;}\n \n\
- @i_val=($val=~/([^\\s]+)/g);\n \n \
- if ( $#i_val==0)\n {\n if ($check){$loc_che\
-ck=~s/$var/$i_val[0]/g;}\n $loc_com=~s/$var/$i_\
-val[0]/g;\n }\n else\n {\n for ($n=1; $\
-n<=$#i_val+1;$n++ )\n {\n \n $s\
-ub=\"$var$n\";\n \n $loc_com=~s/$sub\
-/$i_val[$n-1]/g;\n if ($check){$loc_check=~\
-s/$var/$i_val[0]/g;}\n }\n }\n if ( $c\
-heck && -e $loc_check)\n {\n print STDERR \"sk\
-ipping $loc_com...\\n\";\n }\n else\n {\\
-n system \"$loc_com\";\n }\n }\n exit;\\
-n }\n\nelsif ($para==1) \n {\n print STDE\
-RR \"do parallel execution of: \\\"$com $list\\\"\\
-\n\";\n \n if ($log==1) \n {\n if ($log_file\
- eq \"stdout\" || $log_file eq \"stderr\" ) \n {\\
-n $log_file=\"\";\n }\n\n else \n \
- {\n system \"echo LOG FILE> $log_file\";\n \n \
- }\n }\n else \n {\n open ( OUT, \">/dev/\
-null\");\n }\n \n \n $id=0;\n $n_sub=0;\n\
- while ($val=<F>) \n { \n $job\
-_log[$id]=\"$HOME/tmp/$unique_prefix.$id.log_file\\
-";\n \n $job=$unique_prefix.\"_$id\";\n \
- open (JOB, \">$job\");\n \n $loc_com=$co\
-m;\n chop $val;\n\n $loc_com=~s/\\$/$val/g\
-;\n \n print JOB \"#!/bin/csh\\n\";\n pri\
-nt JOB \"#\\$ -cwd\\n\";\n print JOB \"#\\$ -N\
- $unique_prefix\\n\";\n if ($queue && !($queue\
- eq \" \")) {print JOB \"#\\$ -l $queue\\n\";}\n \
- print JOB \"#\\n\"; \n print JOB\
- \"$loc_com\\n\";\n print JOB \"echo FINISHED \
- >> $job_log[$id]\\n\";\n print JOB \"pwd\\n\"\
-;\n \n close (JOB);\n if ( $output_all\
-==1)\n {\n system \"qsub $job > $unique_prefix\\
-"; \n }\n else\n {system \"qsub $job\
- -e $stderr_file -o $stdio_file >$unique_prefix\";\
- \n } \n\n\n\n print STDERR \"\
-$id: $output_all\\n\";\n $n_sub++;\n if ( \
-$max_sub_jobs && $n_sub==$max_sub_jobs) \n {\n $\
-n_sub=monitor_process($min_sub_jobs,@job_log); \
-\n \n } \n \n unlink $uniqu\
-e_prefix;\n sleep $pause_time;\n $id++;\n \
- }\n\n close (OUT);\n close (F);\n\n p\
-rint STDERR \"Your $id Jobs Have Been Submited (NA\
-ME=$unique_prefix)\\n\";\n monitor_process (0, \
-@job_log);\n foreach $file(@job_log) {if (-e $f\
-ile) {unlink($file);}}\n \n }\n\nsub monitor\
-_process ( @job_list)\n {\n my (@job_list)=@\
-_;\n my $min_sub_jobs=shift (@job_list);\n m\
-y $n_sub_jobs;\n my $finished;\n my $n=0;\n\\
-n $n_sub_jobs=-1;\n $finished=0;\n print \
-STDERR \"\\nMonitor Batch: [$min_sub_jobs]\";\n \
- \n while (!$finished && (($n_sub_jobs>$min_\
-sub_jobs)|| $n_sub_jobs==-1) ) \n {\n $finished=1;\
-\n $n_sub_jobs=0;\n $n=0;\n foreach $file (@job_li\
-st)\n {\n \n if (-e $file){;}\n else \n \
- {\n $finished=0; $n_sub_jobs++;\n \
- }\n }\n system \"sleep 1\";\n \
- }\n \n return $n_sub_jobs;\n }\n \n \
- \nif ($tmp_file_name){unlink($tmp_file_name);}\n\
-","\n\nforeach ($np=0; $np<=$#ARGV; $np++)\n {\\
-n $value=$ARGV[$np];\n\n if ($value eq \"-fi\
-le\")\n {\n $file= $ARGV[++$np];\n \
-}\n elsif ($value eq \"-type\")\n {\n \
- $type= $ARGV[++$np];\n }\n elsif ($valu\
-e eq \"-institute\")\n {\n $institute=\
- $ARGV[++$np];\n }\n elsif ($value eq \"-a\
-uthor\")\n {\n $author= $ARGV[++$np];\\
-n }\n elsif ($value eq \"-date\")\n {\
-\n $date= $ARGV[++$np];\n }\n elsi\
-f ($value eq \"-program\")\n {\n $prog\
-ram= $ARGV[++$np];\n }\n elsif ($value eq \
-\"-email\")\n {\n $email= $ARGV[++$np]\
-;\n }\n else\n {\n print \"$value is \
-an unkown argument[FATAL]\\n\";\n exit (1);\n \
- }\n }\n\n\n\nopen F, $file || die;\nprint $INSTI\
-TUTE;\nif ( $type eq \"c\"){print \"/*************\
+ \"-output_all\")\n {\n $output_all=1;\n \
+ $np++;\n }\n elsif ($value eq \"-pause\") \\
+n {\n $pause_time=$ARGV[++$np];\n $np+\
++;\n }\n elsif ($value eq \"-log\")\n {\\
+n $log=1;\n \n if ($ARGV[$np+\
+1]=~/\\-\\S+/) \n {\n $log_file=\"std\
+err\";\n }\n else \n {\\
+n $log_file=$ARGV[++$np]; \n ++$np;\n \n \
+ }\n }\n elsif ( $value eq \"-com\")\
+\n {\n \n if (!$ARGV[$np+1]=~/^\\'/) { $com=\
+$ARGV[++$np];}\n else {$com=$ARGV[++$np];}\n\n \
+ $np++;\n }\n elsif ( $value eq \"-check\")\\
+n {\n \n if (!$ARGV[$np+1]=~/^\\'/) { $c\
+heck=$ARGV[++$np];}\n else {$check=$ARGV[++$np\
+];}\n $np++;\n }\n elsif ($com eq \"\") \n \
+ {\n $com_set=1;\n $com=$ARGV[$np];\n \
+ \n $np++;\n }\n elsif ($list eq \"\") \n\
+ {\n $list_set=1;\n $list=$ARGV[$np];\\
+n $np++;\n }\n elsif ( $var_set eq \"\")\n\
+ {\n $var_set=1;\n $var=$ARGV[$np];\n \
+ $np++;\n }\n }\n\n\n\n\nif ( $com eq \"\")\
+{print \"You Need to Provide a Command [FATAL]\\n\\
+";\n die;\n }\n\n\n\nif ($list_set==0) \
+\n {\n $x= int (rand 100000)+1;\n $tmp_fi\
+le_name=\"tmp_file_$x\";\n open ( TMP, \">$tmp_\
+file_name\");\n while (<STDIN>)\n {\n prin\
+t TMP $_;\n }\n close (TMP);\n open (F,\
+ $tmp_file_name);\n }\nelse \n {\n open (\
+F, $list);\n }\n\nif ($para==0) \n {\n\n \
+ @tc_list= <F>;\n close (F); \n \n for\
+each $val(@tc_list) \n {\n \n \n \
+ \n $loc_com=$com;\n if ($check){$\
+loc_check=$check;}\n \n @i_val=($val=~\
+/([^\\s]+)/g);\n \n if ( $#i_val==0)\n\
+ {\n if ($check){$loc_check=~s/$var/$i_val[0]/\
+g;}\n $loc_com=~s/$var/$i_val[0]/g;\n }\n \
+ else\n {\n for ($n=1; $n<=$#i_val+1;$n++ )\n\
+ {\n \n $sub=\"$var$n\";\n \
+ \n $loc_com=~s/$sub/$i_val[$n-1]/g;\n \
+ if ($check){$loc_check=~s/$var/$i_val[0]/g;}\\
+n }\n }\n if ( $check && -e $loc_check\
+)\n {\n print STDERR \"skipping $loc_com...\\n\
+\";\n }\n else\n {\n system \"$loc_co\
+m\";\n }\n }\n exit;\n }\n\nelsif ($par\
+a==1) \n {\n print STDERR \"do parallel exec\
+ution of: \\\"$com $list\\\"\\n\";\n \n if (\
+$log==1) \n {\n if ($log_file eq \"stdout\" || $lo\
+g_file eq \"stderr\" ) \n {\n $log_file=\"\";\n \
+ }\n\n else \n {\n system \"echo L\
+OG FILE> $log_file\";\n \n }\n }\n els\
+e \n {\n open ( OUT, \">/dev/null\");\n }\n \n \
+\n $id=0;\n $n_sub=0;\n while ($val=<F>) \
+\n { \n $job_log[$id]=\"$HOME/tmp\
+/$unique_prefix.$id.log_file\";\n \n $job=\
+$unique_prefix.\"_$id\";\n open (JOB, \">$job\\
+");\n \n $loc_com=$com;\n chop $val;\n\
+\n $loc_com=~s/\\$/$val/g;\n \n print JOB\
+ \"#!/bin/csh\\n\";\n print JOB \"#\\$ -cwd\\n\
+\";\n print JOB \"#\\$ -N $unique_prefix\\n\";\
+\n if ($queue && !($queue eq \" \")) {print JO\
+B \"#\\$ -l $queue\\n\";}\n print JOB \"#\\n\"\
+; \n print JOB \"$loc_com\\n\";\n \
+ print JOB \"echo FINISHED >> $job_log[$id]\\n\\
+";\n print JOB \"pwd\\n\";\n \n close \
+(JOB);\n if ( $output_all==1)\n {\n system \\
+"qsub $job > $unique_prefix\"; \n }\n \
+ else\n {system \"qsub $job -e $stderr_file -o $\
+stdio_file >$unique_prefix\"; \n }\
+ \n\n\n\n print STDERR \"$id: $output_all\\n\"\
+;\n $n_sub++;\n if ( $max_sub_jobs && $n_s\
+ub==$max_sub_jobs) \n {\n $n_sub=monitor_process\
+($min_sub_jobs,@job_log); \n \n } \n \
+ \n unlink $unique_prefix;\n sleep\
+ $pause_time;\n $id++;\n }\n\n close (O\
+UT);\n close (F);\n\n print STDERR \"Your $i\
+d Jobs Have Been Submited (NAME=$unique_prefix)\\n\
+\";\n monitor_process (0, @job_log);\n forea\
+ch $file(@job_log) {if (-e $file) {unlink($file);}\
+}\n \n }\n\nsub monitor_process ( @job_list)\
+\n {\n my (@job_list)=@_;\n my $min_sub_j\
+obs=shift (@job_list);\n my $n_sub_jobs;\n m\
+y $finished;\n my $n=0;\n\n $n_sub_jobs=-1;\\
+n $finished=0;\n print STDERR \"\\nMonitor B\
+atch: [$min_sub_jobs]\";\n \n while (!$fi\
+nished && (($n_sub_jobs>$min_sub_jobs)|| $n_sub_jo\
+bs==-1) ) \n {\n $finished=1;\n $n_sub_jobs=0;\n $\
+n=0;\n foreach $file (@job_list)\n {\n \n \
+ if (-e $file){;}\n else \n {\n $finish\
+ed=0; $n_sub_jobs++;\n }\n }\n\
+ system \"sleep 1\";\n }\n \n return \
+$n_sub_jobs;\n }\n \n \nif ($tmp_file_nam\
+e){unlink($tmp_file_name);}\n","\n\nforeach ($np=0\
+; $np<=$#ARGV; $np++)\n {\n $value=$ARGV[$np\
+];\n\n if ($value eq \"-file\")\n {\n \
+ $file= $ARGV[++$np];\n }\n elsif ($value \
+eq \"-type\")\n {\n $type= $ARGV[++$np\
+];\n }\n elsif ($value eq \"-institute\")\\
+n {\n $institute= $ARGV[++$np];\n \
+ }\n elsif ($value eq \"-author\")\n {\n \
+ $author= $ARGV[++$np];\n }\n elsif (\
+$value eq \"-date\")\n {\n $date= $ARG\
+V[++$np];\n }\n elsif ($value eq \"-progr\
+am\")\n {\n $program= $ARGV[++$np];\n \
+ }\n elsif ($value eq \"-email\")\n {\\
+n $email= $ARGV[++$np];\n }\n else\\
+n {\n print \"$value is an unkown argument[FA\
+TAL]\\n\";\n exit (1);\n }\n }\n\n\n\nopen F\
+, $file || die;\nprint $INSTITUTE;\nif ( $type eq \
+\"c\"){print \"/******************************COPY\
+RIGHT NOTICE*******************************/\\n\";\
+}\nif ( $type eq \"perl\"){print \"###############\
+###############COPYRIGHT NOTICE###################\
+###########/\\n\";}\nif ( $type eq \"txt\"){print \
+\"-------------------------------COPYRIGHT NOTICE-\
+-----------------------------/\\n\";}\n\n\nwhile (\
+<F>)\n {\n s/\\$INSTITUTE/$institute/g;\n s/\\$\
+AUTHOR/$author/g;\n s/\\$DATE/$date/g;\n s/\\$PR\
+OGRAM/$program/g; \n s/\\$EMAIL/$email/g; \n i\
+f ( $type eq \"txt\"){print $_;}\n elsif ($type e\
+q \"c\"){chop $_; print \"\\/*$_*\\/\\n\";}\n els\
+if ($type eq \"perl\"){print \"\\#$_\";}\n}\nclose\
+ (F);\nif ( $type eq \"c\"){print \"/*************\
*****************COPYRIGHT NOTICE*****************\
**************/\\n\";}\nif ( $type eq \"perl\"){pr\
int \"##############################COPYRIGHT NOTI\
CE##############################/\\n\";}\nif ( $ty\
pe eq \"txt\"){print \"---------------------------\
----COPYRIGHT NOTICE------------------------------\
-/\\n\";}\n\n\nwhile (<F>)\n {\n s/\\$INSTITUTE/$\
-institute/g;\n s/\\$AUTHOR/$author/g;\n s/\\$DAT\
-E/$date/g;\n s/\\$PROGRAM/$program/g; \n s/\\$E\
-MAIL/$email/g; \n if ( $type eq \"txt\"){print $\
-_;}\n elsif ($type eq \"c\"){chop $_; print \"\\/\
-*$_*\\/\\n\";}\n elsif ($type eq \"perl\"){print \
-\"\\#$_\";}\n}\nclose (F);\nif ( $type eq \"c\"){p\
-rint \"/******************************COPYRIGHT NO\
-TICE*******************************/\\n\";}\nif ( \
-$type eq \"perl\"){print \"#######################\
-#######COPYRIGHT NOTICE###########################\
-###/\\n\";}\nif ( $type eq \"txt\"){print \"------\
--------------------------COPYRIGHT NOTICE---------\
----------------------/\\n\";}\n\n","\nwhile (<>) \\
-n {\n s/\\=cc/123456789/g;\n s/\\bcc/\\$\\(CC\\)/g\
-;\n s/123456789/\\=cc/g;\n print $_;\n }\n\n","$ve\
-rsion=\"1.00\";\n$rseed= int(rand(100000))+1;\n\n\\
-nif ( $#ARGV==-1)\n {\n print \"msa2bootstrap \
--i <input_file> -input <seq|msa|matrix|tree> -n <N\
--Boostrap> -o <outtree> -tmode <nj|upgma|parsimony\
-|ml> -dmode <kimura> -alignpg <t_coffee | muscle |\
- clustalw> -rtree <file> -stype <prot|cdna|dna> -r\
-ecompute -system <cygwin|unix>\";\n print \"\\n\
-\\t-i: input file, can be sequneces, msa, matrix, \
-trees, type is specified via -input\";\n print \
-\"\\n\\t-input: Type of input data\";\n print \\
-"\\n\\t\\tmsa: msa in fasta format\";\n print \\
-"\\n\\t\\tseq: compute an msa with -alignpg\";\n \
- print \"\\n\\t\\tmatrix: phylipp distance matrix\
- fed directly to method -tmode [caveat: tmode=nj o\
-r upgma]\";\n print \"\\n\\t\\ttree: list of ne\
-wick trees directly fed to consence in order to ge\
-nerate a bootstraped tree\";\n \n print \"\\\
-n\\t-n: number of bootstrap replicates\";\n pri\
-nt \"\\n\\t-o: name of the output tree. Files are \
-not overwritten. Use -recompute to overwrite exist\
-ing file\";\n print \"\\n\\t-tmode: tree mode: \
-nj|upgma|parsimony|ml\";\n print \"\\n\\t-dmode\
-: distance mode\";\n print \"\\n\\t-alignpg: pr\
-ogram for aligning sequences (t_coffee=default)\";\
-\n print \"\\n\\t-rtree: replicate tree file (d\
-efault: no file)\";\n print \"\\n\\t-rmsa: repl\
-icate msa file (default: no file)\";\n print \"\
-\\n\\t-rmat: replicate matrix file (default: no fi\
-le)\";\n print \"\\n\\t-stype: sequence type: p\
-rotein, dna or cdna\";\n print \"\\n\\t-recompu\
-te: force files to be overwritten\";\n print \"\
-\\n\\t-system: cygwin|unix\";\n \n\n \n \
- &my_exit (EXIT_FAILURE);\n }\nforeach $arg (@ARG\
-V){$command.=\"$arg \";}\n\nprint \"CLINE: $comman\
-d\\n\";\n$threshold=100;\n$trim_msa=0;\n$stype=\"p\
-rot\";\nprint \"msa2bootstrap \";\n\n$system=\"cyg\
-win\";\nif(($command=~/\\-system (\\S+)/))\n {\n \
- $system=$1;\n if ( $system eq \"cygwin\")\n \
- {\n $exec_extension=\".exe\";\n }\n e\
-lsif ( $system eq \"unix\")\n {\n $exec_exten\
-sion=\"\";\n print \"system=Unix\";die;\n }\n\
- else\n {\n print \"msa2boostrap: -system=\
-$system is an unknown mode [FATAL]\\n\"; die;\n \
- }\n \n print \"-system $system \";\n }\n\
-if(($command=~/\\-stype (\\S+)/))\n {\n $stype\
-=$1;\n }\nprint \"-stype=$stype \";\n\n\n\nif(($c\
-ommand=~/\\-i (\\S+)/))\n {\n $msa=$1;\n pr\
-int \"-i $msa \";\n }\n\nif(($command=~/\\-rtree \
-(\\S+)/))\n {\n $rtree=$1;\n print \"-rtree\
-=$rtree \";\n }\n\nif(($command=~/\\-rmsa (\\S+)/\
-))\n {\n $rmsa=$1;\n }\nif(($command=~/\\-rma\
-t (\\S+)/))\n {\n $rmat=$1;\n }\n$input=\"seq\
-\";\nif(($command=~/\\-input (\\S+)/))\n {\n $\
-input=$1;\n }\nprint \"-input=$input \";\n\n$dmod\
-e=\"kimura\";\nif(($command=~/\\-dmode (\\S+)/))\n\
- {\n $dmode=$1;\n }\nprint \"-dmode=$dmode \"\
-;\n$alignpg=\"muscle\";\nif(($command=~/\\-alignpg\
- (\\S+)/))\n {\n $alignpg=$1;\n }\nprint \"-a\
-lignpg=$dmode \";\n\n$tmode=\"nj\";\nif(($command=\
-~/\\-tmode (\\S+)/))\n {\n $tmode=$1;\n }\npr\
-int \"-tmode=$tmode \";\n$recompute=0;\nif(($comma\
-nd=~/\\-recompute/))\n {\n $recompute=1;\n \
-print \"-recompute \";\n }\n\n$out=$msa;\n$out=~s\
-/\\..*//;\n$out.=\".bph\";\nif(($command=~/\\-o (\\
-\S+)/))\n {\n $out=$1;\n \n }\nprint \"-ou\
-t=$out \";\nif (-e $out && !$recompute)\n {\n \
-print \"\\nNo Computation Required $out already ex\
-ists\\n\";\n &my_exit (EXIT_SUCCESS);\n \n \
-}\n\n$n=100;\nif(($command=~/\\-n (\\d+)/))\n {\n\
- $n=$1;\n }\nprint \"-n=$n \";\n$seed=3;\nif((\
-$command=~/\\-s (\\d+)/))\n {\n $seed=$1;\n }\
-\nprint \"-s=$seed \";\n\nif(($command=~/\\-run_na\
-me (\\d+)/))\n {\n $suffix=$1;\n }\nelse\n {\
-\n $msa=~/([^.]+)/;\n $suffix=$1;\n }\nprin\
-t \"-run_name=$suffix\\n\";\n\n\nif ( $input eq \"\
-seq\")\n {\n $seq=$msa;\n $msa=\"$suffix.pr\
-ot_msa\";\n \n if ($stype eq \"cdna\")\n \
- {\n $cdna_seq=$seq;\n $clean_cdna_seq=&vtmpnam()\
-;\n $seq=&vtmpnam();\n `t_coffee -other_pg seq_ref\
-ormat -in $cdna_seq -action +clean_cdna >$clean_cd\
-na_seq`;\n `t_coffee -other_pg seq_reformat -in $c\
-lean_cdna_seq -action +translate >$seq`;\n \n \
- }\n\n if (!-e $msa || $recompute)\n {\n p\
-rint \"\\n##### Compute an MSA With $alignpg\\n\\
-";\n \n if ( $alignpg eq \"t_coffee\")\n {`$alig\
-npg $seq -outfile=$msa >/dev/null 2>/dev/null`;}\n\
- elsif ( $alignpg eq \"muscle\")\n {\n `$ali\
-gnpg -in $seq > $msa 2>/dev/null`;\n }\n elsif (\
- $alignpg eq \"clustalw\")\n {\n `$alignpg -\
-infile=$seq -outfile=$msa -quicktree >/dev/null 2>\
-/dev/null`;\n }\n elsif ( $align eq \"mafft\")\n\
- {\n `$alignpg $seq > $msa >/dev/null 2>/dev\
-/null`;\n }\n else\n {\n `$alignpg -in=$se\
-q -outfile=$msa`;\n }\n }\n if (!-e $msa\
-)\n {\n print \"\\nError: $alignpg Could Not \
-produce the MSA $msa [FATAL]\\n\";\n }\n\n \
- if ($stype eq \"cdna\")\n {\n $msa2=\"$suffi\
-x.cdna_msa\";\n `t_coffee -other_pg seq_reformat -\
-in $clean_cdna_seq -in2 $msa -action +thread_dna_o\
-n_prot_aln -output fasta_aln >$msa2`;\n $msa=$msa\
-2;\n }\n \n $input=\"msa\";\n }\n\n\n\\
-n$seqboot_o=&vtmpnam();\n$seqboot_c=&vtmpnam();\n\\
-n$protdist_o=&vtmpnam();\n$protdist_c=&vtmpnam();\\
-nif ( $input eq \"msa\")\n {\n if ($tmode eq \\
-"nj\" || $tmode eq \"upgma\"){$input=\"matrix\";}\\
-n \n $lmsa= &vtmpnam ();\n `t_coffee -oth\
-er_pg seq_reformat -in $msa -output phylip_aln > $\
-lmsa`;\n \n if ( -e \"outfile\"){unlink (\"o\
-utfile\");}\n # run seqboot\n \n if ( $n>1)\
-\n {\n print \"Run SeqBoot .....\";\n open (F\
-, \">$seqboot_c\");\n print F \"$lmsa\\nR\\n$n\\nY\
-\\n$seed\\n\";\n close (F);\n `seqboot$exec_extens\
-ion < $seqboot_c`;\n if ( -e \"outfile\"){ print \
-\"[OK]\\n\";}\n else { print \"[FAILED]\\n\";&my_e\
-xit (EXIT_FAILURE);}\n `mv outfile $seqboot_o`;\n \
- }\n else\n {\n `cp $lmsa $seqboot_o`;\
-\n }\n\n if ($rmsa){`cp $seqboot_o $rmsa`;\
-}\n \n if ($tmode eq \"nj\" || $tmode eq \"u\
-pgma\")\n {\n if ( $stype eq \"prot\")\n {\\
-n # run protdist\n print \"Run Protdist [d\
-mode=$dmode]\";\n if ($dmode eq \"kimura\")\n \
- {\n $dmode=\"P\\nP\\nP\";\n }\n e\
-lse\n {\n print \"\\n$dmode is an unknown m\
-ode for Protdist [FATAL:msa2bootstrap.pl]\\n\";\n \
- &my_exit (EXIT_FAILURE);\n }\n open (F,\
- \">$protdist_c\");\n if ($n>1){print F \"$seq\
-boot_o\\n$dmode\\nM\\nD\\n$n\\nY\\n\";}\n else\
- {printf F \"$seqboot_o\\n$dmode\\nY\\n\";}\n \
-close (F);\n `protdist$exec_extension < $prot\
-dist_c`;\n if ( -e \"outfile\"){ print \"[OK]\\
-\n\";}\n else { print \"[FAILED]\\n\";&my_exit\
- (EXIT_FAILURE);}\n `mv outfile $protdist_o`;\\
-n \n }\n elsif ( $stype eq \"cdna\" || $stype e\
-q \"dna\")\n {\n print \"Run dnadist [dmode=\
-default\";\n open (F, \">$protdist_c\");\n \
- if ($n>1){print F \"$seqboot_o\\nM\\nD\\n$n\\nY\\\
-n\";}\n else {printf F \"$seqboot_o\\nY\\n\";}\
-\n close (F);\n `protdist$exec_extension \
-< $protdist_c`;\n if ( -e \"outfile\"){ print \
-\"[OK]\\n\";}\n else { print \"[FAILED]\\n\";&\
-my_exit (EXIT_FAILURE);}\n `mv outfile $protdi\
-st_o`;\n }\n }\n }\nelsif ( $input eq \"ma\
-trix\")\n {\n $protdist_o=&vtmpnam();\n pri\
-nt \"MSA: $msa\\n\";\n `cp $msa $protdist_o`;\n\
- $n=1;\n }\n\n\n\n\n\n$nb_o=&vtmpnam();\n$nb_c\
-=&vtmpnam();\nif ($input eq \"matrix\" && $tmode n\
-e \"parsimony\" && $tmode ne \"ml\")\n {\n pri\
-nt \"Run neighbor [tmode=$tmode]\";\n\n if ($tm\
-ode eq \"nj\")\n {\n $tmode=\"\\nN\\nN\";\n \
- }\n elsif ( $tmode eq \"upgma\")\n {\n\
- $tmode = \"\\nN\";\n }\n else\n {\n \
-print \"\\n ERROR: $tmode is an unknown tree compu\
-tation mode\\n\";\n &my_exit (EXIT_FAILURE);\n \
- }\n\n open (F, \">$nb_c\");\n if ($n>1){pr\
-int F \"$protdist_o$tmode\\nM\\n$n\\n$seed\\nY\\n\\
-";}\n else {print F \"$protdist_o$tmode\\nY\\n\\
-";}\n close (F);\n\n `neighbor$exec_extensio\
-n < $nb_c`;\n if ( -e \"outtree\"){ print \"[N\
-eighbor OK]\\n\";}\n else { print \"[FAILED]\\n\
-\";&my_exit (EXIT_FAILURE);}\n `mv outtree $nb_\
-o`;\n unlink (\"outfile\");\n }\nelsif ($input\
- eq \"msa\" && $tmode eq \"parsimony\")\n {\n \
-if ( -e \"outfile\"){unlink (\"outfile\");}\n i\
-f ( -e \"outtree\"){unlink (\"outtree\");}\n \n\
- if ($stype eq \"prot\")\n {\n print \"Run\
- protpars [tmode=$tmode]\";\n open (F, \">$nb_c\")\
-;\n if ($n>1){print F \"$seqboot_o\\nM\\nD\\n$n\\n\
-$seed\\n10\\nY\\n\";}\n else {print F \"$seqboot_o\
-\\nY\\n\";}\n close (F);\n `protpars$exec_extensio\
-n < $nb_c`;\n }\n elsif ( $stype eq \"dna\
-\" || $stype eq \"cdna\")\n {\n print \"Run d\
-napars [tmode=$tmode]\";\n open (F, \">$nb_c\");\n\
- if ($n>1){print F \"$seqboot_o\\nM\\nD\\n$n\\n$se\
-ed\\n10\\nY\\n\";}\n else {print F \"$seqboot_o\\n\
-Y\\n\";}\n close (F);\n `dnapars$exec_extension <\
- $nb_c`;\n }\n if ( -e \"outtree\"){ print\
- \"[OK]\\n\";}\n else { print \"[FAILED]\\n\";&\
-my_exit (EXIT_FAILURE);}\n `mv outtree $nb_o`;\\
-n unlink (\"outfile\");\n }\nelsif ($input eq \\
-"msa\" && $tmode eq \"ml\")\n {\n if ( -e \"ou\
-tfile\"){unlink (\"outfile\");}\n if ( -e \"out\
-tree\"){unlink (\"outtree\");}\n \n if ($sty\
-pe eq \"prot\")\n {\n print \"Error: ML impos\
-sible with Protein Sequences [ERROR]\";\n &my_exit\
- (EXIT_FAILURE);\n }\n elsif ( $stype eq \\
-"dna\" || $stype eq \"cdna\")\n {\n print \"R\
-un dnaml [tmode=$tmode]\";\n open (F, \">$nb_c\");\
-\n if ($n>1){print F \"$seqboot_o\\nM\\nD\\n$n\\n$\
-seed\\n10\\nY\\n\";}\n else {print F \"$seqboot_o\\
-\nY\\n\";}\n close (F);\n `dnaml$exec_extension <\
- $nb_c`;\n }\n if ( -e \"outtree\"){ print\
- \"[OK]\\n\";}\n else { print \"[FAILED]\\n\";&\
-my_exit (EXIT_FAILURE);}\n `mv outtree $nb_o`;\\
-n unlink (\"outfile\");\n }\n\n\nelse\n {\n \
- `cp $msa $nb_o`;\n $n=2;\n }\n\nif ($rmsa && \
--e $seqboot_o){print \"\\nOutput List of $n Replic\
-ate MSA: $rmsa\\n\";`cp $seqboot_o $rmsa`;}\nif ($\
-rmat && -e $protdist_o){print \"\\nOutput List of \
-$n Replicate MATRICES: $rmat\\n\";`cp $protdist_o \
-$rmat`;}\nif ($rtree && -e $nb_o){print \"\\nOutpu\
-t List of $n Replicate TREES: $rtree\\n\";`cp $nb_\
-o $rtree`;}\n\n\n\n$con_o=&vtmpnam();\n$con_c=&vtm\
-pnam();\nif ($n >1)\n {\n print \"Run Consense\
-.....\";\n open (F, \">$con_c\");\n print F \
-\"$nb_o\\nY\\n\";\n close (F);\n `consense$e\
-xec_extension < $con_c`;\n if ( -s \"outtree\"\
- > 0) { print \"[OK]\\n\";}\n else { print \"[\
-FAILED]\\n\";&my_exit (EXIT_FAILURE);}\n `mv ou\
-ttree $con_o`;\n unlink (\"outfile\");\n }\nel\
-se\n {\n `cp $nb_o $con_o`;\n }\n\n\n`cp $con\
-_o $out`;\nif ( !-e $out)\n {\n print \"Tree C\
-omputation failed [FAILED]\\n\";\n &my_exit (EX\
-IT_FAILURE);\n }\nelsif ($n>1)\n {\n print \"\
-\\nOutput Bootstrapped Tree: $out\\n\";\n $avg=\
-`t_coffee -other_pg seq_reformat -in $out -action \
-+avg_bootstrap`;\n $avg=~s/\\n//g;\n print \\
-"$avg\\n\";\n }\nelse\n {\n print \"\\nOutput\
- Tree: $out\\n\";\n }\n\nopen (F, \"$out\");\nwhi\
-le (<F>)\n {\n \n $tree.=$_;\n }\nclose (F\
-);\n$tree=~s/\\n//g;\nprint \"BPH: $tree\\n\";\n\n\
-\n&my_exit (EXIT_SUCCESS);\n\nsub my_exit \n {\n \
- my $m=@_[0];\n &clean_vtmpnam();\n exit (\
-$m);\n }\nsub vtmpnam \n {\n my $file;\n\n\n \
- $ntmp++;\n $file=\"tmp4msa2bootstrap.$rseed.\
-$$.$ntmp\";\n \n push (@tmpfile, $file);\n \
- return $file;\n }\nsub clean_vtmpnam \n {\n \
- my $t;\n foreach $t (@tmpfile)\n {\n if (\
- -e $t){unlink ($t)};\n }\n }\n","use Env;\n\
-$seq_reformat=\"t_coffee -other_pg seq_reformat \"\
-;\n$VersionTag=\"1.00\";\n$step=1;\n$unset=\"\";\n\
-$scoreT1=$scoreT2=$nseqT=$dp_limit=$unset;\n@tl=()\
-;\nchomp($tc_version=`t_coffee -version`);$tc_vers\
-ion=~s/PROGRAM: //;\n\n\nprint STDERR \"\\n*******\
-**************************************************\
-********\";\nprint STDERR \"\\n* HIGH LE\
-VEL PROGRAM: T-COFFEE_DPA Version $VersionTag\";\n\
-print STDERR \"\\n* LOW LEVEL PROGRAM: \
-$tc_version \";\nprint STDERR \"\\n***************\
-**************************************************\
-\";\n\nif (!@ARGV)\n {\n print \"t_coffee_dpa \
-accepts every t_coffee_flag.\\nType t_coffee to ob\
-tain a list\\n\";\n print \"Requires $TC_VERSIO\
-N\\n\";\n print \"Requires \";\n print \"t_c\
-offee_dpa specific flags:\\n\";\n print \"\\t-d\
-pa_master_aln....................Master alignment:\
- provided OR computed\\n\";\n print \"\\t-dpa_m\
-aster_aln....................By default, Computed \
-with t_coffee -very_fast\\n\";\n print \"\\t-dp\
-a_master_aln=<file>.............Use file, (must be\
- an aln in Fasta or ClustalW\\n\";\n print \"\\\
-t-dpa_master_aln=<program>..........Compute aln wi\
-th pg -in seq -out aln`\\n\";\n print \"\\t-dpa\
-_maxnseq.......................Maximum number of s\
-equences in subgroups\\n\";\n print \"\\t-dpa_m\
-in_score1....................Minimum Id for two se\
-quences to be grouped in ref_aln\\n\";\n print \
-\"\\t-dpa_min_score2....................Minimum Id\
- within a subgroup\\n\";\n print \"\\t-dpa_debu\
-g.........................Keep Tmp File (for debug\
- purpose)\\n\\n\";\n \n exit (0);\n }\nfore\
-ach $arg (@ARGV)\n {\n $arg_list.=\" $arg\";\n\
- }\n$arg_list=~s/[=,;]/ /g;\n\n\n($seq0, $arg_lis\
-t)=&extract_val_from_arg_list(\"^\",$arg_list, \"S\
-PLICE\",\"unset\");\n($seq1, $arg_list)=&extract_v\
-al_from_arg_list(\"-seq\",$arg_list, \"SPLICE\",\"\
-unset\");\n($seq2, $arg_list)=&extract_val_from_ar\
-g_list(\"-in\",$arg_list, \"KEEP\",\"unset\");\n($\
-seq3, $arg_list)=&extract_val_from_arg_list(\"-inf\
-ile\",$arg_list, \"SPLICE\",\"unset\");\n($prf, $\
-arg_list)=&extract_val_from_arg_list(\"-profile\",\
-$arg_list, \"SPLICE\",\"unset\");\n\n$gl{'Seq'}=$s\
-eq=&vtmpnam();#file containing all the sequences\n\
-\n #1-remove sequences from -in\nif ( $arg_list \
-=~/\\-in\\b/)\n {\n my $save, $name;\n whil\
-e($arg_list=~/\\-in\\b[^-]+(\\bS[\\w.]+)/)\n \
-{\n $name=$1;$name=~s/^.//;\n if ( !-e $name){$sav\
-e.=\" S$name \";}\n\n $arg_list=~s/S$name/ /;\n \
- }\n $arg_list=~s/\\-in\\b/\\-in $save /;\n \
-}\n #2-prepare \n\nif (!($arg_list=~/\\-outorder\
-/))\n {\n \n $output_cl .=\" -outorder=$seq\
-\";\n }\n@output_flag=(\"-output\",\"-outfile\", \
-\"-run_name\", \"-outorder\"); \nforeach $v1 (@out\
-put_flag)\n {\n ($v2, $arg_list)=&extract_val_\
-from_arg_list($v1,$arg_list, \"SPLICE\",\"unset\")\
-;\n if ($v2 ne \"\")\n {\n\n if ($v1 eq \"\
--run_name\"){$run_name=$v2;$output_cl .=\" $v1 $v2\
- \";}\n elsif ( $v1 eq \"-outorder\")\n {\n \
-if ( $v2 eq \"input\"){$v2=$seq;}\n $outorder=\
-$v2;$output_cl .=\" $v1 $v2 \";\n }\n else\n {\
-\n $output_cl .=\" $v1 $v2 \";\n }\n }\\
-n }\n\n\n($dpa_master_aln, $arg_list) =&extract_v\
-al_from_arg_list(\"-dpa_master_aln\",$arg_list, \"\
-SPLICE\", \"t_coffee\");\n$dpa_master_aln=~s/\\s//\
-g;\n($nseqT, $arg_list) =&extract_val_fr\
-om_arg_list(\"-dpa_maxnseq\",$arg_list, \"SPLICE\"\
-, 30);\n($scoreT1, $arg_list) =&extract_va\
-l_from_arg_list(\"-dpa_min_score1\",$arg_list, \"S\
-PLICE\", 80);\n($scoreT2, $arg_list) =&ext\
-ract_val_from_arg_list(\"-dpa_min_score2\" ,$ar\
-g_list, \"SPLICE\", 30);\n($dpa_limit, $arg_list) \
- =&extract_val_from_arg_list(\"-dpa_limit\" \
- ,$arg_list, \"SPLICE\", 0);\n($dpa_delta_id,\
- $arg_list) =&extract_val_from_arg_list(\"-dpa_\
-delta_id\" ,$arg_list, \"SPLICE\", 1);\n($d\
-pa_debug, $arg_list) =&extract_val_from_arg_\
-list(\"-dpa_debug\" ,$arg_list, \"SPLICE\
-\", 0);\n\n\n$in_seq=$seq0.\" \".$seq1.\" \".$seq2\
-.\" \".$seq3;\n$in_prf=(($prf ne $unset)?\"$prf \"\
-:\"\");\n&exit_dpa (($in_seq eq \"\" && $in_prf eq\
- \"\")?1:0, \"ERROR: You did not Provide any seque\
-nces. Use the -seq flag [FATAL: t_coffee_dpa]\\n\"\
-, EXIT_FAILURE);\n\n\nprint STDERR \"\\nSTART DPA \
-COMPUTATION\";\n\n\n\nif ($in_seq=~/\\S+/)\n {\n \
- \n print STDERR \"\\n Step $step: Gather all\
- the sequences into the tmp file: [$seq]\";$step++\
-; \n &my_system (\"t_coffee $in_seq -convert -q\
-uiet -output fasta_seq -outfile=$seq -maxnseq 0\")\
-;\n }\n\nif ( !-e $seq){$seq=\"\";}\n\nif ($in_pr\
-f=~/\\S+/)\n {\n $seq_in_type=\"profile\"; \n \
- $seq.= $in_prf; \n }\nif ($seq eq \"\"){ &exit\
-_dpa (1, \"\\nERROR: No Sequence FOund. Provide Se\
-quences with the -seq flag [FATAL: t_coffee_dpa]\"\
-, EXIT_FAILURE);}\n\n \n\nif ( $run_name)\n {\n \
- $suffix=$run_name;\n }\nelsif ($in_seq=~/\\b(S[\
-\\w.]+\\b)/)\n {\n my $suffix1, $sufffix2;\n \
- $suffix1=$suffix2=$1;\n $suffix2=~s/^S//;\n \
- if ( -e $suffix1){$suffix=$suffix1;}\n elsif \
-( -e $suffix2){$suffix=$suffix2;}\n else\n \
- {\n $suffix=&vtmpnam(); \n }\n $suffix=~s\
-/\\.\\w+//;\n }\n\nelse\n {\n $suffix=&vtmpna\
-m();\n }\n\n\nif (!$run_name){$output_cl.=\" -run\
-_name $suffix \";}\n\n\n$gl{'Tree'}=&seq2dpa_tree \
-($seq, \"$suffix.dpadnd\");\n\nprint STDERR \"\\n \
-Step $step: Prepare guide tree: $gl{'Tree'}\";$ste\
-p++;\n\nprint STDERR \"\\n Step $step: Identify an\
-d Align Closely Related Groups\";$step++;\n%gl=&ma\
-ke_one_pass (0, $scoreT1,\"Align\",%gl);\n\nprint \
-STDERR \"\\n Step $step: Make Multiple Group Align\
-ment\";$step++;\nwhile (!%gl ||$gl{'Ng'}>$nseqT)\n\
- {\n %gl=&make_one_pass ($nseqT, $scoreT2,\"t_\
-coffee\",%gl);\n if ( $gl{'Newgroups'}==0){$sco\
-reT2--;} \n }\nprint STDERR \"\\n Step $step: \
-Make The Final Alignment\";$step++;\n\n\n$arg_list\
- .=$output_cl;\n\n\n%gl=&tree2group (0,0, %gl);\n$\
-gl{$gl{'0'}{'File'}}{'Output'}=\"\";\n$a=0;\n&alig\
-n_groups (\"t_coffee\",'0', $arg_list, \" \", %gl)\
-;\n\n\n\nif ( !$dpa_keep_tmpfile){&clean_tmp_file \
-(@tl);}\n\n\n\nsub seq2dpa_tree \n {\n my $seq\
-=@_[0];\n my $newtree=@_[1];\n my $aln=&vtmp\
-nam ();\n\n &my_system (\"t_coffee -special_mod\
-e quickaln -in $seq -outfile $aln -quiet\");\n \
-&my_system (\"$seq_reformat -in $aln -action +aln2\
-tree +tree2dpatree -output newick >$newtree\");\n \
- return $newtree;\n } \nsub seq2dpa_tree_old \n\
- {\n my $aln=@_[0];\n my $newtree=@_[1];\n \
- \n \n &my_system(\"$seq_reformat -in $aln\
- -action +seq2dpatree -output newick > $newtree\")\
-;\n return $newtree;\n }\nsub aln2dpa_tree \n \
- {\n my $aln=@_[0];\n my $newtree=&vtmpnam()\
-;\n \n &my_system(\"$seq_reformat -in $aln -\
-action +aln2tree +tree2dpatree -output newick > $n\
-ewtree\");\n return $newtree;\n }\nsub group_f\
-ile2ngroups\n {\n my $file=@_[0];\n my $n;\\
-n \n open ( F, $file);\n while (<F>)\n \
- {\n $n+=/\\>/;\n }\n close (F);\n re\
-turn $n;\n }\n\nsub make_one_pass\n {\n my ($\
-N, $ID,$pg, %gl)=@_;\n my $a;\n\n %gl=&tree2\
-group ($N,$ID,%gl);\n if (!$gl{'Newgroups'}){re\
-turn %gl;}\n else\n {\n for ( $a=0; $a< $n\
-g; $a++)\n {\n if ($gl{$gl{$a}{'File'}}{'Ng'\
-}>1){&display_group($a, %gl);}\n &align_groups\
- ($pg, $a, $arg_list, \" -quiet=quiet \", %gl);\n \
- }\n return %gl;\n }\n }\n\nsub tree2group \
-\n {\n my ($N, $ID, %gl)=@_;\n my $prefix=&\
-vtmpnam();\n my $group_file=&vtmpnam();\n my\
- $file;\n my $oldtree=&vtmpnam();\n my $n;\n\
- my $tree;\n\n\n if ( $gl{'Ng'}==1){return %\
-gl;}\n $tree=$gl{'Tree'}; \n \n #1 extrac\
-t the groups\n &my_system (\"$seq_reformat -in \
-$tree -action +tree2group $N $ID $prefix > $group_\
-file\");\n $n=group_file2ngroups($group_file);\\
-n \n \n $gl{'Newgroups'}=1;\n if ( $n=\
-=$gl{'Ng'})\n {\n $gl{'Newgroups'}=0;\n retur\
-n %gl;\n }\n $gl{'Iteration'}++;\n $gl{\
-'MaxNseq'}=$N;$gl{'MinID'}=$ID;\n $gl{'GroupFil\
-e'}=$group_file;$gl{'Ng'}=$ng=0;\n #2 Process t\
-he group list into the hash\n open (F, $group_f\
-ile);\n while (<F>)\n {\n $gl{'File'}.=$_;\
-\n if (/\\>/)\n {\n $line=$_;\n $line=~s\
-/\\>//;\n @list=($line=~/(\\S+)/g);\n $fil\
-e=$gl{$ng}{'File'}=shift @list;\n $gl{$file}{'\
-Output'}=$file;\n \n $gl{$file}{'Ng'}=$#li\
-st+1;\n if ($gl{$file}{'Ng'}>1){ $gl{$file}{'T\
-list'}=$gl{$file}{'Alist'}=\"(\";}\n foreach $\
-l (@list)\n {\n \n $gl{$file}{'List'}.=\" $\
-l \";\n \n if (!$gl{$l}{'Tlist'})\n {\n \
-$gl{$l}{'Tlist'}=\"$l\";\n $gl{$l}{'Alist'}=\\
-"$l\";\n $gl{$l}{'Nseq'}=1;\n $gl{$l}{'N\
-g'}=1;\n }\n $gl{$file}{'Tlist'}.=\"$gl{$l}{'T\
-list'},\";\n $gl{$file}{'Alist'}.=\"$gl{$l}{'Tlis\
-t'}|\";\n $gl{$file}{'Nseq'}+=$gl{$l}{'Nseq'};\n \
- }\n \n\n chop($gl{$file}{'Tlist'});c\
-hop($gl{$file}{'Alist'});\n if ($gl{$file}{'Ng\
-'}>1){$gl{$file}{'Tlist'}.=\")\"; $gl{$file}{'Alis\
-t'}.=\");\";}\n $ng++;\n } \n }\n $g\
-l{'Ng'}=$ng;\n close (F);\n \n #3 Update \
-the old tree with the new groups\n $gl{'Tree'}=\
-&vtmpnam();\n &my_system (\"$seq_reformat -in $\
-tree -action +collapse_tree $group_file -output ne\
-wick > $gl{'Tree'}\");\n \n return %gl;\n }\
-\n\nsub display_group \n {\n my ($g,%gl)=@_;\n\
- my $f;\n \n if ( $g==-1)\n {\n prin\
-t STDERR \"\\nIteration $gl{'Iteration'} [MaxN=$gl\
-{'MaxNseq'}][MinID=$gl{'MinID'}]\";\n }\n \
-else\n {\n\n $f=$gl{$g}{'File'};\n $action=($\
-gl{$f}{'Ng'}==1 || $gl{'Iteration'}==1)?\"KEEP \"\
-:\"ALIGN \";\n print STDERR \"\\n\\t[$actio\
-n][MaxN=$gl{'MaxNseq'}][MinID=$gl{'MinID'}][File $\
-f][Nseq=$gl{$f}{'Nseq'}][Ngroups=$gl{$f}{'Ng'}][$g\
-l{$f}{'Alist'}]\";\n }\n }\n \n\n\nsub \
-align_groups\n {\n my ($pg, $g, $arg, $extra_a\
-rg,%gl)=@_;\n my $f;\n my $Output,$Outflag;\\
-n \n \n $f=$gl{$g}{'File'};\n $Output=\
-($gl{$f}{'Output'});\n \n if ( $pg eq \"Alig\
-n\")\n {\n if ( !-e $f)\n {\n $command=\
-\"$seq_reformat -in $gl{'Seq'} -action +extract_a\
-ln $gl{'GroupFile'}\";\n if ($gl{$f}{'Ng'}>1)\\
-n {\n &my_system ($command);\n $command=\"\
-t_coffee -special_mode quick_aln S$f -outfile=$Ou\
-tput -quiet\";\n }\n }\n else \n {$comma\
-nd=\"\";}\n }\n elsif ( -e $f)\n { \n\
- $Outflag=($Output)?\"-outfile=$Output\":\"\";\n $\
-command=\"$pg -infile $f $Outflag -quiet stdout $a\
-rg $extra_arg -maxnseq 0 -convert -quiet stdout\";\
-\n }\n elsif ( $gl{$f}{'Ng'}==1)\n {\\
-n $action=($dpa_debug)?\"cp\":\"mv\";\n $command=\\
-"$action $gl{$f}{'List'} $Output\";\n }\n \
-else\n {\n $Outflag=($Output)?\"-outfile=$Out\
-put\":\"\";\n $command=\"$pg -profile $gl{$f}{'Lis\
-t'} $Outflag $arg $extra_arg -maxnseq 0\";\n \
-}\n \n &my_system ($command);\n return $o\
-utfile;\n }\n \nsub my_system \n {\n my $c\
-ommand=@_[0];\n my $force=@_[1];\n my $statu\
-s;\n\n if ( $dpa_debug) {print STDERR \"\\nCOMM\
-AND: $command\";}\n $status=system ($command);\\
-n\n if (!$force)\n {\n &exit_dpa (($stat\
-us==1), \"Failed in Command:\\n$command\\n[FATAL: \
-t_coffee_dpa]\\n\", EXIT_FAILURE);\n }\n \
-\n return $status;\n }\n\nsub vtmpnam\n {\n \
- my $prefix=@_[0];\n my $tmp_file_name;\n\n \
- $tmp_prefix=($prefix)?$prefix:\"dpa_tmp_file_$$\"\
-;\n \n $tmp_count++;\n $tmp_file_name=\"$t\
-mp_prefix\".\"$tmp_count\";\n $tl[$#tl+1]=$tmp_\
-file_name;\n return $tmp_file_name;\n }\n\nsub\
- clean_tmp_file\n {\n\n my $list;\n my $fil\
-e;\n \n if ($dpa_debug){return;}\n $list=\
-vtmpnam();\n `ls -1 | grep $tmp_prefix>$list`;\\
-n \n open (F,$list);\n while ( <F>)\n \
- {\n $file=$_;\n chop $file;\n if ( -e $file){unl\
-ink $file;}\n }\n close (F);\n unlink $\
-list;\n }\n\n\nsub exit_dpa\n {\n my $condition\
-=@_[0];\n my $error_msg=@_[1];\n my $exit_value=\
-@_[2];\n if ( $condition)\n {\n print \"$\
-error_msg\\n\";\n exit ($exit_value);\n }\\
-n else\n {\n return;\n }\n \n}\nsub e\
-xtract_val_from_arg_list\n {\n my $arg=@_[0];\\
-n my $arg_list=@_[1];\n my $keep_flag=@_[2];\
-\n my $default_value=@_[3];\n my $val=\"\";\\
-n \n #protect\n $arg_list=~s/\\s-/ \\@/g;\
-\n $arg=~s/-/\\@/g;\n \n #search\n if \
-($arg eq \"^\")\n {\n $arg_list=~/^([^@]*)/;\\
-n $val=$1;\n }\n else\n {$arg_list=~/\
-$arg ([^@]*)/;$val=$1;}\n \n #remove trailin\
-g spaces\n $val=~s/\\s*$//;\n \n #remove \
-the parsed sequence if needed\n if (($val ne \"\
-\") && $keep_flag ne \"KEEP\")\n {\n if ( $ar\
-g eq \"^\"){$arg_list=~s/$val/ /;}\n else {$arg_li\
-st=~s/($arg [^@]*)/ /;}\n }\n \n #unprotec\
-t\n $arg_list=~s/\\@/-/g;\n $arg=~s/\\@/-/g;\
-\n \n if (($val eq \"\") && $default_value n\
-e \"unset\"){$val=$default_value;}\n \n retu\
-rn $val, $arg_list;\n }\n$program=\"T-COFFEE (r25\
-3)\";\n\n","\n$DEBUG=1;\n$dpa_nseq=10;\n$dpa_sim=0\
-;\nif (!@ARGV)\n {\n `t_coffee`;\n exit (0)\
-;\n }\nforeach $arg (@ARGV)\n {\n $arg_list.=\
-\" $arg\";\n }\n$max_nseq=10;\n($seq0, $arg_list)\
-=&extract_val_from_arg_list(\"^\",$arg_list);\n($s\
-eq1, $arg_list)=&extract_val_from_arg_list(\"-seq\\
-",$arg_list);\n($seq2, $arg_list)=&extract_val_fro\
-m_arg_list(\"-in\",$arg_list, \"KEEP\");\n($seq3, \
-$arg_list)=&extract_val_from_arg_list(\"-infile\",\
-$arg_list);\n$in_seq=$seq0.\" \".$seq1.\" \".$seq2\
-.\" \".$seq3;\n\n$seq=vtmpnam();\n`t_coffee $in_se\
-q -convert -output fasta_seq -outfile=$seq`;\n\n\n\
-($dpa_nseq, $arg_list)=&extract_val_from_arg_list(\
-\"-dpa_nseq\",$arg_list);\n($master_aln, $arg_list\
-)=&extract_val_from_arg_list(\"-master_aln\",$arg_\
-list);\n($sim_matrix, $arg_list)=&extract_val_from\
-_arg_list(\"-sim_matrix\",$arg_list);\n($core_seq,\
- $arg_list)=&extract_val_from_arg_list(\"-core_seq\
-\",$arg_list);\n($dpa_sim, $arg_list)=&extract_val\
-_from_arg_list(\"-dpa_sim\",$arg_list);\n($run_nam\
-e, $arg_list)=&extract_val_from_arg_list(\"-run_na\
-me\",$arg_list);\n($output, $arg_list)=&extract_va\
-l_from_arg_list(\"-output\",$arg_list);\n\n\n\nif \
-(!$sim_mat && !$master_aln)#Compute the fast align\
-ment\n {\n $ref_aln=vtmpnam();\n `t_coffee \
--seq=$seq -very_fast -outfile=$ref_aln -quiet`;\n \
- \n }\n\nif (!$sim_mat)\n {\n $sim_mat=vtmp\
-nam();\n `seq_reformat -in $ref_aln -output sim\
- > $sim_mat`;\n }\n\nif ( !$core_seq)\n {\n $\
-core_seq=vtmpnam();\n `seq_reformat -in $ref_al\
-n -action +trimTC N$max_nseq -output fasta_seq > $\
-core_seq`;\n }\n@core_name=`seq_reformat -in $cor\
-e_seq -output name `; \n\n@tot_name=`seq_reformat \
--in $seq -output name `;\n\nforeach $s (@core_name\
-){$s=~s/\\s//g;$hcore{$s}=1;}\nforeach $s (@tot_na\
-me){$s=~s/\\s//g;}\nprint STDERR \"T-Coffee_dpa:\\\
-n\";\nprint STDERR \"\\tTOTAL SEQ: @tot_name\\n\"\
-;\nprint STDERR \"\\tCHOSEN SEQ: @core_name\\n\";\\
-n\n\n\nopen (F, $sim_mat);\nwhile ( <F>)\n {\n \
- @l=($_=~/(\\b[\\S]+\\b)/g);\n if (($l[0] eq \"\
-TOP\" || $l[0] eq \"BOT\"))\n {\n $s1=$l[1];$\
-s2=$l[2];$v=$l[3];\n if ($hcore{$s1} && !$hcore{$s\
-2})\n {\n if (!$hseq{$s2}{\"sim\"} || $v>$hs\
-eq{$s2}{\"sim\"})\n {\n $hseq{$s2}{\"sim\"}\
-=$v;$hseq{$s2}{\"seq\"}=$s1;\n }\n }\n \
- }\n }\nclose (F);\nforeach $s (@tot_name)\n {\\
-n\n if ( !$hseq{$s}{\"seq\"}){;}\n else\n \
- {\n $s2=$hseq{$s}{\"seq\"};\n $v=$hseq{$s}{\"si\
-m\"};\n \n if ($v>$dpa_sim)\n {\n $hseq{$s}\
-{'used'}=1;\n $seq_list{$s2}{$seq_list{$s2}{'n\
-seq'}++}=$s;\n }\n }\n }\nforeach $s (@cor\
-e_name){$seq_list{$s}{$seq_list{$s}{'nseq'}++}=$s;\
-$hseq{$s}{'used'}=1;}\nforeach $s (@tot_name){if (\
-!$hseq{$s}{'used'}){$seq_list{'unused'}{$seq_list{\
-'unused'}{'nseq'}++}=$s;}}\n\n\n$n=0;\nforeach $s \
-(@core_name)\n {\n $ng++;\n $n=$seq_list{$s\
-}{'nseq'};\n for (@g_list=(), $a=0; $a<$n; $a++\
-){@g_list=(@g_list,$seq_list{$s}{$a});}\n\n $g_\
-seq=vtmpnam();\n $g_aln=vtmpnam();\n \n p\
-rint STDERR \"Group $ng: $#g_list Seq: @g_list: \"\
-;\n \n \n `seq_reformat -in $seq -action \
-+lower +keep_name +extract_seq @g_list -output fa\
-sta_seq > $g_seq`;\n \n \n if ( $#g_list=\
-=0)\n {\n print STDERR \"[No aln]\\n\";\n $g_\
-aln=$g_seq;\n }\n elsif ($#g_list<$max_nse\
-q) \n {\n print STDERR \"[t_coffee]\\n\";\n `\
-t_coffee $g_seq -outfile=$g_aln -quiet $arg_list`;\
-\n }\n else\n {\n print STDERR \"[t_c\
-offee_dpa]\\n\";\n `t_coffee_dpa2 $g_seq -outfile=\
-$g_aln $arg_list -sim_matrix $sim_matrix -dpa_nseq\
- $dpa_nseq`;\n }\n @profile_list=(@profile\
-_list, $g_aln);\n }\n\n\nprint \"UNUSED $seq_list\
-{'unused'}{'nseq'}\";\n\nif ($seq_list{'unused'}{'\
-nseq'})\n {\n $prf=vtmpnam();\n \n \
- `t_coffee -profile @profile_list $arg_list -out\
-file=$prf -quiet`;\n $n=$seq_list{\"unused\"}\
-{'nseq'};\n $new_seq=vtmpnam();\n $new_p\
-rf=vtmpnam();\n for ($a=0; $a<$n-1; $a++)\n {\
-\n $s=$seq_list{\"unused\"}{$a};\n print STDER\
-R \"\\nADD Sequence $s\";\n \n `seq_reformat -\
-in $seq -action +lower +keep_name +extract_seq $s \
- -output fasta_seq > $new_seq`;\n `t_coffee -pro\
-file $prf $new_seq $arg_list -outfile=$new_prf`;\n\
- `cp $new_prf $prf`;\n }\n $s=$seq_list{\"u\
-nused\"}{$a};\n `seq_reformat -in $seq -actio\
-n +lower +keep_name +extract_seq $s -output fasta\
-_seq > $new_seq`;\n @profile_list=($prf, $new\
-_seq);\n }\n \n \nif ($run_name){$arg_l\
-ist.=\" -run_name $run_name\";}\nelse \n {\n $\
-in_seq=~/([\\w-]+)/;\n $arg_list.=\" -run_name \
-$1\";\n }\nif ( $output){$arg_list.=\" -output $o\
-utput \";}\n\n`t_coffee -profile @profile_list $ar\
-g_list`;\n\n\n&clean (@tmp_file_list);\n\n\nsub vt\
-mpnam\n {\n my $tmp_file_name;\n $tmp_name_\
-counter++;\n $tmp_file_name=\"tmp_file_$tmp_nam\
-e_counter\\_Pid$$\";\n $tmp_file_list[$ntmp_fil\
-e++]=$tmp_file_name;\n return $tmp_file_name;\n\
- }\nsub clean\n {\n my @fl=@_;\n my $file;\n \
-return;\n\n foreach $file ( @fl)\n {\n if\
- ( -e $file){unlink($file);}\n }\n}\nsub extrac\
-t_val_from_arg_list\n {\n my $arg=@_[0];\n \
-my $arg_list=@_[1];\n my $keep_flag=@_[2];\n \
- #protect\n $arg_list=~s/\\s-/ \\@/g;\n $arg\
-=~s/-/\\@/g;\n \n #search\n if ($arg eq \\
-"^\")\n {\n $arg_list=~/^([^@]*)/;\n $val=$1;\
-\n }\n else\n {$arg_list=~/$arg ([^@]\
-*)/;$val=$1;}\n \n #remove the parsed sequen\
-ce if needed\n if ($val && $keep_flag ne \"KEEP\
-\")\n {\n if ( $arg eq \"^\"){$arg_list=~s/$v\
-al/ /;}\n else {$arg_list=~s/($arg [^@]*)/ /;}\n \
- }\n \n #unprotect\n $arg_list=~s/\\@/-/g\
-;\n $arg=~s/\\@/-/g;\n \n return $val, $a\
-rg_list;\n }\n\n","use Env;\nuse FileHandle;\nuse\
- Cwd;\nuse File::Path;\nuse Sys::Hostname;\n\nour \
-$PIDCHILD;\nour $ERROR_DONE;\nour @TMPFILE_LIST;\n\
-our $EXIT_FAILURE=1;\nour $EXIT_SUCCESS=0;\n\nour \
-$REFDIR=getcwd;\nour $EXIT_SUCCESS=0;\nour $EXIT_F\
-AILURE=1;\n\nour $PROGRAM=\"tc_generic_method.pl\"\
-;\nour $CL=$PROGRAM;\n\nour $CLEAN_EXIT_STARTED;\n\
-our $debug_lock=$ENV{\"DEBUG_LOCK\"};\nour $debug_\
-cmd_exec=$ENV{\"DEBUG_CMD_EXEC\"};\nour $LOCKDIR=$\
-ENV{\"LOCKDIR_4_TCOFFEE\"};\nif (!$LOCKDIR){$LOCKD\
-IR=getcwd();}\nour $ERRORDIR=$ENV{\"ERRORDIR_4_TCO\
-FFEE\"};\nour $ERRORFILE=$ENV{\"ERRORFILE_4_TCOFFE\
-E\"};\n&set_lock ($$);\nif (isshellpid(getppid()))\
-{lock4tc(getppid(), \"LLOCK\", \"LSET\", \"$$\\n\"\
-);}\n \n\n\n\n\nour $BLAST_MAX_NRUNS=2;\nour \
-$COMMAND;\nour $PIDCHILD;\n\n$REF_EMAIL=\"\";\n$tm\
-p_dir=\"\";\n$init_dir=\"\";\n\n\n$test=0;\nif ($t\
-est==1)\n {\n $SERVER=\"NCBI\";\n $query=$A\
-RGV[0];\n $hitf=$ARGV[1];\n %s=read_fasta_se\
-q($query);\n @sl=keys(%s);\n &blast_xml2prof\
-ile (\"xx\", $s{$sl[0]}{seq},$maxid,$minid,$mincov\
-, $hitf);\n myexit ($EXIT_FAILURE);\n }\n\nfor\
-each $v(@ARGV){$cl.=\"$v \";}\n$COMMAND=$cl;\n($mo\
-de)=&my_get_opt ( $cl, \"-mode=\",1,0);\n\n($A)=(&\
-my_get_opt ( $cl, \"-name1=\",0,0));\n($B)=(&my_ge\
-t_opt ( $cl, \"-name2=\",0,0));\n($TMPDIR)=(&my_ge\
-t_opt ( $cl, \"-tmpdir=\",0,0));\n($CACHE)=(&my_ge\
-t_opt ( $cl, \"-cache=\",0,0));\n($SERVER)=((&my_g\
-et_opt ( $cl, \"-server=\",0,0)));\n($EMAIL)=((&my\
-_get_opt ( $cl, \"-email=\",0,0)));\n\nif (!$A){$A\
-=\"A\";}\nif (!$B){$B=\"B\";}\n\n\nif (!$TMPDIR)\n\
- {\n $HOME=$ENV{HOME};\n if ($ENV{TMP_4_TCO\
-FFEE}){$TMPDIR=$ENV{TMP_4_TCOFFEE};}\n else{$TM\
-PDIR=\"$HOME/.t_coffee/tmp/\";}\n }\nif ( ! -d $T\
-MPDIR)\n {\n mkdir $TMPDIR;\n }\nif ( ! -d $T\
-MPDIR)\n {\n print \"ERROR: Could not create t\
-emporary dir: $TMPDIR\\n\";\n myexit ($EXIT_FAI\
-LURE);\n }\n\n$EMAIL=~s/XEMAILX/\\@/g;\nif (!$EMA\
-IL)\n {\n if ($ENV{EMAIL_4_TCOFFEE}){$EMAIL=$E\
-NV{EMAIL_4_TCOFFEE};}\n elsif ($ENV{EMAIL}){$EM\
-AIL=$ENV{EMAIL};}\n else {$EMAIL=$REF_EMAIL;}\n\
- }\n\n($maxid,$minid,$mincov)=(&my_get_opt ( $cl,\
- \"-maxid=\",0,0, \"-minid=\",0,0,\"-mincov=\",0,0\
-));\nif (!$cl=~/\\-maxid\\=/){$maxid=95;}\nif (!$c\
-l=~/\\-minid\\=/){$minid=35;}\nif (!$cl=~/\\-minco\
-v\\=/){$mincov=80;}\n\n\n\n\nif ($mode eq \"seq_ms\
-a\")\n {\n &seq2msa($mode,&my_get_opt ( $cl, \\
-"-infile=\",1,1, \"-method=\",1,2, \"-param=\",0,0\
-,\"-outfile=\",1,0, \"-database=\",0,0));\n }\nel\
-sif ( $mode eq \"tblastx_msa\")\n {\n &seq2tbl\
-astx_lib ($mode,&my_get_opt ( $cl, \"-infile=\",1,\
-1, \"-outfile=\",1,0));\n }\nelsif ( $mode eq \"t\
-blastpx_msa\")\n {\n &seq2tblastpx_lib ($mode,\
-&my_get_opt ( $cl, \"-infile=\",1,1, \"-outfile=\"\
-,1,0));\n }\nelsif ( $mode eq \"thread_pair\")\n \
- {\n &seq2thread_pair($mode,&my_get_opt ( $cl, \
-\"-infile=\",1,1, \"-pdbfile1=\",1,1, \"-method=\"\
-,1,2,\"-param=\",0,0, \"-outfile=\",1,0, ));\n }\\
-nelsif ( $mode eq \"pdbid_pair\")\n {\n &seq2p\
-dbid_pair($mode,&my_get_opt ( $cl, \"-pdbfile1=\",\
-1,0, \"-pdbfile2=\",1,0, \"-method=\",1,2,\"-param\
-=\",0,0, \"-outfile=\",1,0, ));\n }\nelsif ( $mod\
-e eq \"pdb_pair\")\n {\n &seq2pdb_pair($mode,&\
-my_get_opt ( $cl, \"-pdbfile1=\",1,1, \"-pdbfile2=\
-\",1,1, \"-method=\",1,2,\"-param=\",0,0, \"-outfi\
-le=\",1,0, ));\n }\nelsif ( $mode eq \"profile_pa\
-ir\")\n {\n &seq2profile_pair($mode,&my_get_o\
-pt ( $cl, \"-profile1=\",1,1, \"-profile2=\",1,1, \
-\"-method=\",1,2,\"-param=\",0,0, \"-outfile=\",1,\
-0 ));\n }\nelsif ($mode eq \"pdb_template_test\")\
-\n {\n &blast2pdb_template_test ($mode,&my_get\
-_opt ( $cl, \"-infile=\",1,1));\n\n }\nelsif ($mo\
-de eq \"psi_template_test\")\n {\n &psiblast2p\
-rofile_template_test ($mode,&my_get_opt ( $cl, \"-\
-seq=\",1,1,\"-blast=\",1,1));\n\n }\n\nelsif ( $m\
-ode eq \"pdb_template\")\n {\n &blast2pdb_temp\
-late ($mode,&my_get_opt ( $cl, \"-infile=\",1,1, \\
-"-database=\",1,0, \"-method=\",1,0, \"-outfile=\"\
-,1,0,\"-pdb_type=\",1,0));\n }\n\nelsif ( $mode e\
-q \"profile_template\")\n {\n \n &psiblast2\
-profile_template ($mode,&my_get_opt ( $cl, \"-infi\
-le=\",1,1, \"-database=\",1,0, \"-method=\",1,0, \\
-"-outfile=\",1,0));\n }\nelsif ( $mode eq \"psipr\
-ofile_template\")\n {\n &psiblast2profile_temp\
-late ($mode,&my_get_opt ( $cl, \"-infile=\",1,1, \\
-"-database=\",1,0, \"-method=\",1,0, \"-outfile=\"\
-,1,0));\n }\nelsif ( $mode eq \"RNA_template\")\n\
- {\n &seq2RNA_template ($mode,&my_get_opt ( $c\
-l, \"-infile=\",1,1, \"-outfile=\",1,0));\n }\nel\
-sif ( $mode eq \"tm_template\")\n {\n &seq2tm_\
-template ($mode, \"\", &my_get_opt ( $cl, \"-infil\
-e=\",1,1,\"-arch=\",1,1,\"-psv=\",1,1, \"-outfile=\
-\",1,0,));\n }\nelsif ( $mode eq \"psitm_template\
-\")\n {\n &seq2tm_template ($mode,&my_get_opt \
-( $cl, \"-database=\",1,0, \"-infile=\",1,1, \"-ar\
-ch=\",1,1,\"-psv=\",1,1, \"-outfile=\",1,0,));\n \
-}\nelsif ( $mode eq \"ssp_template\")\n {\n &s\
-eq2ssp_template ($mode,&my_get_opt ( $cl, \"-infil\
-e=\",1,1,\"-seq=\",1,1,\"-obs=\",1,1, \"-outfile=\\
-",1,0));\n }\nelsif ( $mode eq \"psissp_template\\
-")\n {\n &seq2ssp_template ($mode,&my_get_opt \
-( $cl, \"-infile=\",1,1,\"-seq=\",1,1,\"-obs=\",1,\
-1, \"-outfile=\",1,0));\n }\n\nelsif ( $mode eq \\
-"rna_pair\")\n{\n &seq2rna_pair($mode,&my_get_o\
-pt ( $cl, \"-pdbfile1=\",1,1, \"-pdbfile2=\",1,1, \
-\"-method=\",1,2,\"-param=\",0,0, \"-outfile=\",1,\
-0, ));\n}\nelsif ( $mode eq \"calc_rna_template\")\
-\n{\n &calc_rna_template($mode,&my_get_opt ( $c\
-l, \"-infile=\",1,1,\"-pdbfile=\",1,1, \"-outfile=\
-\",1,0));\n}\nelse\n {\n myexit(flush_error( \\
-"$mode is an unknown mode of tc_generic_method.pl\\
-"));\n }\nmyexit ($EXIT_SUCCESS);\n\n\nsub seq2ss\
-p_template\n {\n my ($mode, $infile,$gor_seq,$go\
-r_obs,$outfile)=@_;\n my %s, %h;\n my $result;\n\
- my (@profiles);\n &set_temporary_dir (\"set\",$\
-infile,\"seq.pep\");\n %s=read_fasta_seq (\"seq.p\
-ep\");\n\n \n open (R, \">result.aln\");\n \n \
-#print stdout \"\\n\";\n foreach $seq (keys(%s))\\
-n {\n \n open (F, \">seqfile\");\n \
- $s{$seq}{seq}=uc$s{$seq}{seq};\n print (F \
-\">$s{$seq}{name}\\n$s{$seq}{seq}\\n\");\n cl\
-ose (F);\n $lib_name=\"$s{$seq}{name}.ssp\";\\
-n $lib_name=&clean_file_name ($lib_name);\n \
- \n if ($mode eq \"ssp_template\"){&seq2go\
-r_prediction ($s{$seq}{name},$s{$seq}{seq}, \"seqf\
-ile\", $lib_name,$gor_seq, $gor_obs);}\n elsi\
-f ($mode eq \"psissp_template\")\n {\n &seq2msa_\
-gor_prediction ($s{$seq}{name},$s{$seq}{seq},\"seq\
-file\", $lib_name,$gor_seq, $gor_obs);\n }\n \n\
- if ( !-e $lib_name)\n {\n myexit(flush_err\
-or(\"GORIV failed to compute the secondary structu\
-re of $s{$seq}{name}\"));\n myexit ($EXIT_FAILUR\
-E);\n }\n else\n {\n print stdout \"\\tProc\
-ess: >$s{$seq}{name} _E_ $lib_name \\n\";\n prin\
-t R \">$s{$seq}{name} _E_ $lib_name\\n\";\n }\n \
- unshift (@profiles, $lib_name);\n }\n close\
- (R);\n &set_temporary_dir (\"unset\",$mode, $met\
-hod,\"result.aln\",$outfile, @profiles);\n}\n\nsub\
- seq2tm_template\n {\n my ($mode, $db, $infile,$\
-arch,$psv,$outfile)=@_;\n my %s, %h;\n my $resul\
+/\\n\";}\n\n","\nwhile (<>) \n {\n s/\\=cc/1234567\
+89/g;\n s/\\bcc/\\$\\(CC\\)/g;\n s/123456789/\\=cc\
+/g;\n print $_;\n }\n\n","$version=\"1.00\";\n$rse\
+ed= int(rand(100000))+1;\n\n\nif ( $#ARGV==-1)\n \
+{\n print \"msa2bootstrap -i <input_file> -inpu\
+t <seq|msa|matrix|tree> -n <N-Boostrap> -o <outtre\
+e> -tmode <nj|upgma|parsimony|ml> -dmode <kimura> \
+-alignpg <t_coffee | muscle | clustalw> -rtree <fi\
+le> -stype <prot|cdna|dna> -recompute -system <cyg\
+win|unix>\";\n print \"\\n\\t-i: input file, ca\
+n be sequneces, msa, matrix, trees, type is specif\
+ied via -input\";\n print \"\\n\\t-input: Type \
+of input data\";\n print \"\\n\\t\\tmsa: msa in\
+ fasta format\";\n print \"\\n\\t\\tseq: comput\
+e an msa with -alignpg\";\n print \"\\n\\t\\tma\
+trix: phylipp distance matrix fed directly to meth\
+od -tmode [caveat: tmode=nj or upgma]\";\n prin\
+t \"\\n\\t\\ttree: list of newick trees directly f\
+ed to consence in order to generate a bootstraped \
+tree\";\n \n print \"\\n\\t-n: number of boo\
+tstrap replicates\";\n print \"\\n\\t-o: name o\
+f the output tree. Files are not overwritten. Use \
+-recompute to overwrite existing file\";\n prin\
+t \"\\n\\t-tmode: tree mode: nj|upgma|parsimony|ml\
+\";\n print \"\\n\\t-dmode: distance mode\";\n \
+ print \"\\n\\t-alignpg: program for aligning se\
+quences (t_coffee=default)\";\n print \"\\n\\t-\
+rtree: replicate tree file (default: no file)\";\n\
+ print \"\\n\\t-rmsa: replicate msa file (defau\
+lt: no file)\";\n print \"\\n\\t-rmat: replicat\
+e matrix file (default: no file)\";\n print \"\\
+\n\\t-stype: sequence type: protein, dna or cdna\"\
+;\n print \"\\n\\t-recompute: force files to be\
+ overwritten\";\n print \"\\n\\t-system: cygwin\
+|unix\";\n \n\n \n &my_exit (EXIT_FAILU\
+RE);\n }\nforeach $arg (@ARGV){$command.=\"$arg \\
+";}\n\nprint \"CLINE: $command\\n\";\n$threshold=1\
+00;\n$trim_msa=0;\n$stype=\"prot\";\nprint \"msa2b\
+ootstrap \";\n\n$system=\"cygwin\";\nif(($command=\
+~/\\-system (\\S+)/))\n {\n $system=$1;\n i\
+f ( $system eq \"cygwin\")\n {\n $exec_extens\
+ion=\".exe\";\n }\n elsif ( $system eq \"u\
+nix\")\n {\n $exec_extension=\"\";\n print \"\
+system=Unix\";die;\n }\n else\n {\n p\
+rint \"msa2boostrap: -system=$system is an unknown\
+ mode [FATAL]\\n\"; die;\n }\n \n print\
+ \"-system $system \";\n }\nif(($command=~/\\-sty\
+pe (\\S+)/))\n {\n $stype=$1;\n }\nprint \"-s\
+type=$stype \";\n\n\n\nif(($command=~/\\-i (\\S+)/\
+))\n {\n $msa=$1;\n print \"-i $msa \";\n \
+}\n\nif(($command=~/\\-rtree (\\S+)/))\n {\n $\
+rtree=$1;\n print \"-rtree=$rtree \";\n }\n\ni\
+f(($command=~/\\-rmsa (\\S+)/))\n {\n $rmsa=$1\
+;\n }\nif(($command=~/\\-rmat (\\S+)/))\n {\n \
+ $rmat=$1;\n }\n$input=\"seq\";\nif(($command=~/\\
+\-input (\\S+)/))\n {\n $input=$1;\n }\nprint\
+ \"-input=$input \";\n\n$dmode=\"kimura\";\nif(($c\
+ommand=~/\\-dmode (\\S+)/))\n {\n $dmode=$1;\n\
+ }\nprint \"-dmode=$dmode \";\n$alignpg=\"muscle\\
+";\nif(($command=~/\\-alignpg (\\S+)/))\n {\n \
+$alignpg=$1;\n }\nprint \"-alignpg=$dmode \";\n\n\
+$tmode=\"nj\";\nif(($command=~/\\-tmode (\\S+)/))\\
+n {\n $tmode=$1;\n }\nprint \"-tmode=$tmode \\
+";\n$recompute=0;\nif(($command=~/\\-recompute/))\\
+n {\n $recompute=1;\n print \"-recompute \"\
+;\n }\n\n$out=$msa;\n$out=~s/\\..*//;\n$out.=\".b\
+ph\";\nif(($command=~/\\-o (\\S+)/))\n {\n $ou\
+t=$1;\n \n }\nprint \"-out=$out \";\nif (-e $o\
+ut && !$recompute)\n {\n print \"\\nNo Computa\
+tion Required $out already exists\\n\";\n &my_e\
+xit (EXIT_SUCCESS);\n \n }\n\n$n=100;\nif(($co\
+mmand=~/\\-n (\\d+)/))\n {\n $n=$1;\n }\nprin\
+t \"-n=$n \";\n$seed=3;\nif(($command=~/\\-s (\\d+\
+)/))\n {\n $seed=$1;\n }\nprint \"-s=$seed \"\
+;\n\nif(($command=~/\\-run_name (\\d+)/))\n {\n \
+ $suffix=$1;\n }\nelse\n {\n $msa=~/([^.]+)/\
+;\n $suffix=$1;\n }\nprint \"-run_name=$suffix\
+\\n\";\n\n\nif ( $input eq \"seq\")\n {\n $seq\
+=$msa;\n $msa=\"$suffix.prot_msa\";\n \n \
+if ($stype eq \"cdna\")\n {\n $cdna_seq=$seq;\
+\n $clean_cdna_seq=&vtmpnam();\n $seq=&vtmpnam();\\
+n `t_coffee -other_pg seq_reformat -in $cdna_seq -\
+action +clean_cdna >$clean_cdna_seq`;\n `t_coffee \
+-other_pg seq_reformat -in $clean_cdna_seq -action\
+ +translate >$seq`;\n \n }\n\n if (!-e $ms\
+a || $recompute)\n {\n print \"\\n##### Com\
+pute an MSA With $alignpg\\n\";\n \n if ( $alignpg\
+ eq \"t_coffee\")\n {`$alignpg $seq -outfile=$ms\
+a >/dev/null 2>/dev/null`;}\n elsif ( $alignpg eq \
+\"muscle\")\n {\n `$alignpg -in $seq > $msa \
+2>/dev/null`;\n }\n elsif ( $alignpg eq \"clusta\
+lw\")\n {\n `$alignpg -infile=$seq -outfile=\
+$msa -quicktree >/dev/null 2>/dev/null`;\n }\n e\
+lsif ( $align eq \"mafft\")\n {\n `$alignpg \
+$seq > $msa >/dev/null 2>/dev/null`;\n }\n else\\
+n {\n `$alignpg -in=$seq -outfile=$msa`;\n \
+ }\n }\n if (!-e $msa)\n {\n print \"\
+\\nError: $alignpg Could Not produce the MSA $msa \
+[FATAL]\\n\";\n }\n\n if ($stype eq \"cdna\
+\")\n {\n $msa2=\"$suffix.cdna_msa\";\n `t_co\
+ffee -other_pg seq_reformat -in $clean_cdna_seq -i\
+n2 $msa -action +thread_dna_on_prot_aln -output fa\
+sta_aln >$msa2`;\n $msa=$msa2;\n }\n \n \
+ $input=\"msa\";\n }\n\n\n\n$seqboot_o=&vtmpnam(\
+);\n$seqboot_c=&vtmpnam();\n\n$protdist_o=&vtmpnam\
+();\n$protdist_c=&vtmpnam();\nif ( $input eq \"msa\
+\")\n {\n if ($tmode eq \"nj\" || $tmode eq \"\
+upgma\"){$input=\"matrix\";}\n \n $lmsa= &vt\
+mpnam ();\n `t_coffee -other_pg seq_reformat -i\
+n $msa -output phylip_aln > $lmsa`;\n \n if \
+( -e \"outfile\"){unlink (\"outfile\");}\n # ru\
+n seqboot\n \n if ( $n>1)\n {\n print \"R\
+un SeqBoot .....\";\n open (F, \">$seqboot_c\");\n\
+ print F \"$lmsa\\nR\\n$n\\nY\\n$seed\\n\";\n clos\
+e (F);\n `seqboot$exec_extension < $seqboot_c`;\n\
+ if ( -e \"outfile\"){ print \"[OK]\\n\";}\n else \
+{ print \"[FAILED]\\n\";&my_exit (EXIT_FAILURE);}\\
+n `mv outfile $seqboot_o`;\n }\n else\n \
+ {\n `cp $lmsa $seqboot_o`;\n }\n\n if (\
+$rmsa){`cp $seqboot_o $rmsa`;}\n \n if ($tmo\
+de eq \"nj\" || $tmode eq \"upgma\")\n {\n if\
+ ( $stype eq \"prot\")\n {\n # run protdist\\
+n print \"Run Protdist [dmode=$dmode]\";\n \
+ if ($dmode eq \"kimura\")\n {\n $dmode=\"P\
+\\nP\\nP\";\n }\n else\n {\n prin\
+t \"\\n$dmode is an unknown mode for Protdist [FAT\
+AL:msa2bootstrap.pl]\\n\";\n &my_exit (EXIT_FAILU\
+RE);\n }\n open (F, \">$protdist_c\");\n\
+ if ($n>1){print F \"$seqboot_o\\n$dmode\\nM\\\
+nD\\n$n\\nY\\n\";}\n else {printf F \"$seqboot\
+_o\\n$dmode\\nY\\n\";}\n close (F);\n `pro\
+tdist$exec_extension < $protdist_c`;\n if ( -\
+e \"outfile\"){ print \"[OK]\\n\";}\n else { p\
+rint \"[FAILED]\\n\";&my_exit (EXIT_FAILURE);}\n \
+ `mv outfile $protdist_o`;\n \n }\n elsif ( $\
+stype eq \"cdna\" || $stype eq \"dna\")\n {\n \
+ print \"Run dnadist [dmode=default\";\n open\
+ (F, \">$protdist_c\");\n if ($n>1){print F \"\
+$seqboot_o\\nM\\nD\\n$n\\nY\\n\";}\n else {pri\
+ntf F \"$seqboot_o\\nY\\n\";}\n close (F);\n \
+ `protdist$exec_extension < $protdist_c`;\n \
+ if ( -e \"outfile\"){ print \"[OK]\\n\";}\n e\
+lse { print \"[FAILED]\\n\";&my_exit (EXIT_FAILURE\
+);}\n `mv outfile $protdist_o`;\n }\n }\
+\n }\nelsif ( $input eq \"matrix\")\n {\n $pr\
+otdist_o=&vtmpnam();\n print \"MSA: $msa\\n\";\\
+n `cp $msa $protdist_o`;\n $n=1;\n }\n\n\n\\
+n\n\n$nb_o=&vtmpnam();\n$nb_c=&vtmpnam();\nif ($in\
+put eq \"matrix\" && $tmode ne \"parsimony\" && $t\
+mode ne \"ml\")\n {\n print \"Run neighbor [tm\
+ode=$tmode]\";\n\n if ($tmode eq \"nj\")\n \
+ {\n $tmode=\"\\nN\\nN\";\n }\n elsif ( $t\
+mode eq \"upgma\")\n {\n $tmode = \"\\nN\";\n\
+ }\n else\n {\n print \"\\n ERROR: $t\
+mode is an unknown tree computation mode\\n\";\n &\
+my_exit (EXIT_FAILURE);\n }\n\n open (F, \\
+">$nb_c\");\n if ($n>1){print F \"$protdist_o$t\
+mode\\nM\\n$n\\n$seed\\nY\\n\";}\n else {print \
+F \"$protdist_o$tmode\\nY\\n\";}\n close (F);\n\
+\n `neighbor$exec_extension < $nb_c`;\n if \
+( -e \"outtree\"){ print \"[Neighbor OK]\\n\";}\n \
+ else { print \"[FAILED]\\n\";&my_exit (EXIT_FAI\
+LURE);}\n `mv outtree $nb_o`;\n unlink (\"ou\
+tfile\");\n }\nelsif ($input eq \"msa\" && $tmode\
+ eq \"parsimony\")\n {\n if ( -e \"outfile\"){\
+unlink (\"outfile\");}\n if ( -e \"outtree\"){u\
+nlink (\"outtree\");}\n \n if ($stype eq \"p\
+rot\")\n {\n print \"Run protpars [tmode=$tmo\
+de]\";\n open (F, \">$nb_c\");\n if ($n>1){print F\
+ \"$seqboot_o\\nM\\nD\\n$n\\n$seed\\n10\\nY\\n\";}\
+\n else {print F \"$seqboot_o\\nY\\n\";}\n close (\
+F);\n `protpars$exec_extension < $nb_c`;\n }\
+\n elsif ( $stype eq \"dna\" || $stype eq \"cdn\
+a\")\n {\n print \"Run dnapars [tmode=$tmode]\
+\";\n open (F, \">$nb_c\");\n if ($n>1){print F \"\
+$seqboot_o\\nM\\nD\\n$n\\n$seed\\n10\\nY\\n\";}\n \
+else {print F \"$seqboot_o\\nY\\n\";}\n close (F);\
+\n `dnapars$exec_extension < $nb_c`;\n }\n \
+ if ( -e \"outtree\"){ print \"[OK]\\n\";}\n e\
+lse { print \"[FAILED]\\n\";&my_exit (EXIT_FAILURE\
+);}\n `mv outtree $nb_o`;\n unlink (\"outfile\
+\");\n }\nelsif ($input eq \"msa\" && $tmode eq \\
+"ml\")\n {\n if ( -e \"outfile\"){unlink (\"ou\
+tfile\");}\n if ( -e \"outtree\"){unlink (\"out\
+tree\");}\n \n if ($stype eq \"prot\")\n \
+ {\n print \"Error: ML impossible with Protein Se\
+quences [ERROR]\";\n &my_exit (EXIT_FAILURE);\n \
+ }\n elsif ( $stype eq \"dna\" || $stype eq \\
+"cdna\")\n {\n print \"Run dnaml [tmode=$tmod\
+e]\";\n open (F, \">$nb_c\");\n if ($n>1){print F \
+\"$seqboot_o\\nM\\nD\\n$n\\n$seed\\n10\\nY\\n\";}\\
+n else {print F \"$seqboot_o\\nY\\n\";}\n close (F\
+);\n `dnaml$exec_extension < $nb_c`;\n }\n \
+ if ( -e \"outtree\"){ print \"[OK]\\n\";}\n e\
+lse { print \"[FAILED]\\n\";&my_exit (EXIT_FAILURE\
+);}\n `mv outtree $nb_o`;\n unlink (\"outfile\
+\");\n }\n\n\nelse\n {\n `cp $msa $nb_o`;\n \
+ $n=2;\n }\n\nif ($rmsa && -e $seqboot_o){print \
+\"\\nOutput List of $n Replicate MSA: $rmsa\\n\";`\
+cp $seqboot_o $rmsa`;}\nif ($rmat && -e $protdist_\
+o){print \"\\nOutput List of $n Replicate MATRICES\
+: $rmat\\n\";`cp $protdist_o $rmat`;}\nif ($rtree \
+&& -e $nb_o){print \"\\nOutput List of $n Replicat\
+e TREES: $rtree\\n\";`cp $nb_o $rtree`;}\n\n\n\n$c\
+on_o=&vtmpnam();\n$con_c=&vtmpnam();\nif ($n >1)\n\
+ {\n print \"Run Consense.....\";\n open (F\
+, \">$con_c\");\n print F \"$nb_o\\nY\\n\";\n \
+ close (F);\n `consense$exec_extension < $con\
+_c`;\n if ( -s \"outtree\" > 0) { print \"[OK]\
+\\n\";}\n else { print \"[FAILED]\\n\";&my_exit\
+ (EXIT_FAILURE);}\n `mv outtree $con_o`;\n u\
+nlink (\"outfile\");\n }\nelse\n {\n `cp $nb_\
+o $con_o`;\n }\n\n\n`cp $con_o $out`;\nif ( !-e $\
+out)\n {\n print \"Tree Computation failed [FA\
+ILED]\\n\";\n &my_exit (EXIT_FAILURE);\n }\nel\
+sif ($n>1)\n {\n print \"\\nOutput Bootstrappe\
+d Tree: $out\\n\";\n $avg=`t_coffee -other_pg s\
+eq_reformat -in $out -action +avg_bootstrap`;\n \
+ $avg=~s/\\n//g;\n print \"$avg\\n\";\n }\nels\
+e\n {\n print \"\\nOutput Tree: $out\\n\";\n \
+}\n\nopen (F, \"$out\");\nwhile (<F>)\n {\n \n\
+ $tree.=$_;\n }\nclose (F);\n$tree=~s/\\n//g;\\
+nprint \"BPH: $tree\\n\";\n\n\n&my_exit (EXIT_SUCC\
+ESS);\n\nsub my_exit \n {\n my $m=@_[0];\n \
+&clean_vtmpnam();\n exit ($m);\n }\nsub vtmpna\
+m \n {\n my $file;\n\n\n $ntmp++;\n $fil\
+e=\"tmp4msa2bootstrap.$rseed.$$.$ntmp\";\n \n \
+ push (@tmpfile, $file);\n return $file;\n }\\
+nsub clean_vtmpnam \n {\n my $t;\n foreach \
+$t (@tmpfile)\n {\n if ( -e $t){unlink ($t)};\
+\n }\n }\n","use Env;\n$seq_reformat=\"t_cof\
+fee -other_pg seq_reformat \";\n$VersionTag=\"1.00\
+\";\n$step=1;\n$unset=\"\";\n$scoreT1=$scoreT2=$ns\
+eqT=$dp_limit=$unset;\n@tl=();\nchomp($tc_version=\
+`t_coffee -version`);$tc_version=~s/PROGRAM: //;\n\
+\n\nprint STDERR \"\\n****************************\
+*************************************\";\nprint ST\
+DERR \"\\n* HIGH LEVEL PROGRAM: T-COFFEE\
+_DPA Version $VersionTag\";\nprint STDERR \"\\n* \
+ LOW LEVEL PROGRAM: $tc_version \";\nprin\
+t STDERR \"\\n************************************\
+*****************************\";\n\nif (!@ARGV)\n \
+ {\n print \"t_coffee_dpa accepts every t_coffe\
+e_flag.\\nType t_coffee to obtain a list\\n\";\n \
+ print \"Requires $TC_VERSION\\n\";\n print \"\
+Requires \";\n print \"t_coffee_dpa specific fl\
+ags:\\n\";\n print \"\\t-dpa_master_aln........\
+............Master alignment: provided OR computed\
+\\n\";\n print \"\\t-dpa_master_aln............\
+........By default, Computed with t_coffee -very_f\
+ast\\n\";\n print \"\\t-dpa_master_aln=<file>..\
+...........Use file, (must be an aln in Fasta or C\
+lustalW\\n\";\n print \"\\t-dpa_master_aln=<pro\
+gram>..........Compute aln with pg -in seq -out al\
+n`\\n\";\n print \"\\t-dpa_maxnseq.............\
+..........Maximum number of sequences in subgroups\
+\\n\";\n print \"\\t-dpa_min_score1............\
+........Minimum Id for two sequences to be grouped\
+ in ref_aln\\n\";\n print \"\\t-dpa_min_score2.\
+...................Minimum Id within a subgroup\\n\
+\";\n print \"\\t-dpa_debug....................\
+.....Keep Tmp File (for debug purpose)\\n\\n\";\n \
+ \n exit (0);\n }\nforeach $arg (@ARGV)\n {\
+\n $arg_list.=\" $arg\";\n }\n$arg_list=~s/[=,\
+;]/ /g;\n\n\n($seq0, $arg_list)=&extract_val_from_\
+arg_list(\"^\",$arg_list, \"SPLICE\",\"unset\");\n\
+($seq1, $arg_list)=&extract_val_from_arg_list(\"-s\
+eq\",$arg_list, \"SPLICE\",\"unset\");\n($seq2, $a\
+rg_list)=&extract_val_from_arg_list(\"-in\",$arg_l\
+ist, \"KEEP\",\"unset\");\n($seq3, $arg_list)=&ext\
+ract_val_from_arg_list(\"-infile\",$arg_list, \"SP\
+LICE\",\"unset\");\n($prf, $arg_list)=&extract_va\
+l_from_arg_list(\"-profile\",$arg_list, \"SPLICE\"\
+,\"unset\");\n\n$gl{'Seq'}=$seq=&vtmpnam();#file c\
+ontaining all the sequences\n\n #1-remove sequen\
+ces from -in\nif ( $arg_list =~/\\-in\\b/)\n {\n \
+ my $save, $name;\n while($arg_list=~/\\-in\\\
+b[^-]+(\\bS[\\w.]+)/)\n {\n $name=$1;$name=~s\
+/^.//;\n if ( !-e $name){$save.=\" S$name \";}\n\n\
+ $arg_list=~s/S$name/ /;\n }\n $arg_list=~\
+s/\\-in\\b/\\-in $save /;\n }\n #2-prepare \n\n\
+if (!($arg_list=~/\\-outorder/))\n {\n \n $\
+output_cl .=\" -outorder=$seq\";\n }\n@output_fla\
+g=(\"-output\",\"-outfile\", \"-run_name\", \"-out\
+order\"); \nforeach $v1 (@output_flag)\n {\n (\
+$v2, $arg_list)=&extract_val_from_arg_list($v1,$ar\
+g_list, \"SPLICE\",\"unset\");\n if ($v2 ne \"\\
+")\n {\n\n if ($v1 eq \"-run_name\"){$run_nam\
+e=$v2;$output_cl .=\" $v1 $v2 \";}\n elsif ( $v1 e\
+q \"-outorder\")\n {\n if ( $v2 eq \"input\"\
+){$v2=$seq;}\n $outorder=$v2;$output_cl .=\" $\
+v1 $v2 \";\n }\n else\n {\n $output_cl .=\\
+" $v1 $v2 \";\n }\n }\n }\n\n\n($dpa_master\
+_aln, $arg_list) =&extract_val_from_arg_list(\"-d\
+pa_master_aln\",$arg_list, \"SPLICE\", \"t_coffee\\
+");\n$dpa_master_aln=~s/\\s//g;\n($nseqT, $arg_lis\
+t) =&extract_val_from_arg_list(\"-dpa_ma\
+xnseq\",$arg_list, \"SPLICE\", 30);\n($scoreT1, $a\
+rg_list) =&extract_val_from_arg_list(\"-dp\
+a_min_score1\",$arg_list, \"SPLICE\", 80);\n($scor\
+eT2, $arg_list) =&extract_val_from_arg_lis\
+t(\"-dpa_min_score2\" ,$arg_list, \"SPLICE\", 3\
+0);\n($dpa_limit, $arg_list) =&extract_val_f\
+rom_arg_list(\"-dpa_limit\" ,$arg_list, \"S\
+PLICE\", 0);\n($dpa_delta_id, $arg_list) =&extr\
+act_val_from_arg_list(\"-dpa_delta_id\" ,$a\
+rg_list, \"SPLICE\", 1);\n($dpa_debug, $arg_list) \
+ =&extract_val_from_arg_list(\"-dpa_debug\" \
+ ,$arg_list, \"SPLICE\", 0);\n\n\n$in_seq=\
+$seq0.\" \".$seq1.\" \".$seq2.\" \".$seq3;\n$in_pr\
+f=(($prf ne $unset)?\"$prf \":\"\");\n&exit_dpa ((\
+$in_seq eq \"\" && $in_prf eq \"\")?1:0, \"ERROR: \
+You did not Provide any sequences. Use the -seq fl\
+ag [FATAL: t_coffee_dpa]\\n\", EXIT_FAILURE);\n\n\\
+nprint STDERR \"\\nSTART DPA COMPUTATION\";\n\n\n\\
+nif ($in_seq=~/\\S+/)\n {\n \n print STDERR\
+ \"\\n Step $step: Gather all the sequences into t\
+he tmp file: [$seq]\";$step++; \n &my_system (\\
+"t_coffee $in_seq -convert -quiet -output fasta_se\
+q -outfile=$seq -maxnseq 0\");\n }\n\nif ( !-e $s\
+eq){$seq=\"\";}\n\nif ($in_prf=~/\\S+/)\n {\n \
+$seq_in_type=\"profile\"; \n $seq.= $in_prf; \n\
+ }\nif ($seq eq \"\"){ &exit_dpa (1, \"\\nERROR: \
+No Sequence FOund. Provide Sequences with the -seq\
+ flag [FATAL: t_coffee_dpa]\", EXIT_FAILURE);}\n\n\
+ \n\nif ( $run_name)\n {\n $suffix=$run_name;\\
+n }\nelsif ($in_seq=~/\\b(S[\\w.]+\\b)/)\n {\n \
+ my $suffix1, $sufffix2;\n $suffix1=$suffix2=$\
+1;\n $suffix2=~s/^S//;\n if ( -e $suffix1){$\
+suffix=$suffix1;}\n elsif ( -e $suffix2){$suffi\
+x=$suffix2;}\n else\n {\n $suffix=&vtmpnam\
+(); \n }\n $suffix=~s/\\.\\w+//;\n }\n\ne\
+lse\n {\n $suffix=&vtmpnam();\n }\n\n\nif (!$\
+run_name){$output_cl.=\" -run_name $suffix \";}\n\\
+n\n$gl{'Tree'}=&seq2dpa_tree ($seq, \"$suffix.dpad\
+nd\");\n\nprint STDERR \"\\n Step $step: Prepare g\
+uide tree: $gl{'Tree'}\";$step++;\n\nprint STDERR \
+\"\\n Step $step: Identify and Align Closely Relat\
+ed Groups\";$step++;\n%gl=&make_one_pass (0, $scor\
+eT1,\"Align\",%gl);\n\nprint STDERR \"\\n Step $st\
+ep: Make Multiple Group Alignment\";$step++;\nwhil\
+e (!%gl ||$gl{'Ng'}>$nseqT)\n {\n %gl=&make_on\
+e_pass ($nseqT, $scoreT2,\"t_coffee\",%gl);\n i\
+f ( $gl{'Newgroups'}==0){$scoreT2--;} \n }\npr\
+int STDERR \"\\n Step $step: Make The Final Alignm\
+ent\";$step++;\n\n\n$arg_list .=$output_cl;\n\n\n%\
+gl=&tree2group (0,0, %gl);\n$gl{$gl{'0'}{'File'}}{\
+'Output'}=\"\";\n$a=0;\n&align_groups (\"t_coffee\\
+",'0', $arg_list, \" \", %gl);\n\n\n\nif ( !$dpa_k\
+eep_tmpfile){&clean_tmp_file (@tl);}\n\n\n\nsub se\
+q2dpa_tree \n {\n my $seq=@_[0];\n my $newt\
+ree=@_[1];\n my $aln=&vtmpnam ();\n\n &my_sy\
+stem (\"t_coffee -special_mode quickaln -in $seq -\
+outfile $aln -quiet\");\n &my_system (\"$seq_re\
+format -in $aln -action +aln2tree +tree2dpatree -o\
+utput newick >$newtree\");\n return $newtree;\n\
+ } \nsub seq2dpa_tree_old \n {\n my $aln=@_[0\
+];\n my $newtree=@_[1];\n \n \n &my_sy\
+stem(\"$seq_reformat -in $aln -action +seq2dpatree\
+ -output newick > $newtree\");\n return $newtre\
+e;\n }\nsub aln2dpa_tree \n {\n my $aln=@_[0]\
+;\n my $newtree=&vtmpnam();\n \n &my_syst\
+em(\"$seq_reformat -in $aln -action +aln2tree +tre\
+e2dpatree -output newick > $newtree\");\n retur\
+n $newtree;\n }\nsub group_file2ngroups\n {\n \
+ my $file=@_[0];\n my $n;\n \n open ( F, \
+$file);\n while (<F>)\n {\n $n+=/\\>/;\n \
+ }\n close (F);\n return $n;\n }\n\nsub \
+make_one_pass\n {\n my ($N, $ID,$pg, %gl)=@_;\\
+n my $a;\n\n %gl=&tree2group ($N,$ID,%gl);\n\
+ if (!$gl{'Newgroups'}){return %gl;}\n else\\
+n {\n for ( $a=0; $a< $ng; $a++)\n {\n \
+if ($gl{$gl{$a}{'File'}}{'Ng'}>1){&display_group($\
+a, %gl);}\n &align_groups ($pg, $a, $arg_list,\
+ \" -quiet=quiet \", %gl);\n }\n return %gl;\n \
+ }\n }\n\nsub tree2group \n {\n my ($N, $I\
+D, %gl)=@_;\n my $prefix=&vtmpnam();\n my $g\
+roup_file=&vtmpnam();\n my $file;\n my $oldt\
+ree=&vtmpnam();\n my $n;\n my $tree;\n\n\n \
+ if ( $gl{'Ng'}==1){return %gl;}\n $tree=$gl{'\
+Tree'}; \n \n #1 extract the groups\n &my\
+_system (\"$seq_reformat -in $tree -action +tree2g\
+roup $N $ID $prefix > $group_file\");\n $n=grou\
+p_file2ngroups($group_file);\n \n \n $gl{\
+'Newgroups'}=1;\n if ( $n==$gl{'Ng'})\n {\\
+n $gl{'Newgroups'}=0;\n return %gl;\n }\n \
+$gl{'Iteration'}++;\n $gl{'MaxNseq'}=$N;$gl{'Mi\
+nID'}=$ID;\n $gl{'GroupFile'}=$group_file;$gl{'\
+Ng'}=$ng=0;\n #2 Process the group list into th\
+e hash\n open (F, $group_file);\n while (<F>\
+)\n {\n $gl{'File'}.=$_;\n if (/\\>/)\n {\n\
+ $line=$_;\n $line=~s/\\>//;\n @list=(\
+$line=~/(\\S+)/g);\n $file=$gl{$ng}{'File'}=sh\
+ift @list;\n $gl{$file}{'Output'}=$file;\n \
+ \n $gl{$file}{'Ng'}=$#list+1;\n if ($gl{$\
+file}{'Ng'}>1){ $gl{$file}{'Tlist'}=$gl{$file}{'Al\
+ist'}=\"(\";}\n foreach $l (@list)\n {\n\
+ \n $gl{$file}{'List'}.=\" $l \";\n \n if (!$gl\
+{$l}{'Tlist'})\n {\n $gl{$l}{'Tlist'}=\"$l\
+\";\n $gl{$l}{'Alist'}=\"$l\";\n $gl{$l}\
+{'Nseq'}=1;\n $gl{$l}{'Ng'}=1;\n }\n $gl{\
+$file}{'Tlist'}.=\"$gl{$l}{'Tlist'},\";\n $gl{$fi\
+le}{'Alist'}.=\"$gl{$l}{'Tlist'}|\";\n $gl{$file}\
+{'Nseq'}+=$gl{$l}{'Nseq'};\n }\n \n\n \
+ chop($gl{$file}{'Tlist'});chop($gl{$file}{'Alist\
+'});\n if ($gl{$file}{'Ng'}>1){$gl{$file}{'Tli\
+st'}.=\")\"; $gl{$file}{'Alist'}.=\");\";}\n $\
+ng++;\n } \n }\n $gl{'Ng'}=$ng;\n clo\
+se (F);\n \n #3 Update the old tree with the\
+ new groups\n $gl{'Tree'}=&vtmpnam();\n &my_\
+system (\"$seq_reformat -in $tree -action +collaps\
+e_tree $group_file -output newick > $gl{'Tree'}\")\
+;\n \n return %gl;\n }\n\nsub display_group\
+ \n {\n my ($g,%gl)=@_;\n my $f;\n \n \
+ if ( $g==-1)\n {\n print STDERR \"\\nIterati\
+on $gl{'Iteration'} [MaxN=$gl{'MaxNseq'}][MinID=$g\
+l{'MinID'}]\";\n }\n else\n {\n\n $f=\
+$gl{$g}{'File'};\n $action=($gl{$f}{'Ng'}==1 || $g\
+l{'Iteration'}==1)?\"KEEP \":\"ALIGN \";\n \
+ print STDERR \"\\n\\t[$action][MaxN=$gl{'MaxNseq'\
+}][MinID=$gl{'MinID'}][File $f][Nseq=$gl{$f}{'Nseq\
+'}][Ngroups=$gl{$f}{'Ng'}][$gl{$f}{'Alist'}]\";\n \
+ }\n }\n \n\n\nsub align_groups\n {\n \
+ my ($pg, $g, $arg, $extra_arg,%gl)=@_;\n my $\
+f;\n my $Output,$Outflag;\n \n \n $f=$\
+gl{$g}{'File'};\n $Output=($gl{$f}{'Output'});\\
+n \n if ( $pg eq \"Align\")\n {\n if ( \
+!-e $f)\n {\n $command=\"$seq_reformat -in $\
+gl{'Seq'} -action +extract_aln $gl{'GroupFile'}\"\
+;\n if ($gl{$f}{'Ng'}>1)\n {\n &my_syst\
+em ($command);\n $command=\"t_coffee -special_mod\
+e quick_aln S$f -outfile=$Output -quiet\";\n \
+ }\n }\n else \n {$command=\"\";}\n }\n \
+ elsif ( -e $f)\n { \n $Outflag=($Output)?\\
+"-outfile=$Output\":\"\";\n $command=\"$pg -infile\
+ $f $Outflag -quiet stdout $arg $extra_arg -maxnse\
+q 0 -convert -quiet stdout\";\n }\n elsif \
+( $gl{$f}{'Ng'}==1)\n {\n $action=($dpa_debug\
+)?\"cp\":\"mv\";\n $command=\"$action $gl{$f}{'Lis\
+t'} $Output\";\n }\n else\n {\n $Outf\
+lag=($Output)?\"-outfile=$Output\":\"\";\n $comman\
+d=\"$pg -profile $gl{$f}{'List'} $Outflag $arg $ex\
+tra_arg -maxnseq 0\";\n }\n \n &my_syst\
+em ($command);\n return $outfile;\n }\n \ns\
+ub my_system \n {\n my $command=@_[0];\n my\
+ $force=@_[1];\n my $status;\n\n if ( $dpa_d\
+ebug) {print STDERR \"\\nCOMMAND: $command\";}\n \
+ $status=system ($command);\n\n if (!$force)\n\
+ {\n &exit_dpa (($status==1), \"Failed in C\
+ommand:\\n$command\\n[FATAL: t_coffee_dpa]\\n\", E\
+XIT_FAILURE);\n }\n \n return $status;\
+\n }\n\nsub vtmpnam\n {\n my $prefix=@_[0];\n\
+ my $tmp_file_name;\n\n $tmp_prefix=($prefix\
+)?$prefix:\"dpa_tmp_file_$$\";\n \n $tmp_coun\
+t++;\n $tmp_file_name=\"$tmp_prefix\".\"$tmp_co\
+unt\";\n $tl[$#tl+1]=$tmp_file_name;\n retur\
+n $tmp_file_name;\n }\n\nsub clean_tmp_file\n {\\
+n\n my $list;\n my $file;\n \n if ($dp\
+a_debug){return;}\n $list=vtmpnam();\n `ls -\
+1 | grep $tmp_prefix>$list`;\n \n open (F,$l\
+ist);\n while ( <F>)\n {\n $file=$_;\n cho\
+p $file;\n if ( -e $file){unlink $file;}\n }\\
+n close (F);\n unlink $list;\n }\n\n\nsub e\
+xit_dpa\n {\n my $condition=@_[0];\n my $error_\
+msg=@_[1];\n my $exit_value=@_[2];\n if ( $condi\
+tion)\n {\n print \"$error_msg\\n\";\n \
+ exit ($exit_value);\n }\n else\n {\n \
+ return;\n }\n \n}\nsub extract_val_from_arg_l\
+ist\n {\n my $arg=@_[0];\n my $arg_list=@_[\
+1];\n my $keep_flag=@_[2];\n my $default_val\
+ue=@_[3];\n my $val=\"\";\n \n #protect\n\
+ $arg_list=~s/\\s-/ \\@/g;\n $arg=~s/-/\\@/g\
+;\n \n #search\n if ($arg eq \"^\")\n \
+ {\n $arg_list=~/^([^@]*)/;\n $val=$1;\n }\n\
+ else\n {$arg_list=~/$arg ([^@]*)/;$val=$1\
+;}\n \n #remove trailing spaces\n $val=~s\
+/\\s*$//;\n \n #remove the parsed sequence i\
+f needed\n if (($val ne \"\") && $keep_flag ne \
+\"KEEP\")\n {\n if ( $arg eq \"^\"){$arg_list\
+=~s/$val/ /;}\n else {$arg_list=~s/($arg [^@]*)/ /\
+;}\n }\n \n #unprotect\n $arg_list=~s/\\
+\@/-/g;\n $arg=~s/\\@/-/g;\n \n if (($val\
+ eq \"\") && $default_value ne \"unset\"){$val=$de\
+fault_value;}\n \n return $val, $arg_list;\n\
+ }\n$program=\"T-COFFEE (Version_11.00.8cbe486)\"\
+;\\n\n","\n$DEBUG=1;\n$dpa_nseq=10;\n$dpa_sim=0;\n\
+if (!@ARGV)\n {\n `t_coffee`;\n exit (0);\n\
+ }\nforeach $arg (@ARGV)\n {\n $arg_list.=\" \
+$arg\";\n }\n$max_nseq=10;\n($seq0, $arg_list)=&e\
+xtract_val_from_arg_list(\"^\",$arg_list);\n($seq1\
+, $arg_list)=&extract_val_from_arg_list(\"-seq\",$\
+arg_list);\n($seq2, $arg_list)=&extract_val_from_a\
+rg_list(\"-in\",$arg_list, \"KEEP\");\n($seq3, $ar\
+g_list)=&extract_val_from_arg_list(\"-infile\",$ar\
+g_list);\n$in_seq=$seq0.\" \".$seq1.\" \".$seq2.\"\
+ \".$seq3;\n\n$seq=vtmpnam();\n`t_coffee $in_seq -\
+convert -output fasta_seq -outfile=$seq`;\n\n\n($d\
+pa_nseq, $arg_list)=&extract_val_from_arg_list(\"-\
+dpa_nseq\",$arg_list);\n($master_aln, $arg_list)=&\
+extract_val_from_arg_list(\"-master_aln\",$arg_lis\
+t);\n($sim_matrix, $arg_list)=&extract_val_from_ar\
+g_list(\"-sim_matrix\",$arg_list);\n($core_seq, $a\
+rg_list)=&extract_val_from_arg_list(\"-core_seq\",\
+$arg_list);\n($dpa_sim, $arg_list)=&extract_val_fr\
+om_arg_list(\"-dpa_sim\",$arg_list);\n($run_name, \
+$arg_list)=&extract_val_from_arg_list(\"-run_name\\
+",$arg_list);\n($output, $arg_list)=&extract_val_f\
+rom_arg_list(\"-output\",$arg_list);\n\n\n\nif (!$\
+sim_mat && !$master_aln)#Compute the fast alignmen\
+t\n {\n $ref_aln=vtmpnam();\n `t_coffee -se\
+q=$seq -very_fast -outfile=$ref_aln -quiet`;\n \
+\n }\n\nif (!$sim_mat)\n {\n $sim_mat=vtmpnam\
+();\n `seq_reformat -in $ref_aln -output sim > \
+$sim_mat`;\n }\n\nif ( !$core_seq)\n {\n $cor\
+e_seq=vtmpnam();\n `seq_reformat -in $ref_aln -\
+action +trimTC N$max_nseq -output fasta_seq > $cor\
+e_seq`;\n }\n@core_name=`seq_reformat -in $core_s\
+eq -output name `; \n\n@tot_name=`seq_reformat -in\
+ $seq -output name `;\n\nforeach $s (@core_name){$\
+s=~s/\\s//g;$hcore{$s}=1;}\nforeach $s (@tot_name)\
+{$s=~s/\\s//g;}\nprint STDERR \"T-Coffee_dpa:\\n\"\
+;\nprint STDERR \"\\tTOTAL SEQ: @tot_name\\n\";\n\
+print STDERR \"\\tCHOSEN SEQ: @core_name\\n\";\n\n\
+\n\nopen (F, $sim_mat);\nwhile ( <F>)\n {\n @l\
+=($_=~/(\\b[\\S]+\\b)/g);\n if (($l[0] eq \"TOP\
+\" || $l[0] eq \"BOT\"))\n {\n $s1=$l[1];$s2=\
+$l[2];$v=$l[3];\n if ($hcore{$s1} && !$hcore{$s2})\
+\n {\n if (!$hseq{$s2}{\"sim\"} || $v>$hseq{\
+$s2}{\"sim\"})\n {\n $hseq{$s2}{\"sim\"}=$v\
+;$hseq{$s2}{\"seq\"}=$s1;\n }\n }\n }\
+\n }\nclose (F);\nforeach $s (@tot_name)\n {\n\n\
+ if ( !$hseq{$s}{\"seq\"}){;}\n else\n \
+{\n $s2=$hseq{$s}{\"seq\"};\n $v=$hseq{$s}{\"sim\"\
+};\n \n if ($v>$dpa_sim)\n {\n $hseq{$s}{'u\
+sed'}=1;\n $seq_list{$s2}{$seq_list{$s2}{'nseq\
+'}++}=$s;\n }\n }\n }\nforeach $s (@core_n\
+ame){$seq_list{$s}{$seq_list{$s}{'nseq'}++}=$s;$hs\
+eq{$s}{'used'}=1;}\nforeach $s (@tot_name){if (!$h\
+seq{$s}{'used'}){$seq_list{'unused'}{$seq_list{'un\
+used'}{'nseq'}++}=$s;}}\n\n\n$n=0;\nforeach $s (@c\
+ore_name)\n {\n $ng++;\n $n=$seq_list{$s}{'\
+nseq'};\n for (@g_list=(), $a=0; $a<$n; $a++){@\
+g_list=(@g_list,$seq_list{$s}{$a});}\n\n $g_seq\
+=vtmpnam();\n $g_aln=vtmpnam();\n \n prin\
+t STDERR \"Group $ng: $#g_list Seq: @g_list: \";\n\
+ \n \n `seq_reformat -in $seq -action +lo\
+wer +keep_name +extract_seq @g_list -output fasta\
+_seq > $g_seq`;\n \n \n if ( $#g_list==0)\
+\n {\n print STDERR \"[No aln]\\n\";\n $g_aln\
+=$g_seq;\n }\n elsif ($#g_list<$max_nseq) \
+\n {\n print STDERR \"[t_coffee]\\n\";\n `t_c\
+offee $g_seq -outfile=$g_aln -quiet $arg_list`;\n \
+ }\n else\n {\n print STDERR \"[t_coff\
+ee_dpa]\\n\";\n `t_coffee_dpa2 $g_seq -outfile=$g_\
+aln $arg_list -sim_matrix $sim_matrix -dpa_nseq $d\
+pa_nseq`;\n }\n @profile_list=(@profile_li\
+st, $g_aln);\n }\n\n\nprint \"UNUSED $seq_list{'u\
+nused'}{'nseq'}\";\n\nif ($seq_list{'unused'}{'nse\
+q'})\n {\n $prf=vtmpnam();\n \n \
+`t_coffee -profile @profile_list $arg_list -outfil\
+e=$prf -quiet`;\n $n=$seq_list{\"unused\"}{'n\
+seq'};\n $new_seq=vtmpnam();\n $new_prf=\
+vtmpnam();\n for ($a=0; $a<$n-1; $a++)\n {\n \
+ $s=$seq_list{\"unused\"}{$a};\n print STDERR \\
+"\\nADD Sequence $s\";\n \n `seq_reformat -in \
+$seq -action +lower +keep_name +extract_seq $s -o\
+utput fasta_seq > $new_seq`;\n `t_coffee -profil\
+e $prf $new_seq $arg_list -outfile=$new_prf`;\n \
+`cp $new_prf $prf`;\n }\n $s=$seq_list{\"unus\
+ed\"}{$a};\n `seq_reformat -in $seq -action +\
+lower +keep_name +extract_seq $s -output fasta_se\
+q > $new_seq`;\n @profile_list=($prf, $new_se\
+q);\n }\n \n \nif ($run_name){$arg_list\
+.=\" -run_name $run_name\";}\nelse \n {\n $in_\
+seq=~/([\\w-]+)/;\n $arg_list.=\" -run_name $1\\
+";\n }\nif ( $output){$arg_list.=\" -output $outp\
+ut \";}\n\n`t_coffee -profile @profile_list $arg_l\
+ist`;\n\n\n&clean (@tmp_file_list);\n\n\nsub vtmpn\
+am\n {\n my $tmp_file_name;\n $tmp_name_cou\
+nter++;\n $tmp_file_name=\"tmp_file_$tmp_name_c\
+ounter\\_Pid$$\";\n $tmp_file_list[$ntmp_file++\
+]=$tmp_file_name;\n return $tmp_file_name;\n }\
+\nsub clean\n {\n my @fl=@_;\n my $file;\n ret\
+urn;\n\n foreach $file ( @fl)\n {\n if ( \
+-e $file){unlink($file);}\n }\n}\nsub extract_v\
+al_from_arg_list\n {\n my $arg=@_[0];\n my \
+$arg_list=@_[1];\n my $keep_flag=@_[2];\n #p\
+rotect\n $arg_list=~s/\\s-/ \\@/g;\n $arg=~s\
+/-/\\@/g;\n \n #search\n if ($arg eq \"^\\
+")\n {\n $arg_list=~/^([^@]*)/;\n $val=$1;\n \
+ }\n else\n {$arg_list=~/$arg ([^@]*)/\
+;$val=$1;}\n \n #remove the parsed sequence \
+if needed\n if ($val && $keep_flag ne \"KEEP\")\
+\n {\n if ( $arg eq \"^\"){$arg_list=~s/$val/\
+ /;}\n else {$arg_list=~s/($arg [^@]*)/ /;}\n \
+ }\n \n #unprotect\n $arg_list=~s/\\@/-/g;\n\
+ $arg=~s/\\@/-/g;\n \n return $val, $arg_\
+list;\n }\n\n","use Env;\nuse FileHandle;\nuse Cw\
+d;\nuse File::Path;\nuse Sys::Hostname;\n\n\nour $\
+PIDCHILD;\nour $ERROR_DONE;\nour @TMPFILE_LIST;\no\
+ur $EXIT_FAILURE=1;\nour $EXIT_SUCCESS=0;\n\nour $\
+REFDIR=getcwd;\nour $EXIT_SUCCESS=0;\nour $EXIT_FA\
+ILURE=1;\n\nour $PROGRAM=\"tc_generic_method.pl\";\
+\nour $CL=$PROGRAM;\n\nour $CLEAN_EXIT_STARTED;\no\
+ur $debug_lock=$ENV{\"DEBUG_LOCK\"};\nour $debug_g\
+eneric_method=$ENV{\"DEBUG_GENERIC_METHOD\"};\nour\
+ $LOCKDIR=$ENV{\"LOCKDIR_4_TCOFFEE\"};\nif (!$LOCK\
+DIR){$LOCKDIR=getcwd();}\nour $ERRORDIR=$ENV{\"ERR\
+ORDIR_4_TCOFFEE\"};\nour $ERRORFILE=$ENV{\"ERRORFI\
+LE_4_TCOFFEE\"};\n&set_lock ($$);\nif (isshellpid(\
+getppid())){lock4tc(getppid(), \"LLOCK\", \"LSET\"\
+, \"$$\\n\");}\nour %RECODE;\nour $RECODE_N;\n\n\n\
+\n\nour $BLAST_MAX_NRUNS=2;\nour $COMMAND;\nour $P\
+IDCHILD;\n\n$REF_EMAIL=\"\";\n$tmp_dir=\"\";\n$ini\
+t_dir=\"\";\n\n\n$test=0;\nif ($test==1)\n {\n \
+ $SERVER=\"NCBI\";\n $query=$ARGV[0];\n $hit\
+f=$ARGV[1];\n %s=read_fasta_seq($query);\n @\
+sl=keys(%s);\n &blast_xml2profile (\"xx\", $s{$\
+sl[0]}{seq},$maxid,$minid,$mincov, $hitf);\n my\
+exit ($EXIT_FAILURE);\n }\n\nforeach $v(@ARGV){$c\
+l.=\"$v \";}\n$COMMAND=$cl;\n($mode)=&my_get_opt (\
+ $cl, \"-mode=\",1,0);\n\n($A)=(&my_get_opt ( $cl,\
+ \"-name1=\",0,0));\n($B)=(&my_get_opt ( $cl, \"-n\
+ame2=\",0,0));\n($TMPDIR)=(&my_get_opt ( $cl, \"-t\
+mpdir=\",0,0));\n($CACHE)=(&my_get_opt ( $cl, \"-c\
+ache=\",0,0));\n($SERVER)=((&my_get_opt ( $cl, \"-\
+server=\",0,0)));\n($EMAIL)=((&my_get_opt ( $cl, \\
+"-email=\",0,0)));\n\nif (!$A){$A=\"A\";}\nif (!$B\
+){$B=\"B\";}\n\n\nif (!$TMPDIR)\n {\n $HOME=$E\
+NV{HOME};\n if ($ENV{TMP_4_TCOFFEE}){$TMPDIR=$E\
+NV{TMP_4_TCOFFEE};}\n else{$TMPDIR=\"$HOME/.t_c\
+offee/tmp/\";}\n }\nif ( ! -d $TMPDIR)\n {\n \
+mkdir $TMPDIR;\n }\nif ( ! -d $TMPDIR)\n {\n \
+print \"ERROR: Could not create temporary dir: $TM\
+PDIR\\n\";\n myexit ($EXIT_FAILURE);\n }\n\n$E\
+MAIL=~s/XEMAILX/\\@/g;\nif (!$EMAIL)\n {\n if \
+($ENV{EMAIL_4_TCOFFEE}){$EMAIL=$ENV{EMAIL_4_TCOFFE\
+E};}\n elsif ($ENV{EMAIL}){$EMAIL=$ENV{EMAIL};}\
+\n else {$EMAIL=$REF_EMAIL;}\n }\n\n($maxid,$m\
+inid,$mincov)=(&my_get_opt ( $cl, \"-maxid=\",0,0,\
+ \"-minid=\",0,0,\"-mincov=\",0,0));\nif (!$cl=~/\\
+\-maxid\\=/){$maxid=95;}\nif (!$cl=~/\\-minid\\=/)\
+{$minid=35;}\nif (!$cl=~/\\-mincov\\=/){$mincov=80\
+;}\n\n\n\n\nif ($mode eq \"seq_msa\")\n {\n &s\
+eq2msa($mode,&my_get_opt ( $cl, \"-infile=\",1,1, \
+\"-method=\",1,2, \"-param=\",0,0,\"-outfile=\",1,\
+0, \"-database=\",0,0));\n }\nelsif ( $mode eq \"\
+tblastx_msa\")\n {\n &seq2tblastx_lib ($mode,&\
+my_get_opt ( $cl, \"-infile=\",1,1, \"-outfile=\",\
+1,0));\n }\nelsif ( $mode eq \"tblastpx_msa\")\n \
+ {\n &seq2tblastpx_lib ($mode,&my_get_opt ( $cl\
+, \"-infile=\",1,1, \"-outfile=\",1,0));\n }\nels\
+if ( $mode eq \"thread_pair\")\n {\n &seq2thre\
+ad_pair($mode,&my_get_opt ( $cl, \"-infile=\",1,1,\
+ \"-pdbfile1=\",1,1, \"-method=\",1,2,\"-param=\",\
+0,0, \"-outfile=\",1,0, ));\n }\nelsif ( $mode eq\
+ \"pdbid_pair\")\n {\n &seq2pdbid_pair($mode,&\
+my_get_opt ( $cl, \"-pdbfile1=\",1,0, \"-pdbfile2=\
+\",1,0, \"-method=\",1,2,\"-param=\",0,0, \"-outfi\
+le=\",1,0, ));\n }\nelsif ( $mode eq \"pdb_pair\"\
+)\n {\n &seq2pdb_pair($mode,&my_get_opt ( $cl,\
+ \"-pdbfile1=\",1,1, \"-pdbfile2=\",1,1, \"-method\
+=\",1,2,\"-param=\",0,0, \"-outfile=\",1,0, ));\n \
+ }\nelsif ( $mode eq \"rnapdb_pair\")\n{\n &seq\
+2rnapdb_pair($mode,&my_get_opt ( $cl, \"-pdbfile1=\
+\",1,1, \"-pdbfile2=\",1,1, \"-method=\",1,2,\"-pa\
+ram=\",0,0, \"-outfile=\",1,0, ));\n}\nelsif ( $mo\
+de eq \"profile_pair\")\n {\n &seq2profile_pa\
+ir($mode,&my_get_opt ( $cl, \"-profile1=\",1,1, \"\
+-profile2=\",1,1, \"-method=\",1,2,\"-param=\",0,0\
+, \"-outfile=\",1,0 ));\n }\nelsif ($mode eq \"pd\
+b_template_test\")\n {\n &blast2pdb_template_t\
+est ($mode,&my_get_opt ( $cl, \"-infile=\",1,1));\\
+n\n }\nelsif ($mode eq \"psi_template_test\")\n \
+{\n &psiblast2profile_template_test ($mode,&my_\
+get_opt ( $cl, \"-seq=\",1,1,\"-blast=\",1,1));\n\\
+n }\n\nelsif ( $mode eq \"pdb_template\")\n {\n \
+ &blast2pdb_template ($mode,&my_get_opt ( $cl, \\
+"-infile=\",1,1, \"-database=\",1,0, \"-method=\",\
+1,0, \"-outfile=\",1,0,\"-pdb_type=\",1,0));\n }\\
+n\nelsif ( $mode eq \"profile_template\")\n {\n\n\
+ &psiblast2profile_template ($mode,&my_get_opt \
+( $cl, \"-infile=\",1,1, \"-database=\",1,0, \"-me\
+thod=\",1,0, \"-outfile=\",1,0));\n }\nelsif ( $m\
+ode eq \"psiprofile_template\")\n {\n &psiblas\
+t2profile_template ($mode,&my_get_opt ( $cl, \"-in\
+file=\",1,1, \"-database=\",1,0, \"-method=\",1,0,\
+ \"-outfile=\",1,0));\n }\nelsif ( $mode eq \"RNA\
+_template\")\n {\n &seq2RNA_template ($mode,&m\
+y_get_opt ( $cl, \"-infile=\",1,1,\"-pdbfile=\",1,\
+1,\"-outfile=\",1,0));\n }\nelsif ( $mode eq \"tm\
+_template\")\n {\n &seq2tm_template ($mode, \"\
+\", &my_get_opt ( $cl, \"-infile=\",1,1,\"-arch=\"\
+,1,1,\"-psv=\",1,1, \"-outfile=\",1,0,));\n }\nel\
+sif ( $mode eq \"psitm_template\")\n {\n &seq2\
+tm_template ($mode,&my_get_opt ( $cl, \"-database=\
+\",1,0, \"-infile=\",1,1, \"-arch=\",1,1,\"-psv=\"\
+,1,1, \"-outfile=\",1,0,));\n }\nelsif ( $mode eq\
+ \"ssp_template\")\n {\n &seq2ssp_template ($m\
+ode,&my_get_opt ( $cl, \"-infile=\",1,1,\"-seq=\",\
+1,1,\"-obs=\",1,1, \"-outfile=\",1,0));\n }\nelsi\
+f ( $mode eq \"psissp_template\")\n {\n &seq2s\
+sp_template ($mode,&my_get_opt ( $cl, \"-infile=\"\
+,1,1,\"-seq=\",1,1,\"-obs=\",1,1, \"-outfile=\",1,\
+0));\n }\n\n\n\nelse\n {\n myexit(flush_error\
+( \"$mode iss an unknown mode of tc_generic_method\
+.pl\"));\n }\nmyexit ($EXIT_SUCCESS);\n\n\nsub se\
+q2ssp_template\n {\n my ($mode, $infile,$gor_seq\
+,$gor_obs,$outfile)=@_;\n my %s, %h;\n my $resul\
t;\n my (@profiles);\n &set_temporary_dir (\"set\
\",$infile,\"seq.pep\");\n %s=read_fasta_seq (\"s\
-eq.pep\");\n\n \n open (R, \">result.aln\");\n \
-\n #print stdout \"\\n\";\n foreach $seq (keys(%\
-s))\n {\n open (F, \">seqfile\");\n p\
-rint (F \">$s{$seq}{name}\\n$s{$seq}{seq}\\n\");\n\
- close (F);\n $lib_name=\"$s{$seq}{name}\
-.tmp\";\n $lib_name=&clean_file_name ($lib_na\
-me);\n\n if ($mode eq \"tm_template\")\n {\n \
- &safe_system (\"t_coffee -other_pg fasta_seq2hmm\
-top_fasta.pl -in=seqfile -out=$lib_name -arch=$arc\
-h -psv=$psv\");\n }\n elsif ( $mode eq \"psit\
-m_template\")\n {\n &seq2msa_tm_prediction ($s{$\
-seq}{name},$s{$seq}{seq}, $db, \"seqfile\", $lib_n\
-ame,$arch, $psv);\n }\n if ( !-e $lib_name)\n\
- {\n myexit(flush_error(\"RNAplfold failed to co\
-mpute the secondary structure of $s{$seq}{name}\")\
-);\n myexit ($EXIT_FAILURE);\n }\n else\n {\
-\n print stdout \"\\tProcess: >$s{$seq}{name} _T\
-_ $lib_name\\n\";\n print R \">$s{$seq}{name} _T\
-_ $lib_name\\n\";\n }\n unshift (@profiles, $\
-lib_name);\n }\n close (R);\n &set_temporary_\
-dir (\"unset\",$mode, $method,\"result.aln\",$outf\
-ile, @profiles);\n}\n\nsub seq2RNA_template\n {\n\
- my ($mode, $infile,$outfile)=@_;\n my %s, %h, ;\
-\n my $result;\n my (@profiles);\n &set_tempora\
-ry_dir (\"set\",$infile,\"seq.pep\");\n %s=read_f\
-asta_seq (\"seq.pep\");\n\n \n open (R, \">resul\
-t.aln\");\n \n #print stdout \"\\n\";\n foreach\
- $seq (keys(%s))\n {\n open (F, \">seqfile\
-\");\n print (F \">$s{$seq}{name}\\n$s{$seq}{\
-seq}\\n\");\n close (F);\n $lib_name=\"$\
-s{$seq}{name}.rfold\";\n $lib_name=&clean_fil\
-e_name ($lib_name);\n &safe_system (\"t_coffe\
-e -other_pg RNAplfold2tclib.pl -in=seqfile -out=$l\
-ib_name\");\n \n if ( !-e $lib_name)\n {\
-\n myexit(flush_error(\"RNAplfold failed to compu\
-te the secondary structure of $s{$seq}{name}\"));\\
-n myexit ($EXIT_FAILURE);\n }\n else\n {\n \
- print stdout \"\\tProcess: >$s{$seq}{name} _F_ $\
-lib_name\\n\";\n print R \">$s{$seq}{name} _F_ $\
-lib_name\\n\";\n }\n unshift (@profiles, $lib\
-_name);\n }\n close (R);\n &set_temporary_dir\
- (\"unset\",$mode, $method,\"result.aln\",$outfile\
-, @profiles);\n}\nsub psiblast2profile_template_te\
-st\n {\n my ($mode, $seq,$blast)=@_;\n my %s, %\
-h, ;\n my ($result,$psiblast_output,$profile_name\
-,@profiles);\n my $trim=0;\n my $maxid=100;\n m\
-y $minid=0;\n my $mincov=0;\n my $maxcov=100;\n \
- \n %s=read_fasta_seq ($seq);\n open (R, \">resu\
-lt.aln\");\n \n #print stdout \"\\n\";\n foreac\
-h $seq (keys(%s))\n {\n \n open (F, \\
-">seqfile\");\n print (F \">$A\\n$s{$seq}{seq\
-}\\n\");\n close (F);\n $psiblast_output\
-=$blast;\n if ( -e $psiblast_output)\n {\n \
-%profile=blast_xml2profile($s{$seq}{name}, $s{$seq\
-}{seq},$maxid, $minid,$mincov,$psiblast_output);\n\
-\n\n \n $profile_name=\"$s{$seq}{name}.prf\";\\
-n $profile_name=&clean_file_name ($profile_name)\
-;\n unshift (@profiles, $profile_name);\n outp\
-ut_profile ($profile_name, \\%profile, $trim);\n \
- print stdout \"\\tProcess: >$s{$seq}{name} _R_ $p\
-rofile_name [$profile{n} Seq.] [$SERVER/blast/$db]\
-[$CACHE_STATUS]\\n\";\n print R \">$s{$seq}{name\
-} _R_ $profile_name\\n\";\n }\n }\n close (R);\
-\n \n die;\n}\nsub psiblast2profile_template \n \
- {\n my ($mode, $infile, $db, $method, $outfile)=\
-@_;\n my %s, %h, ;\n my ($result,$psiblast_outpu\
-t,$profile_name,@profiles);\n my $trim=0;\n &set\
-_temporary_dir (\"set\",$infile,\"seq.pep\");\n %\
-s=read_fasta_seq (\"seq.pep\");\n open (R, \">res\
-ult.aln\");\n \n #print stdout \"\\n\";\n forea\
-ch $seq (keys(%s))\n {\n open (F, \">seqfi\
+eq.pep\");\n\n\n open (R, \">result.aln\");\n\n \
+#print stdout \"\\n\";\n foreach $seq (keys(%s))\\
+n {\n\n open (F, \">seqfile\");\n $s{\
+$seq}{seq}=uc$s{$seq}{seq};\n print (F \">$s{\
+$seq}{name}\\n$s{$seq}{seq}\\n\");\n close (F\
+);\n $lib_name=\"$s{$seq}{name}.ssp\";\n \
+ $lib_name=&clean_file_name ($lib_name);\n\n \
+if ($mode eq \"ssp_template\"){&seq2gor_prediction\
+ ($s{$seq}{name},$s{$seq}{seq}, \"seqfile\", $lib_\
+name,$gor_seq, $gor_obs);}\n elsif ($mode eq \
+\"psissp_template\")\n {\n &seq2msa_gor_predicti\
+on ($s{$seq}{name},$s{$seq}{seq},\"seqfile\", $lib\
+_name,$gor_seq, $gor_obs);\n }\n\n if ( !-e $\
+lib_name)\n {\n myexit(flush_error(\"GORIV faile\
+d to compute the secondary structure of $s{$seq}{n\
+ame}\"));\n myexit ($EXIT_FAILURE);\n }\n e\
+lse\n {\n print stdout \"!\\tProcess: >$s{$seq}{\
+name} _E_ $lib_name \\n\";\n print R \">$s{$seq}\
+{name} _E_ $lib_name\\n\";\n }\n unshift (@pr\
+ofiles, $lib_name);\n }\n close (R);\n &set_t\
+emporary_dir (\"unset\",$mode, $method,\"result.al\
+n\",$outfile, @profiles);\n}\n\nsub seq2tm_templat\
+e\n {\n my ($mode, $db, $infile,$arch,$psv,$outf\
+ile)=@_;\n my %s, %h;\n my $result;\n my (@prof\
+iles);\n &set_temporary_dir (\"set\",$infile,\"se\
+q.pep\");\n %s=read_fasta_seq (\"seq.pep\");\n\n\\
+n open (R, \">result.aln\");\n\n #print stdout \\
+"\\n\";\n foreach $seq (keys(%s))\n {\n o\
+pen (F, \">seqfile\");\n print (F \">$s{$seq}\
+{name}\\n$s{$seq}{seq}\\n\");\n close (F);\n \
+ $lib_name=\"$s{$seq}{name}.tmp\";\n $lib\
+_name=&clean_file_name ($lib_name);\n\n if ($\
+mode eq \"tm_template\")\n {\n &safe_system (\"t\
+_coffee -other_pg fasta_seq2hmmtop_fasta.pl -in=se\
+qfile -out=$lib_name -arch=$arch -psv=$psv\");\n }\
+\n elsif ( $mode eq \"psitm_template\")\n {\n\
+ &seq2msa_tm_prediction ($s{$seq}{name},$s{$seq}\
+{seq}, $db, \"seqfile\", $lib_name,$arch, $psv);\n\
+ }\n if ( !-e $lib_name)\n {\n myexit(flush\
+_error(\"hmmtop failed to compute the secondary st\
+ructure of $s{$seq}{name}\"));\n myexit ($EXIT_F\
+AILURE);\n }\n else\n {\n print stdout \"!\\
+\tProcess: >$s{$seq}{name} _T_ $lib_name\\n\";\n \
+ print R \">$s{$seq}{name} _T_ $lib_name\\n\";\n }\
+\n unshift (@profiles, $lib_name);\n }\n \
+close (R);\n &set_temporary_dir (\"unset\",$mode,\
+ $method,\"result.aln\",$outfile, @profiles);\n}\n\
+\n\n\nsub seq2RNA_template\n {\n \n my ($mo\
+de, $infile, $pdbfile, $outfile)=@_;\n my %s, %\
+h ;\n my $result;\n my (@profiles);\n my \
+($seq_mode, $pdb_mode, $pwd);\n \n #use $seq\
+_mode to estimate the template of sequences WITHOU\
+T a PDB\n #use $pdb_mode to estimate the templa\
+te of sequences WITH a PDB\n\n $seq_mode=$EN\
+V{\"SEQ2TEMPLATE4_F_\"};\n $pdb_mode=$ENV{\"PDB\
+2TEMPLATE4_F_\"};\n \n if (!$pdb_mode){$pdb_\
+mode=\"find_pair-p\";}\n if (!$seq_mode){$seq_m\
+ode=\"RNAplfold\";}\n \n my $cwd = cwd();\n \
+ &set_temporary_dir (\"set\",$infile,\"seq.pep\"\
+);\n %s=read_fasta_seq (\"seq.pep\");\n %pdb\
+_template_h = &read_template_file($pdbfile);\n \
+my $pdb_chain;\n \n \n open (R, \">res\
+ult.aln\");\n #print stdout \"\\n\";\n forea\
+ch $seq (keys(%s))\n {\n \n open (F, \">seqfi\
+le\");\n print (F \">$s{$seq}{name}\\n$s{$seq}{seq\
+}\\n\");\n close (F);\n $pdb_chain = $pdb_template\
+_h{$seq};\n $lib_name=\"$s{$seq}{name}.rfold\";\n \
+$lib_name=&clean_file_name ($lib_name);\n if ($pdb\
+_template_h{$seq} eq \"\")\n {\n if ($seq\
+_mode eq \"RNAplfold\"){RNAplfold2lib (\"seqfile\"\
+, \"$lib_name\");}\n elsif ($seq_mode eq \"no\\
+"){$lib_name=0;}\n else\n {\n myexit(ad\
+d_error (EXIT_FAILURE,$$,$$,getppid(), \"seq2RNA_t\
+emplate failure::method $seq_mode not available fo\
+r sequences without PDB structures\"));\n }\\
+n }\n elsif ($pdb_template_h{$seq} ne \"\")\n \
+{\n my $pdbf;\n if (-e \"$cwd/$pdb_chain\"\
+){$pdbf=\"$cwd/$pdb_chain\";}\n else {$pdbf=\"\
+$CACHE$pdb_chain\";}\n \n\n if($pdb_mode e\
+q \"x3dna-ssr\")\n {\n x3dnassr2lib (\"seqf\
+ile\", \"$pdbf\", \"$lib_name\");\n }\n \
+elsif ($pdb_mode eq \"find_pair-p\")\n {\n \
+x3dna_find_pair2lib (\"seqfile\", \"$pdbf\", \"$li\
+b_name\", \"find_pair -p\");\n }\n elsif\
+ ($pdb_mode eq \"find_pair\")\n {\n x3dna_f\
+ind_pair2lib (\"seqfile\", \"$pdbf\", \"$lib_name\\
+", \"find_pair\");\n }\n elsif ($pdb_mod\
+e eq \"RNAplfold\")\n {\n RNAplfold2lib (\"\
+seqfile\", \"$lib_name\");\n }\n elsif (\
+$pdb_mode eq \"no\"){$lib_name=0;}\n else\n \
+ {\n myexit(add_error (EXIT_FAILURE,$$,$$,getp\
+pid(), \"seq2RNA_template failure::Could not find \
+method $pdb_mode\"));\n }\n }\n if ($lib_n\
+ame)\n {\n print stdout \"!\\tProcess: >$s{$\
+seq}{name} _F_ $lib_name\\n\";\n print R \">$s\
+{$seq}{name} _F_ $lib_name\\n\";\n unshift (@p\
+rofiles, $lib_name);\n }\n }\n close (R)\
+;\n &set_temporary_dir (\"unset\",$mode, $metho\
+d,\"result.aln\",$outfile, @profiles);\n }\n\n\n\\
+nsub psiblast2profile_template_test\n {\n my ($m\
+ode, $seq,$blast)=@_;\n my %s, %h, ;\n my ($resu\
+lt,$psiblast_output,$profile_name,@profiles);\n m\
+y $trim=0;\n my $maxid=100;\n my $minid=0;\n my\
+ $mincov=0;\n my $maxcov=100;\n\n %s=read_fasta_\
+seq ($seq);\n open (R, \">result.aln\");\n\n #pr\
+int stdout \"\\n\";\n foreach $seq (keys(%s))\n \
+ {\n\n open (F, \">seqfile\");\n print \
+(F \">$A\\n$s{$seq}{seq}\\n\");\n close (F);\\
+n $psiblast_output=$blast;\n if ( -e $ps\
+iblast_output)\n {\n %profile=blast_xml2profile(\
+$s{$seq}{name}, $s{$seq}{seq},$maxid, $minid,$minc\
+ov,$psiblast_output);\n\n\n\n $profile_name=\"$s\
+{$seq}{name}.prf\";\n $profile_name=&clean_file_\
+name ($profile_name);\n unshift (@profiles, $pro\
+file_name);\n output_profile ($profile_name, \\%\
+profile, $trim);\n print stdout \"!\\tProcess: >\
+$s{$seq}{name} _R_ $profile_name [$profile{n} Seq.\
+] [$SERVER/blast/$db][$CACHE_STATUS]\\n\";\n pri\
+nt R \">$s{$seq}{name} _R_ $profile_name\\n\";\n }\
+\n }\n close (R);\n\n die;\n}\nsub psiblast2p\
+rofile_template\n {\n my ($mode, $infile, $db, $\
+method, $outfile)=@_;\n my %s, %h, ;\n my ($resu\
+lt,$psiblast_output,$profile_name,@profiles);\n m\
+y $trim=0;\n &set_temporary_dir (\"set\",$infile,\
+\"seq.pep\");\n %s=read_fasta_seq (\"seq.pep\");\\
+n open (R, \">result.aln\");\n\n #print stdout \\
+"\\n\";\n foreach $seq (keys(%s))\n {\n o\
+pen (F, \">seqfile\");\n print (F \">$A\\n$s{\
+$seq}{seq}\\n\");\n close (F);\n $psibla\
+st_output=&run_blast ($s{$seq}{name},$method, $db,\
+ \"seqfile\",\"outfile\");\n\nif ( -e $psiblast_ou\
+tput)\n {\n %profile=blast_xml2profile($s{$seq}{\
+name}, $s{$seq}{seq},$maxid, $minid,$mincov,$psibl\
+ast_output);\n unlink ($psiblast_output);\n\n \
+$profile_name=\"$s{$seq}{name}.prf\";\n $profile\
+_name=&clean_file_name ($profile_name);\n unshif\
+t (@profiles, $profile_name);\n output_profile (\
+$profile_name, \\%profile, $trim);\n print stdou\
+t \"!\\tProcess: >$s{$seq}{name} _R_ $profile_name\
+ [$profile{n} Seq.] [$SERVER/blast/$db][$CACHE_STA\
+TUS]\\n\";\n print R \">$s{$seq}{name} _R_ $prof\
+ile_name\\n\";\n }\n }\n close (R);\n &set_te\
+mporary_dir (\"unset\",$mode, $method,\"result.aln\
+\",$outfile, @profiles);\n}\nsub blast2pdb_templat\
+e_test\n {\n my ($mode,$infile)=@_;\n \
+ my ($maxid,$minid,$mincov);\n $maxid=100;\n \
+ $minid=0;\n $mincov=0;\n\n print \"\
+$infile\\n\";\n\n %p=blast_xml2profile($s{$se\
+q}{name}, $s{$seq}{seq},$maxid, $minid,$mincov,$in\
+file);\n $c=1;\n print stdout \"!\\tProc\
+ess: >$s{$seq}{name} [$SERVER/blast/$db][$CACHE_ST\
+ATUS]\\n\";\n while (!$found && $c<$p{n})\n {\
+\n $pdbid=&id2pdbid($p{$c}{identifyer});\n if \
+( length ($pdbid)>5){$pdbid=id2pdbid($p{$c}{defini\
+tion});}\n\n if ( length ($pdbid)>5)\n {\n \
+ myexit(add_error (EXIT_FAILURE,$$,$$,getppid(\
+), \"BLAST_FAILURE::Could Not Parse PDBID ($p{$c}{\
+identifyer},$p{$c}{definition})\"));\n }\n\n\n\
+ if (!&pdb_is_released($pdbid))\n {\n \
+print stdout \"\\t\\t**$pdbid [PDB NOT RELEASED or\
+ WITHDRAWN]\\n\";\n $c++;\n }\n elsif \
+(!&pdb_has_right_type ($pdbid,$type))\n {\n \
+ my $ptype=&pdb2type ($pdbid);\n my $etyp\
+e=&type2etype($type);\n\n print stdout \"\\t\
+\\t**$pdbid [$ptype cannot be used (expected: $ety\
+pe)]\\n\";\n $c++;\n }\n else\n {\\
+n $found=1;\n }\n }\n\n if ($found)\
+\n {\n print stdout \"\\t\\t >$s{$seq}{name} _P_\
+ $pdbid\\n\";\n }\n else\n {\n print stdout\
+ \"\\t\\t >$s{$seq}{name} No Template Selected\\n\\
+";\n }\n die;\n }\nsub blast2pdb_template\\
+n {\n my ($mode, $infile, $db, $method, $outfile\
+,$type)=@_;\n my %s, %h, ;\n my ($result,$blast_\
+output);\n &set_temporary_dir (\"set\",$infile,\"\
+seq.pep\");\n %s=read_fasta_seq (\"seq.pep\");\n \
+ open (R, \">result.aln\");\n\n\n #print stdout \\
+"\\n\";\n foreach $seq (keys(%s))\n {\n m\
+y $c;\n my $found;\n\n open (F, \">seqfi\
le\");\n print (F \">$A\\n$s{$seq}{seq}\\n\")\
-;\n close (F);\n $psiblast_output=&run_b\
-last ($s{$seq}{name},$method, $db, \"seqfile\",\"o\
-utfile\");\n \nif ( -e $psiblast_output)\n {\\
-n %profile=blast_xml2profile($s{$seq}{name}, $s{\
-$seq}{seq},$maxid, $minid,$mincov,$psiblast_output\
-);\n unlink ($psiblast_output);\n \n $profil\
-e_name=\"$s{$seq}{name}.prf\";\n $profile_name=&\
-clean_file_name ($profile_name);\n unshift (@pro\
-files, $profile_name);\n output_profile ($profil\
-e_name, \\%profile, $trim);\n print stdout \"\\t\
-Process: >$s{$seq}{name} _R_ $profile_name [$profi\
-le{n} Seq.] [$SERVER/blast/$db][$CACHE_STATUS]\\n\\
-";\n print R \">$s{$seq}{name} _R_ $profile_name\
-\\n\";\n }\n }\n close (R);\n &set_temporary_\
-dir (\"unset\",$mode, $method,\"result.aln\",$outf\
-ile, @profiles);\n}\nsub blast2pdb_template_test\n\
- {\n my ($mode,$infile)=@_;\n my ($ma\
-xid,$minid,$mincov);\n $maxid=100;\n $mi\
-nid=0;\n $mincov=0;\n \n print \"$i\
-nfile\\n\";\n \n %p=blast_xml2profile($s\
-{$seq}{name}, $s{$seq}{seq},$maxid, $minid,$mincov\
-,$infile);\n $c=1;\n print stdout \"\\tP\
-rocess: >$s{$seq}{name} [$SERVER/blast/$db][$CACHE\
-_STATUS]\\n\";\n while (!$found && $c<$p{n})\\
-n {\n $pdbid=&id2pdbid($p{$c}{identifyer});\n \
-if ( length ($pdbid)>5){$pdbid=id2pdbid($p{$c}{def\
-inition});}\n \n if ( length ($pdbid)>5)\n \
- {\n myexit(add_error (EXIT_FAILURE,$$,$$,ge\
-tppid(), \"BLAST_FAILURE::Could Not Parse PDBID ($\
-p{$c}{identifyer},$p{$c}{definition})\"));\n }\
-\n \n \n if (!&pdb_is_released($pdbid))\n \
- {\n print stdout \"\\t\\t**$pdbid [PDB NOT\
- RELEASED or WITHDRAWN]\\n\";\n $c++;\n \
-}\n elsif (!&pdb_has_right_type ($pdbid,$type))\\
-n {\n my $ptype=&pdb2type ($pdbid);\n \
- my $etype=&type2etype($type);\n \n \
- print stdout \"\\t\\t**$pdbid [$ptype cannot be u\
-sed (expected: $etype)]\\n\";\n $c++;\n \
-}\n else\n {\n $found=1;\n }\n }\n\
-\n if ($found)\n {\n print stdout \"\\t\\t \
->$s{$seq}{name} _P_ $pdbid\\n\";\n }\n else\n\
- {\n print stdout \"\\t\\t >$s{$seq}{name} No Te\
-mplate Selected\\n\";\n }\n die;\n }\nsub \
-blast2pdb_template \n {\n my ($mode, $infile, $d\
-b, $method, $outfile,$type)=@_;\n my %s, %h, ;\n \
- my ($result,$blast_output);\n &set_temporary_dir\
- (\"set\",$infile,\"seq.pep\");\n %s=read_fasta_s\
-eq (\"seq.pep\");\n open (R, \">result.aln\");\n \
- \n \n #print stdout \"\\n\";\n foreach $seq (ke\
-ys(%s))\n {\n my $c;\n my $found;\n \
- \n open (F, \">seqfile\");\n print (\
-F \">$A\\n$s{$seq}{seq}\\n\");\n close (F);\n\
- \n $blast_output=&run_blast ($s{$seq}{na\
-me},$method, $db, \"seqfile\",\"outfile\");\n \
-\n %p=blast_xml2profile($s{$seq}{name}, $s{$s\
-eq}{seq},$maxid, $minid,$mincov,$blast_output);\n \
- unlink ($blast_output);\n \n $c=1;\\
-n print stdout \"\\tProcess: >$s{$seq}{name} \
-[$SERVER/blast/$db][$CACHE_STATUS]\\n\";\n wh\
-ile (!$found && $c<$p{n})\n {\n $pdbid=&id2pdbid\
-($p{$c}{identifyer});\n if ( length ($pdbid)>5){\
-$pdbid=id2pdbid($p{$c}{definition});}\n\n if ( l\
-ength ($pdbid)>5)\n {\n myexit(add_error\
- (EXIT_FAILURE,$$,$$,getppid(), \"BLAST_FAILURE::C\
-ould Not Parse PDBID ($p{$c}{identifyer},$p{$c}{de\
-finition})\"));\n }\n \n\n if (!&pdb_is_re\
-leased($pdbid))\n {\n print stdout \"\\t\
-\\t**$pdbid [PDB NOT RELEASED or WITHDRAWN]\\n\";\\
-n $c++;\n }\n elsif (!&pdb_has_right_t\
-ype ($pdbid,$type))\n {\n my $ptype=&pdb\
-2type ($pdbid);\n my $etype=&type2etype($typ\
-e);\n \n print stdout \"\\t\\t**$pdbid\
- [$ptype cannot be used (expected: $etype)]\\n\";\\
-n $c++;\n }\n else\n {\n $fo\
-und=1;\n }\n }\n\n if ($found)\n {\n pr\
-int R \">$s{$seq}{name} _P_ $pdbid\\n\";\n print\
- stdout \"\\t\\t >$s{$seq}{name} _P_ $pdbid\\n\";\\
-n }\n else\n {\n print R \">$s{$seq}{name}\\
-\n\";\n print stdout \"\\t\\t >$s{$seq}{name} No\
- Template Selected\\n\";\n }\n }\n close (R);\\
-n &set_temporary_dir (\"unset\",$mode, $method,\"\
-result.aln\",$outfile);\n}\nsub type2etype\n {\n \
- my $type=shift;\n my $etype;\n \n if (\
- $type=~/n/){$etype.=\"NMR \";}\n if ( $type=~/\
-d/){$etype.=\"diffraction \";}\n if ( $type=~/m\
-/){$etype.=\"model \";}\n return $etype;\n }\n\
-sub pdb2type\n {\n my $pdb=shift;\n my $f\
-=vtmpnam();\n \n my $value= &safe_system (\
-\"t_coffee -other_pg extract_from_pdb -model_type \
-$pdb > $f\");\n my $r=&file2string ($f);\n \
- chomp($r);\n return $r;\n }\nsub pdb_has_ri\
-ght_type\n {\n my $pdb=shift;\n my $type=sh\
-ift;\n \n my $f=vtmpnam();\n \n my $va\
-lue= &safe_system (\"t_coffee -other_pg extract_fr\
-om_pdb -model_type $pdb > $f\");\n my $r=&file2\
-string ($f);\n chomp($r);\n\n \n if (\
- $r eq \"NMR\" && $type=~/n/){return 1;}\n elsi\
-f ( $r eq \"diffraction\" && $type=~/d/){return 1;\
-}\n elsif ( $r eq \"model\" && $type=~/m/){retu\
-rn 1;}\n else {return 0;}\n }\nsub pdb_is_rele\
-ased\n {\n my $pdb=shift;\n my $f=vtmpnam()\
-;\n \n $value= &safe_system (\"t_coffee -oth\
-er_pg extract_from_pdb -is_released_pdb_name $pdb \
-> $f\");\n my $r=&file2string ($f);\n chomp(\
-$r);\n return $r;\n }\nsub blast_msa\n {\n \
- my ($infile,$db,$outfile)=@_;\n my ($a, %seq);\
-\n my $seqfile;\n my $SEQ=new FileHandle;\n \
- my $seqfile=\"seqfile\";\n my @txt;\n \n \
- \n %s1=&read_fasta_seq ($db);\n \n for\
-each $s (keys (%s1))\n {\n $i=$s1{$s}{order};\
-\n $s{$i}{name}=$s;\n $s{$i}{seq}=$s1{$s}{seq};\n \
-$s{$i}{len}=length( $s{$i}{seq});\n $s{n}++;\n \
- }\n \n &safe_system (\"formatdb -i $db\");\
-\n &safe_system (\"blastall -i $infile -d $db \
--m7 -p blastp -o io\");\n &set_blast_type (\"io\
-\");\n \n %FB=&xml2tag_list (\"io\", \"Itera\
-tion\");\n open (F, \">$outfile\");\n print \
-F \"! TC_LIB_FORMAT_01\\n\";\n print F \"$s{n}\\
-\n\";\n for ( $a=0; $a<$s{n}; $a++)\n {\n \
-print F \"$s{$a}{name} $s{$a}{len} $s{$a}{seq}\\n\\
-";\n }\n\n\n for ( $a=0; $a<$FB{n}; $a++)\\
-n {\n %p=blast_xml2profile ($s{$a}{name}, $s{\
-$a}{seq},100, 0, 0, $FB{$a}{body});\n my $query=$p\
-{0}{name};\n my $i= $s1{$query}{order}+1;\n for ($\
-b=1; $b<$p{n}; $b++)\n {\n my $l=length ($p{\
-$b}{Qseq});\n my $hit=$p{$b}{definition};\n \
- my $Qstart=$p{$b}{Qstart};\n my $Hstart=$p{$\
-b}{Hstart};\n my $identity=$p{$b}{identity};\n\
- my @lrQ=split (//,$p{$b}{Qseq});\n my @lr\
-H=split (//,$p{$b}{Hseq});\n \n my $j= $s1\
-{$hit}{order}+1;\n #if ( $j==$i){next;}\n \
-printf F \"# %d %d\\n\", $i, $j;\n # print F\
- \"\\n$p{$b}{Qseq} ($Qstart)\\n$p{$b}{Hseq} ($Hsta\
-rt)\";\n for ($c=0; $c<$l; $c++)\n {\n \
-my $rQ=$lrQ[$c];\n my $rH=$lrH[$c];\n my $n=0;\n\
- \n if ($rQ ne \"-\"){$n++, $Qstart++;}\n if ($\
-rH ne \"-\"){$n++; $Hstart++;}\n \n if ( $n==2)\\
-n {\n printf F \"\\t%d %d %d\\n\", $Qstart\
--1, $Hstart-1,$identity;\n }\n }\n }\n \
- }\n print F \"! SEQ_1_TO_N\\n\";\n clos\
-e (F);\n return $output;\n \n }\n\nsub blast_\
-msa_old\n {\n my ($infile,$outfile)=@_;\n m\
-y ($a, %seq);\n %s1=&read_fasta_seq ($infile);\\
-n foreach $s (keys (%s1))\n {\n $i=$s1{$s}\
-{order};\n $s{$i}{name}=$s;\n $s{$i}{seq}=$s1{$s}{\
-seq};\n $s{$i}{len}=length( $s{$i}{seq});\n $s{n}+\
-+;\n }\n &safe_system (\"formatdb -i $infi\
-le\");\n &safe_system (\"blastall -i $infile -d\
- $infile -m7 -o io\");\n &set_blast_type (\"io\\
-");\n \n %FB=&xml2tag_list (\"io\", \"Iterat\
-ion\");\n \n open (F, \">$outfile\");\n p\
-rint F \"! TC_LIB_FORMAT_01\\n\";\n print F \"$\
-s{n}\\n\";\n for ( $a=0; $a<$s{n}; $a++)\n \
- {\n print F \"$s{$a}{name} $s{$a}{len} $s{$a}{seq\
-}\\n\";\n }\n for ( $a=0; $a<$FB{n}; $a++)\
-\n {\n %p=blast_xml2profile ($s{$a}{name}, $s\
-{$a}{seq},100, 0, 0, $FB{$a}{body});\n for ($b=1; \
-$b<$p{n}; $b++)\n {\n my $l=length ($p{$b}{Q\
-seq});\n my $hit=$p{$b}{definition};\n my \
-$Qstart=$p{$b}{Qstart};\n my $Hstart=$p{$b}{Hs\
-tart};\n my $identity=$p{$b}{identity};\n \
-my @lrQ=split (//,$p{$b}{Qseq});\n my @lrH=spl\
-it (//,$p{$b}{Hseq});\n my $i= $s1{$s{$a}{name\
-}}{order}+1;\n my $j= $s1{$hit}{order}+1;\n \
- #if ( $j==$i){next;}\n printf F \"# %d %d\\n\
-\", $i, $j;\n # print F \"\\n$p{$b}{Qseq} ($\
-Qstart)\\n$p{$b}{Hseq} ($Hstart)\";\n for ($c=\
-0; $c<$l; $c++)\n {\n my $rQ=$lrQ[$c];\n m\
-y $rH=$lrH[$c];\n my $n=0;\n \n if ($rQ ne \"-\\
-"){$n++, $Qstart++;}\n if ($rH ne \"-\"){$n++; $H\
-start++;}\n \n if ( $n==2)\n {\n printf \
-F \"\\t%d %d %d\\n\", $Qstart-1, $Hstart-1,$identi\
-ty;\n }\n }\n }\n }\n print F \\
-"! SEQ_1_TO_N\\n\";\n close (F);\n return $o\
-utput;\n \n }\n\nsub seq2msa\n {\n my ($mode\
-, $infile, $method, $param, $outfile,$database)=@_\
-;\n &set_temporary_dir (\"set\",$infile,\"seq.p\
-ep\", $database, \"db.pep\");\n $param.=\" >/de\
-v/null 2>&1 \";\n \n \n #make sure test.p\
+;\n close (F);\n\n $blast_output=&run_bl\
+ast ($s{$seq}{name},$method, $db, \"seqfile\",\"ou\
+tfile\");\n\n %p=blast_xml2profile($s{$seq}{n\
+ame}, $s{$seq}{seq},$maxid, $minid,$mincov,$blast_\
+output);\n unlink ($blast_output);\n\n $\
+c=1;\n print stdout \"!\\tProcess: >$s{$seq}{\
+name} [$SERVER/blast/$db][$CACHE_STATUS]\\n\";\n \
+ while (!$found && $c<$p{n})\n {\n $pdbid=&id\
+2pdbid($p{$c}{identifyer});\n if ( length ($pdbi\
+d)>5){$pdbid=id2pdbid($p{$c}{definition});}\n\n \
+if ( length ($pdbid)>5)\n {\n myexit(add\
+_error (EXIT_FAILURE,$$,$$,getppid(), \"BLAST_FAIL\
+URE::Could Not Parse PDBID ($p{$c}{identifyer},$p{\
+$c}{definition})\"));\n }\n\n\n if (!&pdb_is\
+_released($pdbid))\n {\n print stdout \"\
+\\t\\t**$pdbid [PDB NOT RELEASED or WITHDRAWN]\\n\\
+";\n $c++;\n }\n elsif (!&pdb_has_righ\
+t_type ($pdbid,$type))\n {\n my $ptype=&\
+pdb2type ($pdbid);\n my $etype=&type2etype($\
+type);\n\n print stdout \"\\t\\t**$pdbid [$p\
+type cannot be used (expected: $etype)]\\n\";\n \
+ $c++;\n }\n else\n {\n $found=\
+1;\n }\n }\n\n if ($found)\n {\n print \
+R \">$s{$seq}{name} _P_ $pdbid\\n\";\n print std\
+out \"\\t\\t >$s{$seq}{name} _P_ $pdbid\\n\";\n }\\
+n else\n {\n print R \">$s{$seq}{name}\\n\"\
+;\n print stdout \"\\t\\t >$s{$seq}{name} No Tem\
+plate Selected\\n\";\n }\n }\n close (R);\n &\
+set_temporary_dir (\"unset\",$mode, $method,\"resu\
+lt.aln\",$outfile);\n}\nsub type2etype\n {\n m\
+y $type=shift;\n my $etype;\n\n if ( $type=~\
+/n/){$etype.=\"NMR \";}\n if ( $type=~/d/){$ety\
+pe.=\"diffraction \";}\n if ( $type=~/m/){$etyp\
+e.=\"model \";}\n return $etype;\n }\nsub pdb2\
+type\n {\n my $pdb=shift;\n my $f=vtmpnam\
+();\n\n my $value= &safe_system (\"t_coffee -o\
+ther_pg extract_from_pdb -model_type $pdb > $f\");\
+\n my $r=&file2string ($f);\n chomp($r);\n\
+ return $r;\n }\nsub pdb_has_right_type\n {\
+\n my $pdb=shift;\n my $type=shift;\n\n m\
+y $f=vtmpnam();\n\n my $value= &safe_system (\"\
+t_coffee -other_pg extract_from_pdb -model_type $p\
+db > $f\");\n my $r=&file2string ($f);\n cho\
+mp($r);\n\n\n if ( $r eq \"NMR\" && $type=~/n/)\
+{return 1;}\n elsif ( $r eq \"diffraction\" && \
+$type=~/d/){return 1;}\n elsif ( $r eq \"model\\
+" && $type=~/m/){return 1;}\n else {return 0;}\\
+n }\nsub pdb_is_released\n {\n my $pdb=shift;\
+\n my $f=vtmpnam();\n\n $value= &safe_system\
+ (\"t_coffee -other_pg extract_from_pdb -is_releas\
+ed_pdb_name $pdb > $f\");\n my $r=&file2string \
+($f);\n chomp($r);\n return $r;\n }\nsub bl\
+ast_msa\n {\n my ($blast,$infile,$db,$outfile)\
+=@_;\n my ($a, %s1, %s, %qs, %qs1);\n my $se\
+qfile;\n my $SEQ=new FileHandle;\n my $seqfi\
+le=\"seqfile\";\n my @txt;\n\n\n %s1=&read_f\
+asta_seq ($db);\n %s=&fasta_hash2index_hash(%s1\
+);\n %qs1=&read_fasta_seq ($infile);\n %qs=&\
+fasta_hash2index_hash(%qs1);\n\n\n #&safe_syste\
+m (\"formatdb -i $db\");\n if ($blast eq \"blas\
+tp\"){&safe_system (\"blastall -i $infile -d $db \
+-m7 -p blastp -o io\");}\n elsif ($blast eq \"b\
+lastn\"){&safe_system (\"blastn -query $infile -d\
+b $db -outfmt 5 -word_size 4 -out io\");}\n\n &\
+set_blast_type (\"io\");\n\n\n my %FB=&xml2tag_\
+list (\"io\", \"Iteration\");\n open (F, \">$ou\
+tfile\");\n print F \"! TC_LIB_FORMAT_01\\n\";\\
+n print F \"$s{n}\\n\";\n for ( my $a=0; $a<\
+$s{n}; $a++)\n {\n print F \"$s{$a}{name} $s{\
+$a}{len} $s{$a}{seq}\\n\";\n }\n\n\n for (\
+ my $a=0; $a<$FB{n}; $a++)\n {\n my %p=blast_\
+xml2profile ($qs{$a}{name}, $qs{$a}{seq},100, 0, 0\
+, $FB{$a}{body});\n my $query=$p{0}{name};\n my $i\
+= $s1{$query}{order}+1;\n for (my $b=1; $b<$p{n}; \
+$b++)\n {\n my $l=length ($p{$b}{Qseq});\n \
+ my $hit=$p{$b}{definition};\n my $Qstart=$p\
+{$b}{Qstart};\n my $Hstart=$p{$b}{Hstart};\n \
+ my $identity=$p{$b}{identity};\n my @lrQ=sp\
+lit (//,$p{$b}{Qseq});\n my @lrH=split (//,$p{\
+$b}{Hseq});\n\n my $j= $s1{$hit}{order}+1;\n \
+ #if ( $j==$i){next;}\n printf F \"# %d %d\\\
+n\", $i, $j;\n # print F \"\\n$p{$b}{Qseq} (\
+$Qstart)\\n$p{$b}{Hseq} ($Hstart)\";\n for ($c\
+=0; $c<$l; $c++)\n {\n my $rQ=$lrQ[$c];\n \
+my $rH=$lrH[$c];\n my $n=0;\n\n if ($rQ ne \"-\"\
+){$n++, $Qstart++;}\n if ($rH ne \"-\"){$n++; $Hs\
+tart++;}\n\n if ( $n==2)\n {\n printf F \\
+"\\t%d %d %d\\n\", $Qstart-1, $Hstart-1,$identity;\
+\n }\n }\n }\n }\n print F \"! \
+SEQ_1_TO_N\\n\";\n close (F);\n return $outp\
+ut;\n }\n\nsub blast_msa_old\n {\n my ($infil\
+e,$outfile)=@_;\n my ($a, %seq);\n %s1=&read\
+_fasta_seq ($infile);\n foreach $s (keys (%s1))\
+\n {\n $i=$s1{$s}{order};\n $s{$i}{name}=$s;\\
+n $s{$i}{seq}=$s1{$s}{seq};\n $s{$i}{len}=length( \
+$s{$i}{seq});\n $s{n}++;\n }\n &safe_syste\
+m (\"formatdb -i $infile\");\n &safe_system (\"\
+blastall -i $infile -d $infile -m7 -o io\");\n \
+&set_blast_type (\"io\");\n\n %FB=&xml2tag_list\
+ (\"io\", \"Iteration\");\n\n open (F, \">$outf\
+ile\");\n print F \"! TC_LIB_FORMAT_01\\n\";\n \
+ print F \"$s{n}\\n\";\n for ( $a=0; $a<$s{n}\
+; $a++)\n {\n print F \"$s{$a}{name} $s{$a}{l\
+en} $s{$a}{seq}\\n\";\n }\n for ( $a=0; $a\
+<$FB{n}; $a++)\n {\n %p=blast_xml2profile ($s\
+{$a}{name}, $s{$a}{seq},100, 0, 0, $FB{$a}{body});\
+\n for ($b=1; $b<$p{n}; $b++)\n {\n my $l=le\
+ngth ($p{$b}{Qseq});\n my $hit=$p{$b}{definiti\
+on};\n my $Qstart=$p{$b}{Qstart};\n my $Hs\
+tart=$p{$b}{Hstart};\n my $identity=$p{$b}{ide\
+ntity};\n my @lrQ=split (//,$p{$b}{Qseq});\n \
+ my @lrH=split (//,$p{$b}{Hseq});\n my $i= $\
+s1{$s{$a}{name}}{order}+1;\n my $j= $s1{$hit}{\
+order}+1;\n #if ( $j==$i){next;}\n printf \
+F \"# %d %d\\n\", $i, $j;\n # print F \"\\n$\
+p{$b}{Qseq} ($Qstart)\\n$p{$b}{Hseq} ($Hstart)\";\\
+n for ($c=0; $c<$l; $c++)\n {\n my $rQ=\
+$lrQ[$c];\n my $rH=$lrH[$c];\n my $n=0;\n\n if \
+($rQ ne \"-\"){$n++, $Qstart++;}\n if ($rH ne \"-\
+\"){$n++; $Hstart++;}\n\n if ( $n==2)\n {\n \
+ printf F \"\\t%d %d %d\\n\", $Qstart-1, $Hstart\
+-1,$identity;\n }\n }\n }\n }\n \
+ print F \"! SEQ_1_TO_N\\n\";\n close (F);\n \
+ return $output;\n\n }\n\nsub seq2msa\n {\n m\
+y ($mode, $infile, $method, $param, $outfile,$data\
+base)=@_;\n &set_temporary_dir (\"set\",$infile\
+,\"seq.pep\", $database, \"db.pep\");\n $param.\
+=\" >/dev/null 2>&1 \";\n\n\n #make sure test.p\
ep is in FASTA\n &safe_system (\"t_coffee -othe\
r_pg seq_reformat -in seq.pep -output fasta_seq > \
-x\");\n `mv x seq.pep`;\n \n if ( $method\
- eq \"blastp\")\n {\n &blast_msa (\"seq.pep\"\
-, \"db.pep\",\"result.aln\");\n }\n elsif \
-( $method eq \"muscle\")\n {\n `muscle -in se\
-q.pep -out result.aln $param`;\n }\n elsif\
- ( $method eq \"probcons\")\n {\n `probcons s\
-eq.pep >result.aln 2>/dev/null`;\n }\n els\
-if ( $method eq \"mafft\")\n {\n `mafft --qui\
-et --localpair --maxiterate 1000 seq.pep> result.a\
-ln 2>/dev/null`\n }\n elsif ( $method=~/p\
-rank/)\n {\n `$method -d=seq.pep -o=result.al\
-n -quiet 2>/dev/null`;\n `mv result.aln.1.fas resu\
-lt.aln`;\n }\n else\n {\n `$method -i\
-nfile=seq.pep -outfile=result.aln`;\n }\n \
-\n &set_temporary_dir (\"unset\",$mode, $method\
-,\"result.aln\",$outfile);\n myexit ($EXIT_SUCC\
-ESS);\n }\n\nsub seq2thread_pair\n {\n my ($m\
-ode, $infile, $pdbfile1, $method, $param, $outfile\
-)=@_;\n &set_temporary_dir (\"set\",$infile,\"s\
-eq.pep\",$pdbfile1,\"struc.pdb\");\n if ($metho\
-d eq \"fugueali\")\n {\n #Env Variable that n\
-eed to be defined for Fugue\n if (!$ENV{FUGUE_LIB_\
-LIST}){$ENV{FUGUE_LIB_LIST}=\"DUMMY\";}\n if (!$EN\
-V{HOMSTRAD_PATH}) {$ENV{HOMSTRAD_PATH}=\"DUMMY\";\
-}\n if (!$ENV{HOMS_PATH}){$ENV{HOMS_PATH}=\"DUMMY\\
-";}\n \n `joy struc.pdb >x 2>x`;\n &check_file(\"s\
-truc.tem\", \"Joy failed [FATAL:$PROGRAM/$method]\\
-");\n `melody -t struc.tem >x 2>x`;\n &check_file(\
-\"struc.tem\", \"Melody failed [FATAL:$PROGRAM/$me\
-thod]\");\n `fugueali -seq seq.pep -prf struc.fug \
--print > tmp_result.aln`;\n \n &check_file(\"tmp_r\
-esult.aln\", \"Fugue failed [FATAL:$PROGRAM/$metho\
-d]\");\n &safe_system (\"t_coffee -other_pg seq_re\
-format -in tmp_result.aln -output fasta_aln >resul\
-t.aln\");\n }\n elsif ( $method eq \"t_cof\
-fee\")\n {\n &safe_system (\"t_coffee -in Pst\
-ruc.pdb Sseq.pep Mslow_pair -outfile result.aln -q\
-uiet\");\n }\n else\n {\n &safe_syste\
-m (\"$method -infile=seq.pep -pdbfile1=struc.pdb -\
-outfile=result.aln $param>x 2>x\");\n }\n \
-&set_temporary_dir (\"unset\",$mode,$method,\"resu\
-lt.aln\",$outfile);\n myexit ($EXIT_SUCCESS);\n\
- }\nsub seq2pdbid_pair\n {\n my ($mode, $pdbf\
-ile1, $pdbfile2, $method, $param, $outfile)=@_;\n \
- my ($name);\n\n \n &set_temporary_dir (\"\
-set\");\n $name=$pdbfile1.\" \".$pdbfile2;\n\n \
- if ( &cache_file(\"GET\",\"\",\"$name\",\"$m\
-ethod\",\"dali\",$outfile,\"EBI\"))\n {return\
- $outfile;}\n else\n {\n if ($method eq \"\
-daliweb\")\n {\n $pdbfile1=~/(....)(.)/;\n \
- $id1=$1; $c1=$2;\n \n $pdbfile2=~/(....\
-)(.)/;\n $id2=$1; $c2=$2;\n \n $comman\
-d=\"t_coffee -other_pg dalilite.pl --pdb1 $id1 --c\
-hainid1 $c1 --pdb2 $id2 --chainid2 $c2 --email=$EM\
-AIL >dali_stderr 2>dali_stderr\";\n $dali=`$c\
-ommand`;\n \n open (F, \"dali_stderr\");\n\
- while (<F>)\n {\n if ( /JobId: dalilit\
-e-(\\S+)/)\n {\n $jobid=$1;\n }\n }\n \
- close (F);\n unlink (\"dali_stderr\");\n \
- \n $output1=\"dalilite-$jobid.txt\";\n i\
-f ( -e $output1)\n {\n unlink ($output1);\n\
- &url2file (\"http://www.ebi.ac.uk/Tools/es/cgi-b\
-in/jobresults.cgi/dalilite/dalilite-$jobid/aln.htm\
-l\", \"output2\");\n \n if ( -e \"output2\")\n \
- {\n my ($seq1, $seq2);\n $seq1=$seq2=\\
-"\";\n \n open (F, \"output2\");\n \
-while (<F>)\n {\n $l=$_;\n if ( $l=~/Qu\
-ery\\s+(\\S+)/)\n {\n $seq1.=$1;\n }\
-\n elsif ( $l=~/Sbjct\\s+(\\S+)/)\n {\n \
- $seq2.=$1;\n }\n }\n close (F);\\
-n unlink (\"output2\");\n if ($seq1 ne \\
-"\" && $seq2 ne \"\")\n {\n $output3=\">$\
-A\\n$seq1\\n>$B\\n$seq2\\n\";\n $output3=~s/\\./\
--/g;\n open (F, \">result.aln\");\n print F \"\
-$output3\";\n close (F);\n }\n }\n \
- }\n }\n }\n &cache_file(\"SET\",\"\",\
-\"$name\",\"$method\",\"dali\",\"result.aln\",\"EB\
-I\");\n &set_temporary_dir (\"unset\",$mode, $m\
-ethod, \"result.aln\",$outfile);\n myexit ($EXI\
-T_SUCCESS);\n }\nsub seq2pdb_pair\n {\n my ($\
-mode, $pdbfile1, $pdbfile2, $method, $param, $outf\
-ile)=@_;\n \n &set_temporary_dir (\"set\",$p\
-dbfile1,\"pdb1.pdb\",$pdbfile2,\"pdb2.pdb\");\n \
- if ($method eq \"t_coffee\")\n {\n &safe_sys\
-tem (\"t_coffee -in Ppdb1.pdb Ppdb2.pdb -quiet -ou\
-tfile=result.aln\");\n }\n elsif ( $method\
- eq \"DaliLite\")\n {\n if ( &safe_system (\"\
-DaliLite -pairwise pdb1.pdb pdb2.pdb >tmp1\")==$EX\
-IT_SUCCESS)\n {\n my ($seq1, $seq2);\n \
- $seq1=$seq2=\"\";\n \n open (F, \"tmp1\\
-");\n while (<F>)\n {\n $l=$_;\n i\
-f ( $l=~/Query\\s+(\\S+)/)\n {\n $seq1.=\
-$1;\n }\n elsif ( $l=~/Sbjct\\s+(\\S+)/)\n \
- {\n $seq2.=$1;\n }\n }\n \
-close (F);\n unlink (\"tmp1\");\n if ($s\
-eq1 ne \"\" && $seq2 ne \"\")\n {\n my $o\
-utput3=\">$A\\n$seq1\\n>$B\\n$seq2\\n\";\n $outp\
-ut3=~s/\\./-/g;\n open (F, \">result.aln\");\n \
- print F \"$output3\";\n close (F);\n }\n\
- }\n else\n {\n print \"ERROR: DalLite fa\
-iled to align the considered structures[tc_generic\
-_method.pl]\\n\";\n } \n }\n elsif ( \
-$method eq \"TMalign\")\n {\n if ( &safe_syst\
-em (\"TMalign pdb1.pdb pdb2.pdb >tmp1\")==$EXIT_SU\
-CCESS)\n {\n `tail -4 tmp1 > tmp2`;\n \n\
- open (F, \"tmp2\");\n while (<F>)\n \
- {\n unshift(@l, $_);\n }\n close (F);\\
-n open (F, \">result.aln\");\n $l[3]=~s/[^\
-a-zA-Z0-9-]/\\-/g;\n $l[1]=~s/[^a-zA-Z0-9-]/\\\
--/g;\n print F \">$A\\n$l[3]\\n>$B\\n$l[1]\\n\\
-";\n close (F);\n }\n else\n {\n print\
- \"ERROR: TMalign failed to align the considered s\
-tructures[tc_generic_method.pl]\\n\";\n `rm re\
-sult.aln >/dev/null 2>/dev/null`;\n }\n }\n\
- elsif ( $method eq \"mustang\")\n {\n if \
-( &safe_system (\"mustang -i pdb1.pdb pdb2.pdb -F \
-fasta >/dev/null 2>/dev/null\")==$EXIT_SUCCESS)\n \
- {\n `mv results.afasta result.aln`;\n }\n \
-else\n {\n print \"ERROR: mustang failed to \
-align the considered structures[tc_generic_method.\
-pl]\\n\";\n `rm result.aln >/dev/null 2>/dev/n\
-ull`;\n }\n }\n else\n {\n if ( &sa\
-fe_system (\"$method -pdbfile1=pdb1.pep -pdbfile2=\
-pdb2.pdb -outfile=result.aln $param>x 2>x\")==$EXI\
-T_SUCCESS)\n {\n `mv results.afasta result.a\
-ln`;\n }\n else\n {\n print \"ERROR: $meth\
-od failed to align the considered structures[tc_ge\
-neric_method.pl]\\n\";\n `rm result.aln >/dev/\
-null 2>/dev/null`;\n }\n }\n &set_tempor\
-ary_dir (\"unset\",$mode, $method, \"result.aln\",\
-$outfile);\n myexit ($EXIT_SUCCESS);\n }\n\nsu\
-b seq2profile_pair\n {\n my ($mode, $profile1,\
- $profile2, $method, $param, $outfile)=@_;\n \n\
- \n if ($method eq \"clustalw\")\n {\n \
-&set_temporary_dir (\"set\",$profile1,\"prf1.aln\"\
-,$profile2,\"prf2.aln\");\n `clustalw -profile1=pr\
-f1.aln -profile2=prf2.aln -outfile=result.aln`;\n \
+x\");\n `mv x seq.pep`;\n\n if ( $method eq \
+\"blastp\")\n {\n &blast_msa (\"blastp\",\"se\
+q.pep\",$database,\"result.aln\");\n }\n e\
+lsif ( $method eq \"blastn\")\n {\n &blast_ms\
+a (\"blastn\",\"seq.pep\",$database,\"result.aln\"\
+);\n }\n\n elsif ( $method eq \"muscle\")\\
+n {\n `muscle -in seq.pep -out result.aln $pa\
+ram`;\n }\n elsif ( $method eq \"probcons\\
+")\n {\n `probcons seq.pep >result.aln 2>/dev\
+/null`;\n }\n elsif ( $method eq \"mafft\"\
+)\n {\n `mafft --quiet --localpair --maxitera\
+te 1000 seq.pep> result.aln 2>/dev/null`\n }\
+\n elsif ( $method=~/prank/)\n {\n `$metho\
+d -d=seq.pep -o=result.aln -quiet 2>/dev/null`;\n \
+`mv result.aln.1.fas result.aln`;\n }\n el\
+sif ($method eq \"clustalo\")\n {\n `clustalo\
+ -i seq.pep > result.aln`;\n }\n else\n \
+ {\n `$method -infile=seq.pep -outfile=result.al\
+n`;\n }\n\n &set_temporary_dir (\"unset\",\
+$mode, $method,\"result.aln\",$outfile);\n myex\
+it ($EXIT_SUCCESS);\n }\n\nsub seq2thread_pair\n \
+ {\n my ($mode, $infile, $pdbfile1, $method, $p\
+aram, $outfile)=@_;\n &set_temporary_dir (\"set\
+\",$infile,\"seq.pep\",$pdbfile1,\"struc.pdb\");\n\
+ if ($method eq \"fugueali\")\n {\n #Env V\
+ariable that need to be defined for Fugue\n if (!$\
+ENV{FUGUE_LIB_LIST}){$ENV{FUGUE_LIB_LIST}=\"DUMMY\\
+";}\n if (!$ENV{HOMSTRAD_PATH}) {$ENV{HOMSTRAD_PA\
+TH}=\"DUMMY\";}\n if (!$ENV{HOMS_PATH}){$ENV{HOMS_\
+PATH}=\"DUMMY\";}\n\n `joy struc.pdb >x 2>x`;\n &c\
+heck_file(\"struc.tem\", \"Joy failed [FATAL:$PROG\
+RAM/$method]\");\n `melody -t struc.tem >x 2>x`;\n\
+ &check_file(\"struc.tem\", \"Melody failed [FATAL\
+:$PROGRAM/$method]\");\n `fugueali -seq seq.pep -p\
+rf struc.fug -print > tmp_result.aln`;\n\n &check_\
+file(\"tmp_result.aln\", \"Fugue failed [FATAL:$PR\
+OGRAM/$method]\");\n &safe_system (\"t_coffee -oth\
+er_pg seq_reformat -in tmp_result.aln -output fast\
+a_aln >result.aln\");\n }\n elsif ( $metho\
+d eq \"t_coffee\")\n {\n &safe_system (\"t_co\
+ffee -in Pstruc.pdb Sseq.pep Mslow_pair -outfile r\
+esult.aln -quiet\");\n }\n else\n {\n\
+ &safe_system (\"$method -infile=seq.pep -pdbfile1\
+=struc.pdb -outfile=result.aln $param>x 2>x\");\n \
+ }\n &set_temporary_dir (\"unset\",$mode,$m\
+ethod,\"result.aln\",$outfile);\n myexit ($EXIT\
+_SUCCESS);\n }\nsub seq2pdbid_pair\n {\n my (\
+$mode, $pdbfile1, $pdbfile2, $method, $param, $out\
+file)=@_;\n my ($name);\n\n\n &set_temporary\
+_dir (\"set\");\n $name=$pdbfile1.\" \".$pdbfil\
+e2;\n\n if ( &cache_file(\"GET\",\"\",\"$nam\
+e\",\"$method\",\"dali\",$outfile,\"EBI\"))\n \
+ {return $outfile;}\n else\n {\n if ($meth\
+od eq \"daliweb\")\n {\n $pdbfile1=~/(....)(\
+.)/;\n $id1=$1; $c1=$2;\n\n $pdbfile2=~/(.\
+...)(.)/;\n $id2=$1; $c2=$2;\n\n $command=\
+\"t_coffee -other_pg dalilite.pl --pdb1 $id1 --cha\
+inid1 $c1 --pdb2 $id2 --chainid2 $c2 --email=$EMAI\
+L >dali_stderr 2>dali_stderr\";\n $dali=`$com\
+mand`;\n\n open (F, \"dali_stderr\");\n wh\
+ile (<F>)\n {\n if ( /JobId: dalilite-(\\S+\
+)/)\n {\n $jobid=$1;\n }\n }\n clos\
+e (F);\n unlink (\"dali_stderr\");\n\n $ou\
+tput1=\"dalilite-$jobid.txt\";\n if ( -e $outp\
+ut1)\n {\n unlink ($output1);\n &url2file \
+(\"http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresult\
+s.cgi/dalilite/dalilite-$jobid/aln.html\", \"outpu\
+t2\");\n\n if ( -e \"output2\")\n {\n my \
+($seq1, $seq2);\n $seq1=$seq2=\"\";\n\n \
+open (F, \"output2\");\n while (<F>)\n \
+ {\n $l=$_;\n if ( $l=~/Query\\s+(\\S+)/)\n \
+ {\n $seq1.=$1;\n }\n elsif ( $l=~/Sb\
+jct\\s+(\\S+)/)\n {\n $seq2.=$1;\n }\
+\n }\n close (F);\n unlink (\"out\
+put2\");\n if ($seq1 ne \"\" && $seq2 ne \"\"\
+)\n {\n $output3=\">$A\\n$seq1\\n>$B\\n$s\
+eq2\\n\";\n $output3=~s/\\./-/g;\n open (F, \"\
+>result.aln\");\n print F \"$output3\";\n clos\
+e (F);\n }\n }\n }\n }\n }\\
+n &cache_file(\"SET\",\"\",\"$name\",\"$method\\
+",\"dali\",\"result.aln\",\"EBI\");\n &set_temp\
+orary_dir (\"unset\",$mode, $method, \"result.aln\\
+",$outfile);\n myexit ($EXIT_SUCCESS);\n }\nsu\
+b seq2pdb_pair\n {\n my ($mode, $pdbfile1, $pd\
+bfile2, $method, $param, $outfile)=@_;\n\n &set\
+_temporary_dir (\"set\",$pdbfile1,\"pdb1.pdb\",$pd\
+bfile2,\"pdb2.pdb\");\n if ($method eq \"t_coff\
+ee\")\n {\n &safe_system (\"t_coffee -in Ppdb\
+1.pdb Ppdb2.pdb -quiet -outfile=result.aln\");\n \
+ }\n elsif ( $method eq \"DaliLite\")\n \
+ {\n if ( &safe_system (\"DaliLite -pairwise pdb1.\
+pdb pdb2.pdb >tmp1\")==$EXIT_SUCCESS)\n {\n \
+ my ($seq1, $seq2);\n $seq1=$seq2=\"\";\n\n \
+ open (F, \"tmp1\");\n while (<F>)\n \
+ {\n $l=$_;\n if ( $l=~/Query\\s+(\\S+)/)\n \
+ {\n $seq1.=$1;\n }\n elsif ( $l=~/S\
+bjct\\s+(\\S+)/)\n {\n $seq2.=$1;\n \
+}\n }\n close (F);\n unlink (\"tm\
+p1\");\n if ($seq1 ne \"\" && $seq2 ne \"\")\\
+n {\n my $output3=\">$A\\n$seq1\\n>$B\\n$\
+seq2\\n\";\n $output3=~s/\\./-/g;\n open (F, \\
+">result.aln\");\n print F \"$output3\";\n clo\
+se (F);\n }\n }\n else\n {\n print\
+ \"ERROR: DalLite failed to align the considered s\
+tructures[tc_generic_method.pl]\\n\";\n }\n \
+ }\n elsif ( $method eq \"TMalign\")\n {\n\
+ if ( &safe_system (\"TMalign pdb1.pdb pdb2.pdb >t\
+mp1\")==$EXIT_SUCCESS)\n {\n `tail -4 tmp1 >\
+ tmp2`;\n\n open (F, \"tmp2\");\n while (<\
+F>)\n {\n unshift(@l, $_);\n }\n \
+close (F);\n open (F, \">result.aln\");\n \
+$l[3]=~s/[^a-zA-Z0-9-]/\\-/g;\n $l[1]=~s/[^a-z\
+A-Z0-9-]/\\-/g;\n print F \">$A\\n$l[3]\\n>$B\\
+\n$l[1]\\n\";\n close (F);\n }\n else\n {\\
+n print \"ERROR: TMalign failed to align the c\
+onsidered structures[tc_generic_method.pl]\\n\";\n\
+ `rm result.aln >/dev/null 2>/dev/null`;\n }\
+\n }\n elsif ( $method eq \"mustang\")\n \
+ {\n if ( &safe_system (\"mustang -i pdb1.pdb p\
+db2.pdb -F fasta >/dev/null 2>/dev/null\")==$EXIT_\
+SUCCESS)\n {\n `mv results.afasta result.aln\
+`;\n }\n else\n {\n print \"ERROR: mustang\
+ failed to align the considered structures[tc_gene\
+ric_method.pl]\\n\";\n `rm result.aln >/dev/nu\
+ll 2>/dev/null`;\n }\n }\n else\n {\
+\n if ( &safe_system (\"$method -pdbfile1=pdb1.pep\
+ -pdbfile2=pdb2.pdb -outfile=result.aln $param>x 2\
+>x\")==$EXIT_SUCCESS)\n {\n `mv results.afas\
+ta result.aln`;\n }\n else\n {\n print \"E\
+RROR: $method failed to align the considered struc\
+tures[tc_generic_method.pl]\\n\";\n `rm result\
+.aln >/dev/null 2>/dev/null`;\n }\n }\n \
&set_temporary_dir (\"unset\",$mode, $method, \"re\
-sult.aln\",$outfile);\n }\n elsif ( $metho\
-d eq \"hhalign\")\n {\n hhalign ( $profile1,$\
-profile2,$outfile,$param);\n }\n else\n \
- {\n \n `$method -profile1=prf1.aln -profile2=pr\
-f2.aln -outfile=result.aln $param>x 2>x`;\n }\
-\n \n myexit ($EXIT_SUCCESS);\n }\n\nsub pg_\
-is_installed\n {\n my @ml=@_;\n my ($r, $p,\
- $m);\n my $supported=0;\n \n my $p=shift\
- (@ml);\n if ($p=~/::/)\n {\n if (safe_sys\
-tem (\"perl -M$p -e 1\")==$EXIT_SUCCESS){return 1;\
-}\n else {return 0;}\n }\n else\n {\n\
- $r=`which $p 2>/dev/null`;\n if ($r eq \"\"){$r=0\
-;}\n else {$r=1;}\n \n if ($r==0 && is_blast_packa\
-ge ($p)){return pg_is_installed (\"legacy_blast.pl\
-\");}\n else {return $r;}\n }\n }\n\nsub is_\
-blast_package\n {\n my $p=shift;\n if ( $p=\
-~/blastp/){return 1;}\n elsif ($p=~/blastall/){\
-return 1;}\n elsif ($p=~/blastn/){return 1;}\n \
- elsif ($p=~/blastx/){return 1;}\n elsif ($p=\
-~/formatdb/){return 1;}\n else {return 0;}\n }\
-\n \nsub check_internet_connection\n {\n my\
- $internet;\n my $tmp;\n &check_configuratio\
-n ( \"wget\"); \n \n $tmp=&vtmpnam ();\n \
-\n if (&pg_is_installed (\"wget\")){`wge\
-t www.google.com -O$tmp >/dev/null 2>/dev/null`;}\\
-n elsif (&pg_is_installed (\"curl\")){`curl\
- www.google.com -o$tmp >/dev/null 2>/dev/null`;}\n\
- \n if ( !-e $tmp || -s $tmp < 10){$internet\
-=0;}\n else {$internet=1;}\n if (-e $tmp){un\
-link $tmp;}\n\n return $internet;\n }\nsub che\
-ck_pg_is_installed\n {\n my @ml=@_;\n my $r\
-=&pg_is_installed (@ml);\n if (!$r && $p=~/::/)\
-\n {\n print STDERR \"\\nYou Must Install the\
- perl package $p on your system.\\nRUN:\\n\\tsudo \
-perl -MCPAN -e 'install $pg'\\n\";\n }\n e\
-lsif (!$r)\n {\n myexit(flush_error(\"\\nProg\
-ram $p Supported but Not Installed on your system\\
-"));\n }\n else\n {\n return 1;\n \
- }\n }\nsub set_temporary_dir\n {\n my @list\
-=@_;\n my $dir_mode, $a, $mode, $method;\n \n \
- $dir_mode=shift (@list);\n\n \n if ( $dir\
-_mode eq \"set\")\n {\n $initial_dir=cwd();\n\
- if ( !$tmp_dir)\n {\n $rand=rand (100000);\\
-n $tmp_dir=\"$TMPDIR/tmp4tcoffee_profile_pair_\
-dir_$$\\_P_$rand\";\n }\n if ( !-d $tmp_dir)\n \
- {\n push (@TMPDIR_LIST, $tmp_dir);\n `mkd\
-ir $tmp_dir`;\n }\n \n for ( $a=0; $a<=$#list; $\
-a+=2)\n {\n if (-e $list[$a]){ `cp $list[$a\
-] $tmp_dir/$list[$a+1]`;}\n }\n chdir $tmp_d\
-ir;\n }\n elsif ( $dir_mode eq \"unset\")\\
-n {\n $mode=shift (@list);\n $method=shift (@\
-list);\n \n if (!-e $list[0])\n {\n myexit(fl\
-ush_error(\"Program $method failed to produce $lis\
-t[1]\" ));\n myexit ($EXIT_FAILURE);\n }\n e\
-lse\n {\n chdir $initial_dir;\n # `t_cof\
-fee -other_pg seq_reformat -in $tmp_dir/$list[0] -\
-output fasta_aln -out $tmp_dir/result2.aln`;\n \
- `cp $tmp_dir/$list[0] $tmp_dir/result2.aln`;\n \
- if ( $list[1] eq \"stdout\")\n {\n open (\
-F, \"$tmp_dir/result2.aln\");\n while (<F>){print\
- $_;}close(F);\n }\n else\n {\n `\
-mv $tmp_dir/result2.aln $list[1]`;\n }\n \
- shift (@list); shift (@list);\n foreach $f (@\
-list)\n {\n if (-e (\"$tmp_dir/$f\")){`mv $\
-tmp_dir/$f .`;}\n }\n }\n }\n }\n\n\\
-n\n\nsub my_get_opt\n {\n my @list=@_;\n my\
- $cl, $a, $argv, @argl;\n \n @argl=();\n \
-$cl=shift @list;\n for ( $a=0; $a<=$#list; $a+=\
-3)\n {\n $option=$list[$a];\n $optional=$list\
-[$a+1];\n $status=$list[$a+2];\n $argv=\"\";\n if \
-($cl=~/$option(\\S+)/){$argv=$1;}\n @argl=(@argl,$\
-argv);\n \n \n #$optional:0=>optional\n #$optional\
-:1=>must be set\n #$status: 0=>no requirement\n #$\
-status: 1=>must be an existing file\n #$status: 2=\
->must be an installed package\n \n\n if ($optional\
-==0){;}\n elsif ( $optional==1 && $argv eq \"\")\n\
- {\n myexit(flush_error( \"ERROR: Option $op\
-tion must be set\"));\n myexit ($EXIT_FAILURE)\
-;\n }\n if ($status==0){;}\n elsif ($status ==1 \
-&& $argv ne \"\" && !-e $argv)\n {\n myexit(\
-flush_error( \"File $argv must exist\"));\n my\
-exit ($EXIT_FAILURE);\n }\n elsif ( $status==2 &\
-& $argv ne \"\" && &check_pg_is_installed ($argv)=\
-=0)\n {\n myexit(flush_error( \" $argv is no\
-t installed\"));\n myexit ($EXIT_FAILURE);\n \
- }\n }\n\n return @argl;\n }\n\nsub che\
-ck_file \n {\n my ($file, $msg)=@_;\n\n if \
-( !-e $file)\n {\n myexit(flush_error(\"$msg\\
-"));\n }\n }\nsub hhalign\n {\n my ($a\
-ln1, $aln2, $outfile, $param)=@_;\n my $h1, $h2\
-;\n \n $h{0}{index}=0;\n $h{1}{index}=1;\\
-n \n $h{0}{aln}=$aln1;\n $h{1}{aln}=$aln2\
-;\n\n \n\n %{$h{0}}=aln2psi_profile (%{$h{0}}\
-);\n %{$h{1}}=aln2psi_profile (%{$h{1}});\n\n \
- $param=~s/#S/ /g;\n $param=~s/#M/\\-/g;\n \
-$param=~s/#E/\\=/g;\n \n\n \n $command=\"\
-hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $outfile.t\
-mp -rank 1 -mapt 0 $param\";\n `$command`;\n \
- \n # `hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $\
-outfile.tmp -rank 1 -mapt 0 -gapf 0.8 -gapg 0.8`;\\
-n \n\n # To run global use the following\n \
- \n open (I, \"$outfile.tmp\");\n open (O, \
-\">$outfile\");\n $h{0}{cons}=s/\\./x/g;\n $\
-h{1}{cons}=s/\\./x/g;\n\n print O \"! TC_LIB_FO\
-RMAT_01\\n2\\n$h{0}{name} $h{0}{len} $h{0}{seq}\\n\
-$h{1}{name} $h{1}{len} $h{1}{seq}\\n#1 2\\n\";\n \
- \n while (<I>)\n {\n if (/(\\d+)\\s+(\\d\
-+)\\s+(\\d+)/)\n {\n print O \"\\t$h{0}{$1}\\
-\t$h{1}{$2}\\t$3\\n\";\n }\n }\n print O\
- \"! SEQ_1_TO_N\\n\";\n\n close (O);\n close\
- (I);\n }\n\nsub aln2psi_profile\n {\n my (%h\
-)=@_;\n my ($aln,$i,$hv, $a, @c, $n);\n \n \
- $i=$h{index};\n $aln=$h{aln};\n\n `cp $aln \
-$$.hhh_aln`;\n $command=\"t_coffee -other_pg se\
-q_reformat -in $aln -output hasch\";\n $hv=`$co\
-mmand`;chomp ($hv);\n \n $h{a2m}=\"$tmp/$hv.\
-tmp4hhpred.a2m\";\n $h{a3m}=\"$tmp/$hv.tmp4hhpr\
-ed.a3m\";\n if ( -e $h{a3m}){;}\n else\n \
- {\n `hhconsensus -M 50 -i $h{aln} -oa2m $h{a2m}\
-`;\n if (!-e $h{a2m})\n {\n print STDERR \"P\
-rogram tc_generic_method.pl FAILED to run:\\n\\thh\
-consensus -M 50 -i $h{aln} -oa2m $h{a2m}\";\n \
- myexit ($EXIT_FAILURE);\n }\n \n `hhconsensus \
--M 50 -i $h{aln} -oa3m $h{a3m}`;\n if (!-e $h{a3m}\
-)\n {\n print STDERR \"Program tc_generic_me\
-thod.pl FAILED to run:\\n\\thhconsensus -M 50 -i \
-$h{aln} -oa3m $h{a3m}\";\n myexit ($EXIT_FAILU\
-RE);\n }\n `buildali.pl $h{a3m} -n 1`;\n \
- }\n \n \n $h{a2m_seq}=`head -n 2 $h{a\
-2m} | grep -v \">\"`;chomp ($h{a2m_seq});\n $h{\
-a3m_seq}=`head -n 2 $h{a3m} | grep -v \">\"`;chomp\
- ($h{a3m_seq});\n $h{cons}=$h{a2m_seq};\n $h\
-{seq}=`head -n 2 $h{aln} | grep -v \">\"`;chomp ($\
-h{seq});\n \n \n\n @c=split (//, $h{cons}\
-);\n $h{len}=$#c+1;\n for ($n=0,$a=0, $b=0; \
-$a<$h{len};$a++)\n {\n if ( $c[$a]=~/[A-Z]/)\\
-n {\n $h{++$n}=++$b;\n\n }\n elsif ( $c[$a\
-]=~/[a-z\\.]/)\n {\n ++$b;\n }\n }\n \
- \n $name=`head -n 2 $h{aln} | grep \">\"`;\n\
- $name=~/\\>(\\S+)/;\n $h{name}=$1;\n \n \
- `cp $h{a2m} $i.a2m`;\n `cp $h{a3m} $i.a3m`;\\
-n `cp $h{aln} $i.hh_aln`;\n \n return %h;\
-\n }\n\nsub read_fasta_seq \n {\n my $f=@_[0]\
-;\n my %hseq;\n my (@seq, @com, @name);\n \
- my ($a, $s,$nseq);\n\n open (F, $f);\n whil\
-e (<F>)\n {\n $s.=$_;\n }\n close (F)\
-;\n\n \n @name=($s=~/>(\\S*).*\\n[^>]*/g);\n\
- \n @seq =($s=~/>.*.*\\n([^>]*)/g);\n @co\
-m =($s=~/>\\S*(.*)\\n([^>]*)/g);\n\n \n $nse\
-q=$#name+1;\n \n for ($a=0; $a<$nseq; $a++)\\
-n {\n my $s;\n my $n=$name[$a];\n $hseq{$n}{n\
-ame}=$n;\n $seq[$a]=~s/[^A-Za-z]//g;\n $hseq{$n}{o\
-rder}=$a;\n $hseq{$n}{seq}=$seq[$a];\n $hseq{$n}{c\
-om}=$com[$a];\n \n }\n return %hseq;\n }\\
-n\nsub file_contains \n {\n my ($file, $tag, $\
-max)=(@_);\n my ($n);\n $n=0;\n \n if \
-( !-e $file && ($file =~/$tag/)) {return 1;}\n \
-elsif ( !-e $file){return 0;}\n else \n {\\
-n open (FC, \"$file\");\n while ( <FC>)\n {\n \
- if ( ($_=~/$tag/))\n {\n close (FC);\n r\
-eturn 1;\n }\n elsif ($max && $n>$max)\n\
- {\n close (FC);\n return 0;\n }\n \
- $n++;\n }\n }\n close (FC);\n retu\
-rn 0;\n }\n \n \nsub file2string\n {\n \
-my $f=@_[0];\n my $string, $l;\n open (F,\"$\
-f\");\n while (<F>)\n {\n\n $l=$_;\n #chom\
-p ($l);\n $string.=$l;\n }\n close (F);\n \
- $string=~s/\\r\\n//g;\n $string=~s/\\n//g;\n\
- return $string;\n }\n\n\nsub my_get_opt\n {\\
-n my @list=@_;\n my $cl, $a, $argv, @argl;\n\
- \n @argl=();\n $cl=shift @list;\n for\
- ( $a=0; $a<=$#list; $a+=3)\n {\n $option=$li\
-st[$a];\n $optional=$list[$a+1];\n $status=$list[$\
-a+2];\n $argv=\"\";\n if ($cl=~/$option(\\S+)/){$a\
-rgv=$1;}\n @argl=(@argl,$argv);\n \n \n #$optional\
-:0=>optional\n #$optional:1=>must be set\n #$statu\
-s: 0=>no requirement\n #$status: 1=>must be an exi\
-sting file\n #$status: 2=>must be an installed pac\
-kage\n \n\n if ($optional==0){;}\n elsif ( $option\
-al==1 && $argv eq \"\")\n {\n\n myexit(flush\
-_error(\"Option $option must be set\"));\n \n \
- }\n if ($status==0){;}\n elsif ($status ==1 && $a\
-rgv ne \"\" && !-e $argv)\n {\n myexit(flus\
-h_error(\"File $argv must exist\"));\n \n }\n\
- elsif ( $status==2 && $argv ne \"\" && &check_pg_\
-is_installed ($argv)==0)\n {\n myexit(flush_\
-error(\"$argv is not installed\"));\n \n }\n \
- }\n\n return @argl;\n }\n\nsub tag2valu\
-e \n {\n \n my $tag=(@_[0]);\n my $word=\
-(@_[1]);\n my $return;\n \n $tag=~/$word=\
-\"([^\"]+)\"/;\n $return=$1;\n return $retur\
-n;\n }\n \nsub hit_tag2pdbid\n {\n my $t\
-ag=(@_[0]);\n my $pdbid;\n \n $tag=~/i\
-d=\"(\\S+)\"/;\n $pdbid=$1;\n $pdbid=~s/_//;\
-\n return $pdbid;\n }\nsub id2pdbid\n {\n \
-my $in=@_[0];\n my $id;\n \n $in=~/(\\S+)\
-/;\n $id=$in;\n $id=~s/PDB/pdb/g;\n \n \
+sult.aln\",$outfile);\n myexit ($EXIT_SUCCESS);\
+\n }\n\nsub seq2rnapdb_pair\n {\n my ($mode, \
+$pdbfile1, $pdbfile2, $method, $param, $outfile)=@\
+_;\n \n if ($method eq \"runsara.py\")\n \
+ {\n my $path=$ENV{PATH};\n \n if ($ENV{X3DNA_4_S\
+ARA}){$ENV{PATH}=\"$ENV{X3DNA_4_SARA}:$path\";}\n \
+\n open(TMP,\"<$pdbfile1\");\n my $count = 0;\n my\
+ $line;\n while (<TMP>)\n {\n $line = $_;\n \
+ if ($count ==1)\n {\n last;\n }\n\
+ $count += 1;\n }\n \n \n $chain1 = substr($\
+line,length($line)-3,1);\n \n close TMP;\n open(TM\
+P,\"<$pdbfile2\");\n my $count = 0;\n while (<TMP>\
+)\n {\n $line = $_;\n if ($count ==1)\n \
+ {\n last;\n }\n $count += 1;\n \
+}\n $chain2 = substr($line,length($line)-3,1);\n c\
+lose TMP;\n \n $tmp_file=&vtmpnam();\n \n safe_sys\
+tem(\"runsara.py $pdbfile1 $chain1 $pdbfile2 $chai\
+n2 -s -o $tmp_file --limitation 5000 > /dev/null 2\
+> /dev/null\");\n if ($ENV{X3DNA_4_SARA}){$ENV{PAT\
+H}=$path;}\n \n open(TMP,\"<$tmp_file\") or die \"\
+cannot open the sara tmp file:$!\\n\";\n open(OUT,\
+\">$outfile\") or die \"cannot open the $outfile f\
+ile:$!\\n\";\n \n my $switch = 0;\n my $seqNum = 0\
+;\n foreach my $line (<TMP>)\n {\n next unle\
+ss ($line=~/SARAALI/);\n if ($line=~/>/)\n \
+ {\n $switch =0;\n print OUT \">seq$seqNum\\n\\
+";\n $seqNum++;\n }\n if ($switch < 2){\
+\n $switch++;\n next;\n }\n \n\
+ if ($line =~/REMARK\\s+SARAALI\\s+([^\\*]+)\\\
+*/)\n {\n my $string = $1;\n print OUT \"$\
+string\\n\";\n }\n }\n close TMP;\n close \
+OUT;\n unlink($tmp_file);\n }\n }\nsub seq2p\
+rofile_pair\n{\n my ($mode, $profile1, $profile2, \
+$method, $param, $outfile)=@_;\n\n\n if ($method e\
+q \"clustalw\")\n {\n &set_temporary_dir (\"set\"\
+,$profile1,\"prf1.aln\",$profile2,\"prf2.aln\");\n\
+ `clustalw -profile1=prf1.aln -profile2=prf2.aln \
+-outfile=result.aln`;\n &set_temporary_dir (\"uns\
+et\",$mode, $method, \"result.aln\",$outfile);\n }\
+\n elsif ( $method eq \"clustalo\")\n {\n `clusta\
+lo --p1 $profile1 --p2 $profile2 -o $outfile --for\
+ce`;\n }\n elsif ( $method eq \"hhalign\")\n {\n \
+hhalign ( $profile1,$profile2,$outfile,$param);\n \
+}\n else\n {\n `$method -profile1=prf1.aln -profi\
+le2=prf2.aln -outfile=result.aln $param>x 2>x`;\n \
+}\n myexit ($EXIT_SUCCESS);\n}\n\nsub pg_is_instal\
+led\n {\n my @ml=@_;\n my ($r, $p, $m);\n \
+ my $supported=0;\n\n my $p=shift (@ml);\n \
+if ($p=~/::/)\n {\n if (safe_system (\"perl -\
+M$p -e 1\")==$EXIT_SUCCESS){return 1;}\n else {ret\
+urn 0;}\n }\n else\n {\n $r=`which $p\
+ 2>/dev/null`;\n if ($r eq \"\"){$r=0;}\n else {$r\
+=1;}\n\n if ($r==0 && is_blast_package ($p)){retur\
+n pg_is_installed (\"legacy_blast.pl\");}\n else {\
+return $r;}\n }\n }\n\nsub is_blast_package\\
+n {\n my $p=shift;\n if ( $p=~/blastp/){ret\
+urn 1;}\n elsif ($p=~/blastall/){return 1;}\n \
+ elsif ($p=~/blastn/){return 1;}\n elsif ($p=~\
+/blastx/){return 1;}\n elsif ($p=~/formatdb/){r\
+eturn 1;}\n else {return 0;}\n }\n\nsub check_\
+internet_connection\n {\n my $internet;\n m\
+y $tmp;\n &check_configuration ( \"wget\");\n\n\
+ $tmp=&vtmpnam ();\n\n if (&pg_is_instal\
+led (\"wget\")){`wget www.google.com -O$tmp >/d\
+ev/null 2>/dev/null`;}\n elsif (&pg_is_install\
+ed (\"curl\")){`curl www.google.com -o$tmp >/de\
+v/null 2>/dev/null`;}\n\n if ( !-e $tmp || -s $\
+tmp < 10){$internet=0;}\n else {$internet=1;}\n\
+ if (-e $tmp){unlink $tmp;}\n\n return $inte\
+rnet;\n }\nsub check_pg_is_installed\n {\n my\
+ @ml=@_;\n my $r=&pg_is_installed (@ml);\n i\
+f (!$r && $p=~/::/)\n {\n print STDERR \"\\nY\
+ou Must Install the perl package $p on your system\
+.\\nRUN:\\n\\tsudo perl -MCPAN -e 'install $pg'\\n\
+\";\n }\n elsif (!$r)\n {\n myexit(fl\
+ush_error(\"\\nProgram $p Supported but Not Instal\
+led on your system\"));\n }\n else\n \
+{\n return 1;\n }\n }\nsub set_temporary_dir\
+\n {\n my @list=@_;\n my $dir_mode, $a, $mo\
+de, $method;\n\n $dir_mode=shift (@list);\n\n\n\
+ if ( $dir_mode eq \"set\")\n {\n $initial\
+_dir=cwd();\n if ( !$tmp_dir)\n {\n $rand=ra\
+nd (100000);\n $tmp_dir=\"$TMPDIR/tmp4tcoffee_\
+profile_pair_dir_$$\\_P_$rand\";\n }\n if ( !-d \
+$tmp_dir)\n {\n push (@TMPDIR_LIST, $tmp_dir\
+);\n `mkdir $tmp_dir`;\n }\n\n for ( $a=0; $\
+a<=$#list; $a+=2)\n {\n if (-e $list[$a]){ \
+`cp $list[$a] $tmp_dir/$list[$a+1]`;}\n }\n \
+chdir $tmp_dir;\n }\n elsif ( $dir_mode eq\
+ \"unset\")\n {\n $mode=shift (@list);\n $met\
+hod=shift (@list);\n\n if (!-e $list[0])\n {\n \
+ myexit(flush_error(\"Program $method failed to p\
+roduce $list[1]\" ));\n myexit ($EXIT_FAILURE)\
+;\n }\n else\n {\n chdir $initial_dir;\n \
+ # `t_coffee -other_pg seq_reformat -in $tmp_dir\
+/$list[0] -output fasta_aln -out $tmp_dir/result2.\
+aln`;\n `cp $tmp_dir/$list[0] $tmp_dir/result2\
+.aln`;\n if ( $list[1] eq \"stdout\")\n \
+{\n open (F, \"$tmp_dir/result2.aln\");\n while \
+(<F>){print $_;}close(F);\n }\n else\n \
+ {\n `mv $tmp_dir/result2.aln $list[1]`;\n \
+ }\n shift (@list); shift (@list);\n fo\
+reach $f (@list)\n {\n if (-e (\"$tmp_dir/$\
+f\")){`mv $tmp_dir/$f .`;}\n }\n }\n \
+}\n }\n\n\n\n\nsub my_get_opt\n {\n my @list=\
+@_;\n my ($cl, $a, $argv, @argl);\n\n \n \
+@argl=();\n $cl=shift @list;\n for ( my $a=0\
+; $a<=$#list; $a+=3)\n {\n my $option=$list[$\
+a];\n my $optional=$list[$a+1];\n my $status=$list\
+[$a+2];\n my $argv=\"\";\n if ($cl=~/$option(\\S+)\
+/){$argv=$1;}\n @argl=(@argl,$argv);\n\n\n #$optio\
+nal:0=>optional\n #$optional:1=>must be set\n #$st\
+atus: 0=>no requirement\n #$status: 1=>must be an \
+existing file\n #$status: 2=>must be an installed \
+package\n \n\n if ($optional==0){;}\n elsif ( $opt\
+ional==1 && $argv eq \"\")\n {\n myexit(flus\
+h_error( \"ERROR: Option $option must be set\"));\\
+n myexit ($EXIT_FAILURE);\n }\n if ($status=\
+=0){;}\n elsif ($status ==1 && $argv ne \"\" && !-\
+e $argv)\n {\n myexit(flush_error( \"File [$\
+argv] must exist\"));\n myexit ($EXIT_FAILURE)\
+;\n }\n elsif ( $status==2 && $argv ne \"\" && &\
+check_pg_is_installed ($argv)==0)\n {\n myex\
+it(flush_error( \" $argv is not installed\"));\n \
+ myexit ($EXIT_FAILURE);\n }\n }\n ret\
+urn @argl;\n }\n\nsub check_file\n {\n my (\
+$file, $msg)=@_;\n\n if ( !-e $file)\n {\n\
+ myexit(flush_error(\"$msg\"));\n }\n }\ns\
+ub hhalign\n {\n my ($aln1, $aln2, $outfile, $\
+param)=@_;\n my $h1, $h2;\n\n $h{0}{index}=0\
+;\n $h{1}{index}=1;\n\n $h{0}{aln}=$aln1;\n \
+ $h{1}{aln}=$aln2;\n\n\n\n %{$h{0}}=aln2psi_p\
+rofile (%{$h{0}});\n %{$h{1}}=aln2psi_profile (\
+%{$h{1}});\n\n $param=~s/#S/ /g;\n $param=~s\
+/#M/\\-/g;\n $param=~s/#E/\\=/g;\n\n\n\n $co\
+mmand=\"hhalign -i $h{0}{a3m} -t $h{1}{a3m} -tc $o\
+utfile.tmp -rank 1 -mapt 0 $param\";\n `$comman\
+d`;\n\n # `hhalign -i $h{0}{a3m} -t $h{1}{a3m} -\
+tc $outfile.tmp -rank 1 -mapt 0 -gapf 0.8 -gapg 0.\
+8`;\n\n\n # To run global use the following\n\n\
+ open (I, \"$outfile.tmp\");\n open (O, \">$\
+outfile\");\n $h{0}{cons}=s/\\./x/g;\n $h{1}\
+{cons}=s/\\./x/g;\n\n print O \"! TC_LIB_FORMAT\
+_01\\n2\\n$h{0}{name} $h{0}{len} $h{0}{seq}\\n$h{1\
+}{name} $h{1}{len} $h{1}{seq}\\n#1 2\\n\";\n\n \
+while (<I>)\n {\n if (/(\\d+)\\s+(\\d+)\\s+(\\
+\d+)/)\n {\n print O \"\\t$h{0}{$1}\\t$h{1}{\
+$2}\\t$3\\n\";\n }\n }\n print O \"! SEQ\
+_1_TO_N\\n\";\n\n close (O);\n close (I);\n \
+ }\n\nsub aln2psi_profile\n {\n my (%h)=@_;\n \
+ my ($aln,$i,$hv, $a, @c, $n);\n\n\n $i=$h{in\
+dex};\n $aln=$h{aln};\n\n `cp $aln $$.hhh_al\
+n`;\n $command=\"t_coffee -other_pg seq_reforma\
+t -in $aln -output hasch\";\n $hv=`$command`;ch\
+omp ($hv);\n\n $h{a2m}=\"$tmp/$hv.tmp4hhpred.a2\
+m\";\n $h{a3m}=\"$tmp/$hv.tmp4hhpred.a3m\";\n \
+ if ( -e $h{a3m}){;}\n else\n {\n $x=`whi\
+ch hhconsensus`;\n `hhconsensus -M 50 -i $h{aln} \
+-oa2m $h{a2m}`;\n if (!-e $h{a2m})\n {\n pri\
+nt STDERR \"Program tc_generic_method.pl FAILED to\
+ run:\\n\\thhconsensus -M 50 -i $h{aln} -oa2m $h{\
+a2m}\";\n myexit ($EXIT_FAILURE);\n }\n\n `h\
+hconsensus -M 50 -i $h{aln} -oa3m $h{a3m}`;\n if \
+(!-e $h{a3m})\n {\n print STDERR \"Program t\
+c_generic_method.pl FAILED to run:\\n\\thhconsensu\
+s -M 50 -i $h{aln} -oa3m $h{a3m}\";\n myexit \
+($EXIT_FAILURE);\n }\n `buildali.pl $h{a3m\
+} -n 1`;\n }\n\n\n $h{a2m_seq}=`head -n 2 \
+$h{a2m} | grep -v \">\"`;chomp ($h{a2m_seq});\n \
+ $h{a3m_seq}=`head -n 2 $h{a3m} | grep -v \">\"`;c\
+homp ($h{a3m_seq});\n $h{cons}=$h{a2m_seq};\n \
+ $h{seq}=`head -n 2 $h{aln} | grep -v \">\"`;chom\
+p ($h{seq});\n\n\n\n @c=split (//, $h{cons});\n\
+ $h{len}=$#c+1;\n for ($n=0,$a=0, $b=0; $a<$\
+h{len};$a++)\n {\n if ( $c[$a]=~/[A-Z]/)\n \
+{\n $h{++$n}=++$b;\n\n }\n elsif ( $c[$a]=~/\
+[a-z\\.]/)\n {\n ++$b;\n }\n }\n\n \
+ $name=`head -n 2 $h{aln} | grep \">\"`;\n $nam\
+e=~/\\>(\\S+)/;\n $h{name}=$1;\n\n `cp $h{a2\
+m} $i.a2m`;\n `cp $h{a3m} $i.a3m`;\n `cp $h{\
+aln} $i.hh_aln`;\n\n return %h;\n }\nsub read_\
+fasta_seq_index\n {\n my $f=@_[0];\n my %hs\
+eq;\n my (@seq, @com, @name);\n my ($a, $s,$\
+nseq);\n\n open (F, $f);\n while (<F>)\n \
+ {\n $s.=$_;\n }\n close (F);\n\n\n @n\
+ame=($s=~/>(\\S*).*\\n[^>]*/g);\n\n @seq =($s=~\
+/>.*.*\\n([^>]*)/g);\n @com =($s=~/>\\S*(.*)\\n\
+([^>]*)/g);\n\n\n $nseq=$#name+1;\n\n for ($\
+a=0; $a<$nseq; $a++)\n {\n my $s;\n my $n=$na\
+me[$a];\n $hseq{$a}{name}=$n;\n $seq[$a]=~s/[^A-Za\
+-z]//g;\n $hseq{$a}{order}=$a;\n $hseq{$a}{seq}=$s\
+eq[$a];\n $hseq{$a}{com}=$com[$a];\n\n }\n \
+ return %hseq;\n }\nsub read_fasta_seq\n {\n \
+my $f=@_[0];\n my %hseq;\n my (@seq, @com, @\
+name);\n my ($a, $s,$nseq);\n\n open (F, $f)\
+;\n while (<F>)\n {\n $s.=$_;\n }\n \
+ close (F);\n\n\n @name=($s=~/>(\\S*).*\\n[^>]\
+*/g);\n\n @seq =($s=~/>.*.*\\n([^>]*)/g);\n \
+@com =($s=~/>\\S*(.*)\\n([^>]*)/g);\n\n\n $nseq\
+=$#name+1;\n\n for ($a=0; $a<$nseq; $a++)\n \
+ {\n my $s;\n my $n=$name[$a];\n $hseq{$n}{name}=\
+$n;\n $seq[$a]=~s/[^A-Za-z]//g;\n $hseq{$n}{order}\
+=$a;\n $hseq{$n}{seq}=$seq[$a];\n $hseq{$n}{com}=$\
+com[$a];\n\n }\n return %hseq;\n }\n\n\ns\
+ub read_fasta_aln\n {\n my $f=@_[0];\n my %\
+hseq;\n my (@seq, @com, @name);\n my ($a, $s\
+,$nseq);\n\n open (F, $f);\n while (<F>)\n \
+ {\n $s.=$_;\n }\n close (F);\n\n\n \
+@name=($s=~/>(\\S*).*\\n[^>]*/g);\n\n @seq =($s\
+=~/>.*.*\\n([^>]*)/g);\n @com =($s=~/>\\S*(.*)\\
+\n([^>]*)/g);\n\n\n $nseq=$#name+1;\n\n for \
+($a=0; $a<$nseq; $a++)\n {\n my $s;\n my $n=$\
+name[$a];\n $hseq{$n}{name}=$n;\n $seq[$a]=~s/[^A-\
+Za-z-.()[\\]]//g;\n $hseq{$n}{order}=$a;\n $hseq{$\
+n}{seq}=$seq[$a];\n $hseq{$n}{com}=$com[$a];\n\n \
+ }\n return %hseq;\n }\n\nsub recode_name2\\
+n{\n my ($in)=shift;\n my $mode=shift;\n\n my %seq\
+;\n my $new_name;\n\n if (! -e $in){return;}\n\n #\
+needed by ClustalOmega to avoid very long names\n \
+open (INFILE, \"+<$in\");\n\n my $line;\n\n if ($m\
+ode eq \"code\")\n {\n chomp($line = <INFILE>);\n\
+ my $line_length = length($line);\n $new_name=++\
+$RECODE_N;\n $new_name=\">$new_name\";\n my $new\
+_length = length($new_name);\n $RECODE {$new_name\
+}=$line;\n for ($count = $new_length; $count < $l\
+ine_length; $count++)\n {\n $new_name .= \" \";\
+\n }\n $new_name=\"$new_name\\n\";\n seek INFIL\
+E, 0, 0\n or die \"could not seek: $!\";\n prin\
+t INFILE \"$new_name\";\n }\n else\n {\n my $n_fo\
+und = 0;\n my $file_pos=0;\n $file_pos=tell INFI\
+LE;\n while (<INFILE>)\n {\n $line=$_;\n $li\
+ne =~ s/\\s*$//;\n\n $old_name= $RECODE{$line};\\
+n if ($old_name ne \"\")\n {\n seek INFILE,\
+ $file_pos, 0\n or die \"could not seek: $!\";\
+\n print INFILE \"$old_name\\n\";\n $file_po\
+s++;\n if ($file_pos == 2)\n {\n print \\
+"stop\\n\";\n break;\n }\n }\n $file_po\
+s=tell INFILE;\n }\n\n }\n\n\n close INFILE;\n}\n\
+\n\nsub recode_name\n{\n my ($in)=shift;\n my $mod\
+e=shift;\n my $f=new FileHandle;\n my %seq;\n my $\
+new_name;\n\n if (! -e $in){return;}\n\n #needed b\
+y ClustalOmega to avoid very long names\n %seq=rea\
+d_fasta_aln ($in);\n\n open ($f, \">$in\");\n fore\
+ach my $s (keys(%seq))\n {\n if ($mode eq \"code\\
+")\n {\n $new_name=++$RECODE_N;\n $RECODE {$n\
+ew_name}=$seq{$s}{name};\n }\n else\n {\n $ne\
+w_name=$RECODE{$seq{$s}{name}};\n }\n print $f \\
+">$new_name\\n$seq{$s}{seq}\\n\";\n }\n close $f;\\
+n}\n\nsub fasta_hash2index_hash\n {\n my %s1=@\
+_;\n my %s;\n foreach my $s (keys (%s1))\n \
+ {\n my $i=$s1{$s}{order};\n $s{$i}{name}=$s;\n\
+ $s{$i}{seq}=$s1{$s}{seq};\n $s{$i}{len}=length( $\
+s{$i}{seq});\n $s{n}++;\n }\n return %s;\n\
+ }\nsub file_contains\n {\n my ($file, $tag, \
+$max)=(@_);\n my ($n);\n $n=0;\n\n if ( !\
+-e $file && ($file =~/$tag/)) {return 1;}\n els\
+if ( !-e $file){return 0;}\n else\n {\n op\
+en (FC, \"$file\");\n while ( <FC>)\n {\n if\
+ ( ($_=~/$tag/))\n {\n close (FC);\n retur\
+n 1;\n }\n elsif ($max && $n>$max)\n \
+ {\n close (FC);\n return 0;\n }\n $\
+n++;\n }\n }\n close (FC);\n return 0\
+;\n }\n\n\nsub file2string\n {\n my $f=@_[0];\
+\n my $string, $l;\n open (F,\"$f\");\n w\
+hile (<F>)\n {\n\n $l=$_;\n #chomp ($l);\n $s\
+tring.=$l;\n }\n close (F);\n $string=~\
+s/\\r\\n//g;\n $string=~s/\\n//g;\n return $\
+string;\n }\n\n\nsub tag2value\n {\n\n my $ta\
+g=(@_[0]);\n my $word=(@_[1]);\n my $return;\
+\n\n $tag=~/$word=\"([^\"]+)\"/;\n $return=$\
+1;\n return $return;\n }\n\nsub hit_tag2pdbid\\
+n {\n my $tag=(@_[0]);\n my $pdbid;\n\n \
+$tag=~/id=\"(\\S+)\"/;\n $pdbid=$1;\n $pdbid\
+=~s/_//;\n return $pdbid;\n }\nsub id2pdbid\n \
+ {\n my $in=@_[0];\n my $id;\n\n $in=~/(\\
+\S+)/;\n $id=$in;\n $id=~s/PDB/pdb/g;\n\n \
if ($id =~/pdb(.*)/){$id=$1;}\n elsif ( $id=~/\
(\\S+)\\s+mol:protein/){$id=$1;}\n $id=~s/[:|ï¿\
½ï¿½_]//g;\n return $id;\n }\nsub set_blast_ty\
-pe \n {\n my $file =@_[0];\n if (&file_cont\
-ains ($file,\"EBIApplicationResult\",100)){$BLAST_\
-TYPE=\"EBI\";}\n elsif (&file_contains ($file,\\
-"NCBI_BlastOutput\",100)) {$BLAST_TYPE=\"NCBI\";}\\
-n else\n {\n $BLAST_TYPE=\"\";\n }\n \
- return $BLAST_TYPE;\n }\nsub is_valid_blast_xm\
-l\n {\n my $file=shift;\n my $line;\n\
- \n \n if ( !-e $file) {return 0;}\\
-n $line=&file2tail ($file,100);\n if ( $\
-line=~/<\\/EBIApplicationResult/ || $line=~/<\\/NC\
-BI_BlastOutput/ || $line=~/<\\/BlastOutput/ ){retu\
-rn 1;}\n return 0;\n }\nsub file2blast_fla\
-vor\n {\n my $file=shift;\n if (&file_contain\
-s ($file,\"EBIApplicationResult\",100)){return \"E\
-BI\";}\n elsif (&file_contains ($file,\"NCBI_Blast\
-Output\",100)){return \"NCBI\";}\n else {return \"\
-UNKNOWN\";}\n }\nsub blast_xml2profile \n {\\
-n my ($name,$seq,$maxid, $minid, $mincov, $file\
-)=(@_);\n my (%p, $a, $string, $n);\n \n \
-\n\n if ($BLAST_TYPE eq \"EBI\" || &file_contai\
-ns ($file,\"EBIApplicationResult\",100)){%p=ebi_bl\
-ast_xml2profile(@_);}\n elsif ($BLAST_TYPE eq \\
-"NCBI\" || &file_contains ($file,\"NCBI_BlastOutpu\
-t\",100)){%p=ncbi_blast_xml2profile(@_);}\n els\
-e \n {\n myexit(add_error ( $$,$$,getppid(), \
-\"BLAST_FAILURE::unkown XML\",$CL));\n }\n \
- for ($a=0; $a<$p{n}; $a++)\n {\n my $name=$p\
-{$a}{name};\n $p{$name}{seq}=$p{$a}{seq};\n $p{$na\
-me}{index}=$a;\n }\n return %p;\n }\nsub \
-ncbi_tblastx_xml2lib_file \n {\n my ($outlib,\
-$string)=(@_);\n my ($L,$l, $a,$b,$c,$d,$i,$nhi\
-ts,@identifyerL);\n my (%ITERATION);\n \n \
- open (F, \">>$outlib\");\n \n $seq=~s/[^a\
--zA-Z]//g;\n $L=length ($seq);\n \n %ITER\
-ATION=xml2tag_list ($string, \"Iteration\");\n \
-for ($i=0; $i<$ITERATION{n};$i++)\n {\n my ($\
-qindex, $qlen, %hit, $string);\n $string=$ITERATIO\
-N{$i}{body};\n\n $qindex=xmltag2value($string,\"It\
-eration_iter-num\");\n $qlen =xmltag2value($strin\
-g,\"Iteration_query-len\");\n %hit=&xml2tag_list \
-($string, \"Hit\");\n\n for ($a=0; $a<$hit{n}; $a+\
-+)\n {\n my ($string);\n $string=$hit{$a\
-}{body};\n \n $hindex=xmltag2value($string,\"\
-Hit_accession\")+1;\n if ($hindex<=$qindex){ne\
-xt;}\n else {print F \"# $qindex $hindex\\n\\
-";}\n \n \n $hlen=xmltag2value ($strin\
-g,\"Hit_len\");\n %HSP=&xml2tag_list ($string\
-, \"Hsp\");\n \n for ($b=0; $b<$HSP{n}; $b+\
-+)\n {\n my ($string, $qs,$qe,$qf,$hs,$he,$\
-hf,$s, $d, $e);\n $string=$HSP{$b}{body};\n \n $\
-qs=xmltag2value ($string,\"Hsp_query-from\");\n \
-$qe=xmltag2value ($string,\"Hsp_query-to\");\n $\
-qf=xmltag2value ($string,\"Hsp_query-frame\");\n\\
-n $hs=xmltag2value ($string,\"Hsp_hit-from\");\n\
- $he=xmltag2value ($string,\"Hsp_hit-to\");\n $\
-hf=xmltag2value ($string,\"Hsp_hit-frame\");\n \\
-n $s=xmltag2value ($string,\"Hsp_identity\");\n \
- $l=xmltag2value ($string,\"Hsp_align-len\");\n \
-$s=int(($s*100)/$l);\n \n if ($qf>0)\n {$rqs=\
-$qs; $rqe=$qe;}\n else\n {\n $rqe=($qlen-\
-$qs)+1;\n $rqs=($qlen-$qe)+1;\n }\n \n i\
-f ($hf>0)\n {$rhs=$hs; $rhe=$he;}\n else\n \
-{\n $rhe=($hlen-$hs)+1;\n $rhs=($hlen-$h\
-e)+1;\n }\n for ($d=0,$e=$rqs; $e<$rqe; $e++,$\
-d++)\n {\n my ($r1,$r2);\n $r1=$e;\n \
- $r2=$rhs+$d;\n print F \" $r1 $r2 $s 0\\\
-n\";\n }\n }\n }\n }\n print F \
-\"! SEQ_1_TO_N\\n\";\n \n close (F);\n re\
-turn %lib;\n }\n\nsub ncbi_tblastpx_xml2lib_file \
-\n {\n my ($outlib,$string,%s)=(@_);\n my \
-($L,$l, $a,$b,$c,$d,$i,$nhits,@identifyerL);\n \
-my (%ITERATION,%hdes, %qdes);\n \n open (F\
-, \">>$outlib\");\n \n $seq=~s/[^a-zA-Z]//g;\
-\n $L=length ($seq);\n \n %ITERATION=xml2\
-tag_list ($string, \"Iteration\");\n for ($i=0;\
- $i<$ITERATION{n};$i++)\n {\n my ($qindex, $q\
-len, %hit, $string);\n $string=$ITERATION{$i}{body\
-};\n\n $qdef=xmltag2value($string,\"Iteration_quer\
-y-def\");\n %qdes=&tblastpx_name2description($qdef\
-,%s);\n $qlen =xmltag2value($string,\"Iteration_q\
-uery-len\");\n %hit=&xml2tag_list ($string, \"Hit\
-\");\n\n for ($a=0; $a<$hit{n}; $a++)\n {\n \
-my ($string);\n $string=$hit{$a}{body};\n \
-$hdef=xmltag2value($string,\"Hit_def\");\n %hd\
-es=&tblastpx_name2description($hdef,%s);\n if \
-($hdes{index}<=$qdes{index}){next;}\n else {p\
-rint F \"# $qdes{index} $hdes{index}\\n\";}\n \
- \n \n $hlen=xmltag2value ($string,\"Hit_l\
-en\");\n %HSP=&xml2tag_list ($string, \"Hsp\"\
-);\n \n for ($b=0; $b<$HSP{n}; $b++)\n \
- {\n my ($string, $l,$qs,$qe,$qf,$hs,$he,$hf,$s,\
- $d, $e, @s1, @s2);\n $string=$HSP{$b}{body};\n \\
-n $qs=xmltag2value ($string,\"Hsp_query-from\");\
-\n $qe=xmltag2value ($string,\"Hsp_query-to\");\\
-n $qf=$qdes{frame};\n $qseq=xmltag2value ($stri\
-ng,\"Hsp_qseq\");\n \n $hs=xmltag2value ($strin\
-g,\"Hsp_hit-from\");\n $he=xmltag2value ($string\
-,\"Hsp_hit-to\");\n $hf=$hdes{frame};\n $hseq=xm\
-ltag2value ($string,\"Hsp_hseq\");\n \n $s=xmlt\
-ag2value ($string,\"Hsp_identity\");\n $l=xmltag\
-2value ($string,\"Hsp_align-len\");\n $s=int(($s\
-*100)/$l);\n @s1=tblastpx_hsp2coordinates($qseq,$\
-qs,$qe,%qdes);\n @s2=tblastpx_hsp2coordinates($hs\
-eq,$hs,$he,%hdes);\n \n \n for ($f=0; $f<=$#s1;\
- $f++)\n {\n if ($s1[$f]==-1 || $s2[$f]==-\
-1){next;}\n else \n {\n print F \" $\
+pe\n {\n my $file =@_[0];\n if (&file_conta\
+ins ($file,\"EBIApplicationResult\",100)){$BLAST_T\
+YPE=\"EBI\";}\n elsif (&file_contains ($file,\"\
+NCBI_BlastOutput\",100)) {$BLAST_TYPE=\"NCBI\";}\n\
+ else\n {\n $BLAST_TYPE=\"\";\n }\n \
+ return $BLAST_TYPE;\n }\nsub is_valid_blast_xml\
+\n {\n my $file=shift;\n my $line;\n\\
+n\n if ( !-e $file) {return 0;}\n $line=\
+&file2tail ($file,100);\n\n if ( $line=~/<\\/\
+EBIApplicationResult/ || $line=~/<\\/NCBI_BlastOut\
+put/ || $line=~/<\\/BlastOutput/ ){return 1;}\n \
+ return 0;\n }\nsub file2blast_flavor\n \
+{\n my $file=shift;\n if (&file_contains ($file,\"\
+EBIApplicationResult\",100)){return \"EBI\";}\n el\
+sif (&file_contains ($file,\"NCBI_BlastOutput\",10\
+0)){return \"NCBI\";}\n else {return \"UNKNOWN\";}\
+\n }\nsub blast_xml2profile\n {\n my ($na\
+me,$seq,$maxid, $minid, $mincov, $file)=(@_);\n \
+ my (%p, $a, $string, $n);\n\n\n\n if ($BLAST_T\
+YPE eq \"EBI\" || &file_contains ($file,\"EBIAppli\
+cationResult\",100)){%p=ebi_blast_xml2profile(@_);\
+}\n elsif ($BLAST_TYPE eq \"NCBI\" || &file_con\
+tains ($file,\"NCBI_BlastOutput\",100)){%p=ncbi_bl\
+ast_xml2profile(@_);}\n else\n {\n myexit(\
+add_error ( $$,$$,getppid(), \"BLAST_FAILURE::unko\
+wn XML\",$CL));\n }\n for ($a=0; $a<$p{n};\
+ $a++)\n {\n my $name=$p{$a}{name};\n $p{$nam\
+e}{seq}=$p{$a}{seq};\n $p{$name}{index}=$a;\n \
+ }\n return %p;\n }\nsub ncbi_tblastx_xml2lib_\
+file\n {\n my ($outlib,$string)=(@_);\n my\
+ ($L,$l, $a,$b,$c,$d,$i,$nhits,@identifyerL);\n \
+ my (%ITERATION);\n\n open (F, \">>$outlib\");\\
+n\n $seq=~s/[^a-zA-Z]//g;\n $L=length ($seq)\
+;\n\n %ITERATION=xml2tag_list ($string, \"Itera\
+tion\");\n for ($i=0; $i<$ITERATION{n};$i++)\n \
+ {\n my ($qindex, $qlen, %hit, $string);\n $st\
+ring=$ITERATION{$i}{body};\n\n $qindex=xmltag2valu\
+e($string,\"Iteration_iter-num\");\n $qlen =xmlta\
+g2value($string,\"Iteration_query-len\");\n %hit=&\
+xml2tag_list ($string, \"Hit\");\n\n for ($a=0; $\
+a<$hit{n}; $a++)\n {\n my ($string);\n $\
+string=$hit{$a}{body};\n\n $hindex=xmltag2valu\
+e($string,\"Hit_accession\")+1;\n if ($hindex<\
+=$qindex){next;}\n else {print F \"# $qindex\
+ $hindex\\n\";}\n\n\n $hlen=xmltag2value ($st\
+ring,\"Hit_len\");\n %HSP=&xml2tag_list ($str\
+ing, \"Hsp\");\n\n for ($b=0; $b<$HSP{n}; $b++\
+)\n {\n my ($string, $qs,$qe,$qf,$hs,$he,$h\
+f,$s, $d, $e);\n $string=$HSP{$b}{body};\n\n $qs\
+=xmltag2value ($string,\"Hsp_query-from\");\n $q\
+e=xmltag2value ($string,\"Hsp_query-to\");\n $qf\
+=xmltag2value ($string,\"Hsp_query-frame\");\n\n \
+ $hs=xmltag2value ($string,\"Hsp_hit-from\");\n \
+$he=xmltag2value ($string,\"Hsp_hit-to\");\n $hf\
+=xmltag2value ($string,\"Hsp_hit-frame\");\n\n $\
+s=xmltag2value ($string,\"Hsp_identity\");\n $l=\
+xmltag2value ($string,\"Hsp_align-len\");\n $s=i\
+nt(($s*100)/$l);\n\n if ($qf>0)\n {$rqs=$qs; $\
+rqe=$qe;}\n else\n {\n $rqe=($qlen-$qs)+1\
+;\n $rqs=($qlen-$qe)+1;\n }\n\n if ($hf>0\
+)\n {$rhs=$hs; $rhe=$he;}\n else\n {\n \
+ $rhe=($hlen-$hs)+1;\n $rhs=($hlen-$he)+1;\n \
+ }\n for ($d=0,$e=$rqs; $e<$rqe; $e++,$d++)\n \
+ {\n my ($r1,$r2);\n $r1=$e;\n $r2\
+=$rhs+$d;\n print F \" $r1 $r2 $s 0\\n\";\n \
+ }\n }\n }\n }\n print F \"! SEQ_\
+1_TO_N\\n\";\n\n close (F);\n return %lib;\n\
+ }\n\nsub ncbi_tblastpx_xml2lib_file\n {\n my\
+ ($outlib,$string,%s)=(@_);\n my ($L,$l, $a,$b\
+,$c,$d,$i,$nhits,@identifyerL);\n my (%ITERATIO\
+N,%hdes, %qdes);\n\n open (F, \">>$outlib\");\n\
+\n $seq=~s/[^a-zA-Z]//g;\n $L=length ($seq);\
+\n\n %ITERATION=xml2tag_list ($string, \"Iterat\
+ion\");\n for ($i=0; $i<$ITERATION{n};$i++)\n \
+ {\n my ($qindex, $qlen, %hit, $string);\n $str\
+ing=$ITERATION{$i}{body};\n\n $qdef=xmltag2value($\
+string,\"Iteration_query-def\");\n %qdes=&tblastpx\
+_name2description($qdef,%s);\n $qlen =xmltag2valu\
+e($string,\"Iteration_query-len\");\n %hit=&xml2ta\
+g_list ($string, \"Hit\");\n\n for ($a=0; $a<$hit\
+{n}; $a++)\n {\n my ($string);\n $string\
+=$hit{$a}{body};\n $hdef=xmltag2value($string,\
+\"Hit_def\");\n %hdes=&tblastpx_name2descripti\
+on($hdef,%s);\n if ($hdes{index}<=$qdes{index}\
+){next;}\n else {print F \"# $qdes{index} $h\
+des{index}\\n\";}\n\n\n $hlen=xmltag2value ($\
+string,\"Hit_len\");\n %HSP=&xml2tag_list ($s\
+tring, \"Hsp\");\n\n for ($b=0; $b<$HSP{n}; $b\
+++)\n {\n my ($string, $l,$qs,$qe,$qf,$hs,$\
+he,$hf,$s, $d, $e, @s1, @s2);\n $string=$HSP{$b}{\
+body};\n\n $qs=xmltag2value ($string,\"Hsp_query\
+-from\");\n $qe=xmltag2value ($string,\"Hsp_quer\
+y-to\");\n $qf=$qdes{frame};\n $qseq=xmltag2valu\
+e ($string,\"Hsp_qseq\");\n\n $hs=xmltag2value \
+($string,\"Hsp_hit-from\");\n $he=xmltag2value (\
+$string,\"Hsp_hit-to\");\n $hf=$hdes{frame};\n $\
+hseq=xmltag2value ($string,\"Hsp_hseq\");\n\n $s\
+=xmltag2value ($string,\"Hsp_identity\");\n $l=x\
+mltag2value ($string,\"Hsp_align-len\");\n $s=in\
+t(($s*100)/$l);\n @s1=tblastpx_hsp2coordinates($q\
+seq,$qs,$qe,%qdes);\n @s2=tblastpx_hsp2coordinate\
+s($hseq,$hs,$he,%hdes);\n\n\n for ($f=0; $f<=$#s1\
+; $f++)\n {\n if ($s1[$f]==-1 || $s2[$f]==\
+-1){next;}\n else\n {\n print F \" $\
s1[$f] $s2[$f] $s 0\\n\";\n }\n }\n \
}\n }\n }\n print F \"! SEQ_1_TO_N\\n\\
-";\n \n close (F);\n return %lib;\n }\ns\
-ub tblastpx_hsp2coordinates\n {\n my ($seq, $s\
-, $e, %des)=@_;\n my @list;\n my @sa;\n m\
-y @gap=(-1,-1,-1);\n \n $s=$des{start}+3*($s\
--1);\n \n if ($des{strand} eq \"d\"){;}\n e\
-lse {$s=($des{length}-$s)+1;}\n \n foreach $\
-c (split (//,$seq))\n {\n if ( $c eq '-'){pus\
-h (@list,@gap);}\n elsif ($des{strand} eq \"d\")\n\
- {\n push(@list,$s++,$s++,$s++);\n }\n els\
-e\n {\n push(@list, $s--,$s--,$s--);\n }\n\
- }\n return @list;\n }\n\nsub tblastpx_na\
-me2description\n {\n my ($name, %s)=@_;\n m\
-y @at=split(\"__\", $name);\n my %des;\n\n $\
-des{name}=$at[0];\n $des{strand}=$at[1];\n \\
-n $des{start}=$at[2];\n $des{end}=$at[3];\n \
- $des{length}=$at[4];\n $des{index}=$s{$at[0]\
-}{order}+1;\n return %des;\n } \nsub ncbi_bla\
-st_xml2profile \n {\n my ($name,$seq,$maxid, $\
-minid, $mincov, $string)=(@_);\n my ($L,$l, $a,\
-$b,$c,$d,$nhits,@identifyerL);\n \n \n $s\
-eq=~s/[^a-zA-Z]//g;\n $L=length ($seq);\n \n \
- #This is causing the NCBI parser to fail when I\
-teration_query-def is missing \n #%query=&xml2t\
-ag_list ($string, \"Iteration_query-def\");\n #\
-$name=$query{0}{body};\n \n %hit=&xml2tag_li\
-st ($string, \"Hit\");\n \n \n for ($nhit\
-s=0,$a=0; $a<$hit{n}; $a++)\n {\n my ($ldb,$i\
-d, $identity, $expectation, $start, $end, $coverag\
-e, $r);\n my (%ID,%DE,%HSP);\n \n $ldb=\"\";\n\n %\
-ID=&xml2tag_list ($hit{$a}{body}, \"Hit_id\");\n $\
-identifyer=$ID{0}{body};\n \n %DE=&xml2tag_list ($\
-hit{$a}{body}, \"Hit_def\");\n $definition=$DE{0}{\
-body};\n \n %HSP=&xml2tag_list ($hit{$a}{body}, \"\
-Hsp\");\n for ($b=0; $b<$HSP{n}; $b++)\n {\n \
- my (%START,%END,%E,%I,%Q,%M);\n\n \n %START=\
+";\n\n close (F);\n return %lib;\n }\nsub t\
+blastpx_hsp2coordinates\n {\n my ($seq, $s, $e\
+, %des)=@_;\n my @list;\n my @sa;\n my @g\
+ap=(-1,-1,-1);\n\n $s=$des{start}+3*($s-1);\n\n\
+ if ($des{strand} eq \"d\"){;}\n else {$s=($\
+des{length}-$s)+1;}\n\n foreach $c (split (//,$\
+seq))\n {\n if ( $c eq '-'){push (@list,@gap)\
+;}\n elsif ($des{strand} eq \"d\")\n {\n pus\
+h(@list,$s++,$s++,$s++);\n }\n else\n {\n \
+push(@list, $s--,$s--,$s--);\n }\n }\n r\
+eturn @list;\n }\n\nsub tblastpx_name2description\
+\n {\n my ($name, %s)=@_;\n my @at=split(\"\
+__\", $name);\n my %des;\n\n $des{name}=$at[\
+0];\n $des{strand}=$at[1];\n\n $des{start}=$\
+at[2];\n $des{end}=$at[3];\n $des{length}=$a\
+t[4];\n $des{index}=$s{$at[0]}{order}+1;\n r\
+eturn %des;\n }\nsub ncbi_blast_xml2profile\n {\\
+n my ($name,$seq,$maxid, $minid, $mincov, $stri\
+ng)=(@_);\n my ($L,$l, $a,$b,$c,$d,$nhits,@iden\
+tifyerL);\n\n\n $seq=~s/[^a-zA-Z]//g;\n $L=l\
+ength ($seq);\n\n #This is causing the NCBI par\
+ser to fail when Iteration_query-def is missing\n \
+ #%query=&xml2tag_list ($string, \"Iteration_que\
+ry-def\");\n #$name=$query{0}{body};\n\n %hi\
+t=&xml2tag_list ($string, \"Hit\");\n\n\n for (\
+$nhits=0,$a=0; $a<$hit{n}; $a++)\n {\n my ($l\
+db,$id, $identity, $expectation, $start, $end, $co\
+verage, $r);\n my (%ID,%DE,%HSP);\n\n $ldb=\"\";\n\
+\n %ID=&xml2tag_list ($hit{$a}{body}, \"Hit_id\");\
+\n $identifyer=$ID{0}{body};\n\n %DE=&xml2tag_list\
+ ($hit{$a}{body}, \"Hit_def\");\n $definition=$DE{\
+0}{body};\n\n %HSP=&xml2tag_list ($hit{$a}{body}, \
+\"Hsp\");\n for ($b=0; $b<$HSP{n}; $b++)\n {\n \
+ my (%START,%END,%E,%I,%Q,%M);\n\n\n %START=\
&xml2tag_list ($HSP{$b}{body}, \"Hsp_query-from\")\
;\n %HSTART=&xml2tag_list ($HSP{$b}{body}, \"H\
-sp_hit-from\");\n \n %LEN= &xml2tag_list \
-($HSP{$b}{body}, \"Hsp_align-len\");\n %END= \
-&xml2tag_list ($HSP{$b}{body}, \"Hsp_query-to\");\\
-n %HEND= &xml2tag_list ($HSP{$b}{body}, \"Hsp\
-_hit-to\");\n %E=&xml2tag_list ($HSP{$b}{b\
-ody}, \"Hsp_evalue\");\n %I=&xml2tag_list \
-($HSP{$b}{body}, \"Hsp_identity\");\n %Q=&xml2\
-tag_list ($HSP{$b}{body}, \"Hsp_qseq\");\n \
- %M=&xml2tag_list ($HSP{$b}{body}, \"Hsp_hseq\\
-");\n \n for ($e=0; $e<$Q{n}; $e++)\n\n \
- {\n $qs=$Q{$e}{body};\n $ms=$M{$e}{body};\n \
- \n $expectation=$E{$e}{body};\n $identity=($LEN\
-{$e}{body}==0)?0:$I{$e}{body}/$LEN{$e}{body}*100;\\
-n $start=$START{$e}{body};\n $end=$END{$e}{body}\
-;\n $Hstart=$HSTART{$e}{body};\n $Hend=$HEND{$e}\
-{body};\n \n $coverage=($L)?(($end-$start)*100)/$\
-L:0;\n \n if ($identity>$maxid || $identity<$mini\
-d || $coverage<$mincov){next;}\n @lr1=(split (//,\
-$qs));\n @lr2=(split (//,$ms));\n $l=$#lr1+1;\n \
- for ($c=0;$c<$L;$c++){$p[$nhits][$c]=\"-\";}\n f\
-or ($d=0,$c=0; $c<$l; $c++)\n {\n $r=$lr1[\
-$c];\n if ( $r=~/[A-Za-z]/)\n {\n \n\
- $p[$nhits][$d + $start-1]=$lr2[$c];\n $d++;\n\
- }\n }\n $Qseq[$nhits]=$qs;\n $Hseq[$n\
-hits]=$ms;\n $QstartL[$nhits]=$start;\n $HstartL\
-[$nhits]=$Hstart;\n $identityL[$nhits]=$identity;\
-\n $endL[$nhits]=$end;\n $definitionL[$nhits]=$d\
-efinition;\n $identifyerL[$nhits]=$identifyer;\n \
- $comment[$nhits]=\"$ldb|$identifyer [Eval=$expect\
-ation][id=$identity%][start=$Hstart end=$Hend]\";\\
-n $nhits++;\n }\n }\n }\n \n \\
-n $profile{n}=0;\n $profile{$profile{n}}{nam\
-e}=$name;\n $profile{$profile{n}}{seq}=$seq;\n \
- $profile {n}++;\n \n for ($a=0; $a<$nhits\
-; $a++)\n {\n $n=$a+1;\n \n $profile{$n}{name\
-}=\"$name\\_$a\";\n $profile{$n}{seq}=\"\";\n $pro\
-file{$n}{Qseq}=$Qseq[$a];\n $profile{$n}{Hseq}=$Hs\
-eq[$a];\n $profile{$n}{Qstart}=$QstartL[$a];\n $pr\
-ofile{$n}{Hstart}=$HstartL[$a];\n $profile{$n}{ide\
-ntity}=$identityL[$a];\n $profile{$n}{definition}=\
-$definitionL[$a];\n $profile{$n}{identifyer}=$iden\
-tifyerL[$a];\n $profile{$n}{comment}=$comment[$a];\
-\n\n for ($b=0; $b<$L; $b++)\n {\n if ($p[$a\
-][$b])\n {\n $profile{$n}{seq}.=$p[$a][$b];\
-\n }\n else\n {\n $profile{$n}{se\
-q}.=\"-\";\n }\n }\n }\n \n $pr\
-ofile{n}=$nhits+1;\n return %profile;\n }\nsub\
- ebi_blast_xml2profile \n {\n my ($name,$seq,$\
-maxid, $minid, $mincov, $string)=(@_);\n my ($L\
-,$l, $a,$b,$c,$d,$nhits,@identifyerL,$identifyer);\
-\n \n\n \n $seq=~s/[^a-zA-Z]//g;\n $L=\
-length ($seq);\n %hit=&xml2tag_list ($string, \\
-"hit\");\n \n for ($nhits=0,$a=0; $a<$hit{n}\
-; $a++)\n {\n my ($ldb,$id, $identity, $expec\
-tation, $start, $end, $coverage, $r);\n my (%Q,%M,\
-%E,%I);\n \n $ldb=&tag2value ($hit{$a}{open}, \"da\
-tabase\");\n $identifyer=&tag2value ($hit{$a}{open\
-}, \"id\");\n\n $description=&tag2value ($hit{$a}{\
-open}, \"description\");\n \n %Q=&xml2tag_list ($h\
-it{$a}{body}, \"querySeq\");\n %M=&xml2tag_list ($\
-hit{$a}{body}, \"matchSeq\");\n %E=&xml2tag_list (\
-$hit{$a}{body}, \"expectation\");\n %I=&xml2tag_li\
-st ($hit{$a}{body}, \"identity\");\n \n\n for ($b=\
+sp_hit-from\");\n\n %LEN= &xml2tag_list ($HSP\
+{$b}{body}, \"Hsp_align-len\");\n %END= &xml2\
+tag_list ($HSP{$b}{body}, \"Hsp_query-to\");\n \
+ %HEND= &xml2tag_list ($HSP{$b}{body}, \"Hsp_hit-\
+to\");\n %E=&xml2tag_list ($HSP{$b}{body},\
+ \"Hsp_evalue\");\n %I=&xml2tag_list ($HSP\
+{$b}{body}, \"Hsp_identity\");\n %Q=&xml2tag_l\
+ist ($HSP{$b}{body}, \"Hsp_qseq\");\n %M=&\
+xml2tag_list ($HSP{$b}{body}, \"Hsp_hseq\");\n\
+\n for ($e=0; $e<$Q{n}; $e++)\n\n {\n $\
+qs=$Q{$e}{body};\n $ms=$M{$e}{body};\n\n $expect\
+ation=$E{$e}{body};\n $identity=($LEN{$e}{body}==\
+0)?0:$I{$e}{body}/$LEN{$e}{body}*100;\n $start=$S\
+TART{$e}{body};\n $end=$END{$e}{body};\n $Hstart\
+=$HSTART{$e}{body};\n $Hend=$HEND{$e}{body};\n\n \
+ $coverage=($L)?(($end-$start)*100)/$L:0;\n\n if \
+($identity>$maxid || $identity<$minid || $coverage\
+<$mincov){next;}\n @lr1=(split (//,$qs));\n @lr2\
+=(split (//,$ms));\n $l=$#lr1+1;\n for ($c=0;$c<\
+$L;$c++){$p[$nhits][$c]=\"-\";}\n for ($d=0,$c=0;\
+ $c<$l; $c++)\n {\n $r=$lr1[$c];\n if\
+ ( $r=~/[A-Za-z]/)\n {\n\n $p[$nhits][$d \
++ $start-1]=$lr2[$c];\n $d++;\n }\n }\\
+n $Qseq[$nhits]=$qs;\n $Hseq[$nhits]=$ms;\n $Qs\
+tartL[$nhits]=$start;\n $HstartL[$nhits]=$Hstart;\
+\n $identityL[$nhits]=$identity;\n $endL[$nhits]\
+=$end;\n $definitionL[$nhits]=$definition;\n $id\
+entifyerL[$nhits]=$identifyer;\n $comment[$nhits]\
+=\"$ldb|$identifyer [Eval=$expectation][id=$identi\
+ty%][start=$Hstart end=$Hend]\";\n $nhits++;\n \
+ }\n }\n }\n\n\n $profile{n}=0;\n \
+$profile{$profile{n}}{name}=$name;\n $profile{$\
+profile{n}}{seq}=$seq;\n $profile {n}++;\n\n \
+ for ($a=0; $a<$nhits; $a++)\n {\n $n=$a+1;\n\
+\n $profile{$n}{name}=\"$name\\_$a\";\n $profile{$\
+n}{seq}=\"\";\n $profile{$n}{Qseq}=$Qseq[$a];\n $p\
+rofile{$n}{Hseq}=$Hseq[$a];\n $profile{$n}{Qstart}\
+=$QstartL[$a];\n $profile{$n}{Hstart}=$HstartL[$a]\
+;\n $profile{$n}{identity}=$identityL[$a];\n $prof\
+ile{$n}{definition}=$definitionL[$a];\n $profile{$\
+n}{identifyer}=$identifyerL[$a];\n $profile{$n}{co\
+mment}=$comment[$a];\n\n for ($b=0; $b<$L; $b++)\n\
+ {\n if ($p[$a][$b])\n {\n $profile{$\
+n}{seq}.=$p[$a][$b];\n }\n else\n \
+{\n $profile{$n}{seq}.=\"-\";\n }\n }\n \
+ }\n\n $profile{n}=$nhits+1;\n return %pr\
+ofile;\n }\nsub ebi_blast_xml2profile\n {\n m\
+y ($name,$seq,$maxid, $minid, $mincov, $string)=(@\
+_);\n my ($L,$l, $a,$b,$c,$d,$nhits,@identifyer\
+L,$identifyer);\n\n\n\n $seq=~s/[^a-zA-Z]//g;\n\
+ $L=length ($seq);\n %hit=&xml2tag_list ($st\
+ring, \"hit\");\n\n for ($nhits=0,$a=0; $a<$hit\
+{n}; $a++)\n {\n my ($ldb,$id, $identity, $ex\
+pectation, $start, $end, $coverage, $r);\n my (%Q,\
+%M,%E,%I);\n\n $ldb=&tag2value ($hit{$a}{open}, \"\
+database\");\n $identifyer=&tag2value ($hit{$a}{op\
+en}, \"id\");\n\n $description=&tag2value ($hit{$a\
+}{open}, \"description\");\n\n %Q=&xml2tag_list ($\
+hit{$a}{body}, \"querySeq\");\n %M=&xml2tag_list (\
+$hit{$a}{body}, \"matchSeq\");\n %E=&xml2tag_list \
+($hit{$a}{body}, \"expectation\");\n %I=&xml2tag_l\
+ist ($hit{$a}{body}, \"identity\");\n\n\n for ($b=\
0; $b<$Q{n}; $b++)\n {\n\n $qs=$Q{$b}{body};\
-\n $ms=$M{$b}{body};\n \n $expectation\
-=$E{$b}{body};\n $identity=$I{$b}{body};\n \
- \n \n $start=&tag2value ($Q{$b}{open\
-}, \"start\");\n $end=&tag2value ($Q{$b}{open}\
-, \"end\");\n $startM=&tag2value ($M{$b}{open}\
-, \"start\");\n $endM=&tag2value ($M{$b}{open}\
-, \"end\");\n $coverage=(($end-$start)*100)/$L\
-;\n \n # print \"$id: ID: $identity COV: $c\
-overage [$start $end]\\n\";\n \n if ($iden\
-tity>$maxid || $identity<$minid || $coverage<$minc\
-ov){next;}\n # print \"KEEP\\n\";\n\n \n \
- @lr1=(split (//,$qs));\n @lr2=(split (//,$m\
-s));\n $l=$#lr1+1;\n for ($c=0;$c<$L;$c++)\
-{$p[$nhits][$c]=\"-\";}\n for ($d=0,$c=0; $c<$\
-l; $c++)\n {\n $r=$lr1[$c];\n if ( $r=~/[A\
--Za-z]/)\n {\n \n $p[$nhits][$d + $st\
-art-1]=$lr2[$c];\n $d++;\n }\n }\n \
- \n $Qseq[$nhits]=$qs;\n $Hseq[$nhits]=$ms\
-;\n $QstartL[$nhits]=$start;\n $HstartL[$n\
-hits]=$Hstart;\n $identityL[$nhits]=$identity;\
-\n $endL[$nhits]=$end;\n $definitionL[$nhi\
-ts]=$definition;\n $identifyerL[$nhits]=$ident\
-ifyer;\n $comment[$nhits]=\"$ldb|$identifyer [\
-Eval=$expectation][id=$identity%][start=$startM en\
-d=$endM]\";\n $nhits++;\n }\n }\n \n\
- $profile{n}=0;\n $profile{$profile{n}}{name\
-}=$name;\n $profile{$profile{n}}{seq}=$seq;\n \
- $profile {n}++;\n \n for ($a=0; $a<$nhits;\
- $a++)\n {\n $n=$a+1;\n $profile{$n}{name}=\"\
-$name\\_$a\";\n $profile{$n}{seq}=\"\";\n $profile\
-{$n}{Qseq}=$Qseq[$a];\n $profile{$n}{Hseq}=$Hseq[$\
-a];\n $profile{$n}{Qstart}=$QstartL[$a];\n $profil\
-e{$n}{Hstart}=$HstartL[$a];\n $profile{$n}{identit\
-y}=$identityL[$a];\n $profile{$n}{definition}=$def\
-initionL[$a]; \n $profile{$n}{identifyer}=$identif\
-yerL[$a];\n $profile{$n}{comment}=$comment[$a];\n\\
-n for ($b=0; $b<$L; $b++)\n {\n if ($p[$a][$\
-b])\n {\n $profile{$n}{seq}.=$p[$a][$b];\n \
- }\n else\n {\n $profile{$n}{seq}.\
-=\"-\";\n }\n }\n }\n $profile{n}=\
-$nhits+1;\n \n return %profile;\n }\nsub ou\
-tput_profile\n {\n my ($outfile,$profileR, $tr\
-im)=(@_);\n my ($a);\n my %profile=%$profile\
-R;\n my $P= new FileHandle;\n my $tmp=vtmpna\
-m();\n \n open ($P, \">$tmp\");\n for ($a\
-=0; $a<$profile{n}; $a++)\n {\n print $P \">$\
-profile{$a}{name} $profile{$a}{comment}\\n$profile\
-{$a}{seq}\\n\";\n }\n close ($P);\n\n i\
-f ( $trim)\n {\n &safe_system (\"t_coffee -ot\
-her_pg seq_reformat -in $tmp -action +trim _aln_%%\
-$trim\\_K1 -output fasta_aln -out $outfile\");\n \
- }\n else\n {\n &safe_system (\"mv $tmp\
- $outfile\");\n }\n return;\n }\nsub blas\
-t_xml2hit_list\n {\n my $string=(@_[0]);\n \
-return &xml2tag_list ($string, \"hit\");\n }\nsub\
- xmltag2value\n {\n my ($string_in, $tag)=@_;\\
-n my %TAG;\n %TAG=xml2tag_list ($string_in, \
-$tag);\n return $TAG{0}{body};\n }\n \nsu\
-b xml2tag_list \n {\n my ($string_in,$tag)=@_\
-;\n my $tag_in, $tag_out;\n my %tag;\n \n\
- if (-e $string_in)\n {\n $string=&file2st\
-ring ($string_in);\n }\n else\n {\n $\
-string=$string_in;\n }\n $tag_in1=\"<$tag \
-\";\n $tag_in2=\"<$tag>\";\n $tag_out=\"/$ta\
-g>\";\n $string=~s/>/>##1/g;\n $string=~s/</\
-##2</g;\n $string=~s/##1/<#/g;\n $string=~s/\
-##2/#>/g;\n @l=($string=~/(\\<[^>]+\\>)/g);\n \
- $tag{n}=0;\n $in=0;$n=-1;\n \n \n\n forea\
-ch $t (@l)\n {\n\n $t=~s/<#//;\n $t=~s/#>//;\\
-n \n if ( $t=~/$tag_in1/ || $t=~/$tag_in2/)\n {\\
-n \n $in=1;\n $tag{$tag{n}}{open}=$t;\n \
- $n++;\n \n }\n elsif ($t=~/$tag_out/)\n \
- {\n \n\n $tag{$tag{n}}{close}=$t;\n $\
-tag{n}++;\n $in=0;\n }\n elsif ($in)\n {\n\
- \n $tag{$tag{n}}{body}.=$t;\n }\n }\
-\n \n return %tag;\n }\n\n\nsub seq2gor_predi\
-ction \n {\n my ($name, $seq,$infile, $outfile\
-, $gor_seq, $gor_obs)=(@_);\n my ($l);\n \n \
+\n $ms=$M{$b}{body};\n\n $expectation=$E{$\
+b}{body};\n $identity=$I{$b}{body};\n\n\n \
+$start=&tag2value ($Q{$b}{open}, \"start\");\n \
+ $end=&tag2value ($Q{$b}{open}, \"end\");\n $s\
+tartM=&tag2value ($M{$b}{open}, \"start\");\n \
+$endM=&tag2value ($M{$b}{open}, \"end\");\n $c\
+overage=(($end-$start)*100)/$L;\n\n # print \"$\
+id: ID: $identity COV: $coverage [$start $end]\\n\\
+";\n\n if ($identity>$maxid || $identity<$mini\
+d || $coverage<$mincov){next;}\n # print \"KEE\
+P\\n\";\n\n\n @lr1=(split (//,$qs));\n @lr\
+2=(split (//,$ms));\n $l=$#lr1+1;\n for ($\
+c=0;$c<$L;$c++){$p[$nhits][$c]=\"-\";}\n for (\
+$d=0,$c=0; $c<$l; $c++)\n {\n $r=$lr1[$c];\\
+n if ( $r=~/[A-Za-z]/)\n {\n\n $p[$nhits]\
+[$d + $start-1]=$lr2[$c];\n $d++;\n }\n \
+ }\n\n $Qseq[$nhits]=$qs;\n $Hseq[$nhit\
+s]=$ms;\n $QstartL[$nhits]=$start;\n $Hsta\
+rtL[$nhits]=$Hstart;\n $identityL[$nhits]=$ide\
+ntity;\n $endL[$nhits]=$end;\n $definition\
+L[$nhits]=$definition;\n $identifyerL[$nhits]=\
+$identifyer;\n $comment[$nhits]=\"$ldb|$identi\
+fyer [Eval=$expectation][id=$identity%][start=$sta\
+rtM end=$endM]\";\n $nhits++;\n }\n }\n\
+\n $profile{n}=0;\n $profile{$profile{n}}{na\
+me}=$name;\n $profile{$profile{n}}{seq}=$seq;\n\
+ $profile {n}++;\n\n for ($a=0; $a<$nhits; $\
+a++)\n {\n $n=$a+1;\n $profile{$n}{name}=\"$n\
+ame\\_$a\";\n $profile{$n}{seq}=\"\";\n $profile{$\
+n}{Qseq}=$Qseq[$a];\n $profile{$n}{Hseq}=$Hseq[$a]\
+;\n $profile{$n}{Qstart}=$QstartL[$a];\n $profile{\
+$n}{Hstart}=$HstartL[$a];\n $profile{$n}{identity}\
+=$identityL[$a];\n $profile{$n}{definition}=$defin\
+itionL[$a];\n $profile{$n}{identifyer}=$identifyer\
+L[$a];\n $profile{$n}{comment}=$comment[$a];\n\n f\
+or ($b=0; $b<$L; $b++)\n {\n if ($p[$a][$b])\
+\n {\n $profile{$n}{seq}.=$p[$a][$b];\n \
+ }\n else\n {\n $profile{$n}{seq}.=\"\
+-\";\n }\n }\n }\n $profile{n}=$nh\
+its+1;\n\n return %profile;\n }\nsub output_pr\
+ofile\n {\n my ($outfile,$profileR, $trim)=(@_\
+);\n my ($a);\n my %profile=%$profileR;\n \
+ my $P= new FileHandle;\n my $tmp=vtmpnam();\n\\
+n open ($P, \">$tmp\");\n for ($a=0; $a<$pro\
+file{n}; $a++)\n {\n print $P \">$profile{$a}\
+{name} $profile{$a}{comment}\\n$profile{$a}{seq}\\\
+n\";\n }\n close ($P);\n\n if ( $trim)\\
+n {\n &safe_system (\"t_coffee -other_pg seq_\
+reformat -in $tmp -action +trim _aln_%%$trim\\_K1 \
+-output fasta_aln -out $outfile\");\n }\n \
+else\n {\n &safe_system (\"mv $tmp $outfile\"\
+);\n }\n return;\n }\nsub blast_xml2hit_l\
+ist\n {\n my $string=(@_[0]);\n return &xml\
+2tag_list ($string, \"hit\");\n }\nsub xmltag2val\
+ue\n {\n my ($string_in, $tag)=@_;\n my %TA\
+G;\n %TAG=xml2tag_list ($string_in, $tag);\n \
+ return $TAG{0}{body};\n }\n\nsub xml2tag_list\n \
+ {\n my ($string_in,$tag)=@_;\n my $tag_in, \
+$tag_out;\n my %tag;\n\n if (-e $string_in)\\
+n {\n $string=&file2string ($string_in);\n \
+ }\n else\n {\n $string=$string_in;\n \
+ }\n $tag_in1=\"<$tag \";\n $tag_in2=\"<$t\
+ag>\";\n $tag_out=\"/$tag>\";\n $string=~s/>\
+/>##1/g;\n $string=~s/</##2</g;\n $string=~s\
+/##1/<#/g;\n $string=~s/##2/#>/g;\n @l=($str\
+ing=~/(\\<[^>]+\\>)/g);\n $tag{n}=0;\n $in=0\
+;$n=-1;\n\n\n\n foreach $t (@l)\n {\n\n $t\
+=~s/<#//;\n $t=~s/#>//;\n\n if ( $t=~/$tag_in1/ ||\
+ $t=~/$tag_in2/)\n {\n\n $in=1;\n $tag{$\
+tag{n}}{open}=$t;\n $n++;\n\n }\n elsif ($t=\
+~/$tag_out/)\n {\n\n\n $tag{$tag{n}}{close}=\
+$t;\n $tag{n}++;\n $in=0;\n }\n elsif ($\
+in)\n {\n\n $tag{$tag{n}}{body}.=$t;\n }\n\
+ }\n\n return %tag;\n }\n\n\nsub seq2gor_\
+prediction\n {\n my ($name, $seq,$infile, $out\
+file, $gor_seq, $gor_obs)=(@_);\n my ($l);\n\n \
`gorIV -prd $infile -seq $gor_seq -obs $gor_obs\
> gor_tmp`;\n open (GR, \">$outfile\");\n o\
pen (OG, \"gor_tmp\");\n\n while (<OG>)\n \
-{\n \n $l=$_;\n if ($l=~/\\>/){print GR \"$l\";}\n\
- elsif ( $l=~/Predicted Sec. Struct./)\n {\n \
- $l=~s/Predicted Sec. Struct\\.//;\n print GR \
-\"$l\";\n }\n }\n close (GR);\n close\
- (OG);\n return;\n }\nsub seq2msa_tm_predictio\
-n \n {\n my ($name, $seq, $db, $infile, $outfi\
-le, $arch, $psv)=(@_);\n my (%p,%gseq,%R, $blas\
-t_output, %s, $l);\n my $R2=new FileHandle;\n \
- my $db=\"uniprot\";\n my $method=\"psitm\";\n\
- my $SERVER=\"EBI\";\n \n $blast_output=&\
-run_blast ($name,\"blastp\", $db, $infile, \"outfi\
-le\");\n \n if (&cache_file(\"GET\",$infile,\
-$name,$method,$db,$outfile,$SERVER))\n {\n pr\
-int \"\\tPSITM: USE Cache\\n\";\n return $outfile;\
-\n }\n else\n {\n $CACHE_STATUS=\"COM\
-PUTE CACHE\";\n %p=blast_xml2profile($name,$seq,$m\
-axid, $minid,$mincov,$blast_output);\n \n \n open \
-(F, \">tm_input\");\n for (my $a=0; $a<$p{n}; $a++\
-)\n {\n my $s;\n \n $s=$p{$a}{seq};\\
-n $s=uc($s);\n print F \">$p{$a}{name}\\n$\
-s\\n\";\n #print stdout \">$p{$a}{name}\\n$s\\\
-n\";\n }\n close (F);\n print \"\\tPSITM: kept \
-$p{n} Homologues for Sequence $p{0}{name}\\n\";\n \
-&safe_system (\"t_coffee -other_pg fasta_seq2hmmto\
-p_fasta.pl -in=tm_input -out=$outfile -output=cons\
- -cov=70 -trim=95 -arch=$arch -psv=$psv\");\n unli\
-nk (\"tm_input\");\n &cache_file(\"SET\",$infile,$\
-name,$method,$db,$outfile,$SERVER);\n return;\n \
- }\n }\n\n\nsub seq2msa_gor_prediction \n {\n \
- my ($name, $seq,$infile, $outfile, $gor_seq, $g\
-or_obs)=(@_);\n my (%p,%gseq,%R, $blast_output,\
- %s, $l);\n my $R2=new FileHandle;\n my $db=\
-\"uniprot\";\n my $method=\"psigor\";\n my $\
-SERVER=\"EBI\";\n \n $blast_output=&run_blas\
-t ($name,\"blastp\", \"uniprot\", $infile, \"outfi\
-le\");\n \n if (&cache_file(\"GET\",$infile,\
-$name,$method,$db,$outfile,$SERVER))\n {\n pr\
-int \"\\tPSIGOR: USE Cache\\n\";\n return $outfile\
-;\n }\n else\n {\n $CACHE_STATUS=\"CO\
-MPUTE CACHE\";\n %p=blast_xml2profile($name,$seq,$\
-maxid, $minid,$mincov,$blast_output);\n \n \n open\
- (F, \">gor_input\");\n for (my $a=0; $a<$p{n}; $a\
-++)\n {\n my $s;\n \n $s=$p{$a}{seq}\
-;\n $s=uc($s);\n print F \">$p{$a}{name}\\\
-n$s\\n\";\n #print stdout \">$p{$a}{name}\\n$s\
-\\n\";\n }\n close (F);\n print \"\\tGORTM: kept\
- $p{n} Homologues for Sequence $p{0}{name}\\n\";\\
-n &safe_system (\"t_coffee -other_pg fasta_seq2hmm\
-top_fasta.pl -in=gor_input -out=$outfile -output=c\
-ons -cov=70 -trim=95 -gor_seq=$gor_seq -gor_obs=$g\
-or_obs -mode=gor\");\n unlink (\"tm_input\");\n &c\
-ache_file(\"SET\",$infile,$name,$method,$db,$outfi\
-le,$SERVER);\n return;\n }\n }\n\n\n\nsub ru\
-n_blast\n {\n my ($name, $method, $db, $infile\
-, $outfile, $run)=(@_);\n if (!$run){$run=1;}\n\
- \n \n if (&cache_file(\"GET\",$infile,$n\
-ame,$method,$db,$outfile,$SERVER) && is_valid_blas\
-t_xml ($outfile))\n {return $outfile;}\n e\
-lse\n {\n $CACHE_STATUS=\"COMPUTE CACHE\";\n \
-if ( $SERVER eq \"EBI_SOAP\")\n {\n &check_c\
-onfiguration (\"EMAIL\",\"SOAP::Light\",\"INTERNET\
-\");\n \n $cl_method=$method;\n if ($c\
-l_method =~/wu/)\n {\n $cl_method=~s/wu//;\\
-n if ( $cl_method eq \"psiblast\")\n {\n \
-add_warning($$,$$,\"PSI BLAST cannot be used with \
-the wuBLAST Client. Use server=EBI Or server=LOCAL\
-. blastp will be used instead\");\n $cl_metho\
-d=\"blastp\";\n }\n \n $command=\"t_coffee -o\
-ther_pg wublast.pl --email $EMAIL $infile -D $db -\
-p $cl_method --outfile $outfile -o xml>/dev/null 2\
->/dev/null\";\n &safe_system ( $command);\n if (\
--e \"$outfile.xml\") {`mv $outfile.xml $outfile`;}\
-\n }\n else\n {\n if ($cl_method \
-eq \"psiblast\"){$cl_method =\"blastp -j5\";}\n \\
-n $command=\"t_coffee -other_pg blastpgp.pl --ema\
-il $EMAIL $infile -d $db --outfile $outfile -p $cl\
-_method --mode PSI-Blast>/dev/null 2>/dev/null\";\\
-n &safe_system ( $command);\n \n if (-e \"$outf\
-ile.xml\") {`mv $outfile.xml $outfile`;}\n }\
-\n }\n elsif ($SERVER eq \"EBI_REST\" || $SERVER\
- eq \"EBI\")\n {\n \n $cl_method=$method;\
-\n &check_configuration(\"EMAIL\",\"XML::Simpl\
-e\", \"INTERNET\");\n if ($db eq \"uniprot\"){\
-$db1=\"uniprotkb\";}\n else {$db1=$db;}\n \
-\n\n if ($cl_method =~/wu/)\n {\n $cl_m\
-ethod=~s/wu//;\n if ( $cl_method eq \"psiblast\")\
-{$cl_method=\"blastp\";}\n \n $command=\"t_coffe\
-e -other_pg wublast_lwp.pl --email $EMAIL -D $db1 \
--p $cl_method --outfile $outfile --align 7 --stype\
- protein $infile>/dev/null 2>/dev/null\";\n \n \
- }\n else\n {\n if ( $cl_method =~/p\
-siblast/){$cl_method =\"blastp -j5\";}\n $command\
-=\"t_coffee -other_pg ncbiblast_lwp.pl --email $EM\
-AIL -D $db1 -p $cl_method --outfile $outfile --ali\
-gn 7 --stype protein $infile>/dev/null 2>/dev/null\
-\";\n }\n &safe_system ( $command,5);\n \
- if (-e \"$outfile.out.xml\") {`mv $outfile.out\
-.xml $outfile`;}\n elsif (-e \"$outfile.xml.xm\
-l\"){`mv $outfile.xml.xml $outfile`;}\n elsif \
-(-e \"$outfile.out..xml\") {`mv $outfile.out..xml \
-$outfile`;}\n elsif (-e \"$outfile.xml..xml\")\
-{`mv $outfile.xml..xml $outfile`;}\n }\n elsif (\
-$SERVER eq \"NCBI\")\n {\n &check_configurat\
-ion (\"blastcl3\",\"INTERNET\");\n if ($db eq \
-\"uniprot\"){$cl_db=\"nr\";}\n else {$cl_db=$d\
-b;}\n \n if ( $method eq \"psiblast\")\n \
- {\n add_warning($$,$$,\"PSI BLAST cannot be \
-used with the NCBI BLAST Client. Use server=EBI Or\
- server=LOCAL. blastp will be used instead\");\n \
-$cl_method=\"blastp\";\n }\n else\n \
- {\n $cl_method=$method;\n }\n $comman\
-d=\"blastcl3 -p $cl_method -d $cl_db -i $infile -o\
- $outfile -m 7\";\n &safe_system ($command);\n\
- }\n elsif ($SERVER =~/CLIENT_(.*)/)\n {\n \
- my $client=$1;\n $command=\"$client -p $metho\
-d -d $db -i $infile -o $outfile -m 7\";\n &saf\
-e_system ($command);\n }\n elsif ( $SERVER eq \"\
-LOCAL_blastall\")\n {\n &check_configuration\
- (\"blastall\");\n if ($method eq \"blastp\")\\
-n {\n $command=\"blastall -d $db -i $infile\
- -o $outfile -m7 -p blastp\";\n }\n &saf\
-e_system ($command);\n }\n elsif ( $SERVER eq \"\
-LOCAL\")\n {\n \n if ($ENV{\"BLAST_DB_DI\
-R\"})\n {\n $x=$ENV{\"BLAST_DB_DIR\"};\n $\
-cl_db=\"$x$db\";\n }\n else\n {\n \
- $cl_db=$db;\n }\n \n if ($method eq\
- \"blastp\")\n {\n &check_configuration(\"b\
-lastpgp\");\n $command=\"blastpgp -d $cl_db -i $i\
-nfile -o $outfile -m7 -j1\";\n }\n elsif\
- ($method eq \"psiblast\")\n {\n &check_con\
-figuration(\"blastpgp\");\n $command=\"blastpgp -\
-d $cl_db -i $infile -o $outfile -m7 -j5\";\n \
- }\n elsif ($method eq \"blastn\")\n {\n\
- &check_configuration(\"blastall\");\n $command=\
-\"blastall -p blastn -d $cl_db -i $infile -o $outf\
-ile -m7 -W6\";\n } \n &safe_system ($com\
-mand);\n }\n else\n {\n \n myexit(add_\
-error (EXIT_FAILURE,$$,$$,getppid(), \"BLAST_FAILU\
-RE::UnknownServer\",$CL));\n }\n \n if ( !-e $ou\
-tfile || !&is_valid_blast_xml($outfile))\n {\n \
- \n if ( -e $outfile)\n {\n add_warni\
-ng ($$,$$,\"Corrupted Blast Output (Run $run)\");\\
-n unlink($outfile);\n }\n \n if ( $\
-run==$BLAST_MAX_NRUNS)\n {\n \n myexit(add_\
-error (EXIT_FAILURE,$$,$$,getppid(), \"BLAST_FAILU\
-RE::UnknownReason\", \"$command\"));\n }\n \
- else\n {\n my $out;\n if ($SERVER eq \"\
-NCBI\") {$SERVER=\"EBI\"; }\n elsif ($SERVER eq \\
-"EBI\"){$SERVER=\"NCBI\";}\n add_warning ($$,$$,\\
-"Blast for $name failed (Run: $run out of $BLAST_M\
-AX_NRUNS. Use $SERVER)\");\n $out=&run_blast ($na\
-me, $method, $db,$infile, $outfile, $run+1);\n if\
- ($SERVER eq \"NCBI\") {$SERVER=\"EBI\"; }\n elsi\
-f ($SERVER eq \"EBI\"){$SERVER=\"NCBI\";}\n retur\
-n $out;\n }\n }\n \n &cache_file(\"SET\",$\
-infile,$name,$method,$db,$outfile,$SERVER);\n #sys\
-tem (\"cp $outfile ~/Dropbox/tmp/cedric.out\");\n \
-#die;\n return $outfile;\n }\n }\n\nsub cach\
-e_file\n {\n my ($cache_mode,$infile,$name,$me\
-thod,$db, $outfile,$server)=(@_);\n my $cache_f\
-ile;\n #Protect names so that they can be turne\
-d into legal filenames\n $name=&clean_file_name\
- ($name);\n\n if ($db=~/\\//)\n {\n $db=~/\
-([^\\/]+)$/;\n $db=$1;\n }\n $cache_file_s\
-h=\"$name.$method.$db.$server.tmp\";\n $cache_f\
-ile=\"$CACHE/$name.$method.$db.$server.tmp\";\n \
- \n if ($infile ne \"\")\n {\n $cache_file\
-_infile_sh=\"$name.$method.$db.$server.infile.tmp\\
-";\n $cache_file_infile=\"$CACHE/$name.$method.$db\
-.$server.infile.tmp\";\n }\n \n if ($ca\
-che_mode eq \"GET\")\n {\n if ($CACHE eq \"\"\
- || $CACHE eq \"no\" || $CACHE eq \"ignore\" || $\
-CACHE eq \"local\" || $CACHE eq \"update\"){return\
- 0;}\n elsif ( !-d $CACHE)\n {\n print STDER\
-R \"ERROR: Cache Dir: $CACHE Does not Exist\";\n \
- return 0;\n }\n else\n {\n if ( -e $cac\
-he_file && &fasta_file1_eq_fasta_file2($infile,$ca\
-che_file_infile)==1)\n {\n `cp $cache_file \
-$outfile`;\n $CACHE_STATUS=\"READ CACHE\";\n ret\
-urn 1;\n }\n }\n }\n elsif ($cache\
-_mode eq \"SET\")\n {\n if ($CACHE eq \"\" ||\
- $CACHE eq \"no\" || $CACHE eq \"ignore\" || $CAC\
-HE eq \"local\" || $CACHE eq \"update\"){return 0;\
-}\n elsif ( !-d $CACHE)\n {\n print STDERR \\
-"ERROR: Cache Dir: $CACHE Does not Exist\";\n \
-return 0;\n }\n elsif (-e $outfile)\n {\n \
-`cp $outfile $cache_file`;\n if ($cache_file_i\
-nfile ne \"\"){ `cp $infile $cache_file_infile`;}\\
-n\n #functions for updating the cache\n #`\
-t_coffee -other_pg clean_cache.pl -file $cache_fil\
-e_sh -dir $CACHE`;\n #`t_coffee -other_pg clea\
-n_cache.pl -file $cache_file_infile_sh -dir $CACHE\
-`;\n return 1;\n }\n }\n $CACHE_STAT\
-US=\"COMPUTE CACHE\";\n return 0;\n }\nsub fil\
-e1_eq_file2\n {\n my ($f1, $f2)=@_;\n if ( \
-$f1 eq \"\"){return 1;}\n elsif ( $f2 eq \"\"){\
-return 1;}\n elsif ( !-e $f1){return 0;}\n e\
-lsif ( !-e $f2){return 0;}\n elsif ($f1 eq \"\"\
- || $f2 eq \"\" || `diff $f1 $f2` eq \"\"){return \
-1;}\n \n return 0;\n }\nsub clean_file_name\
- \n {\n my $name=@_[0];\n \n $name=~s/[^\
-A-Za-z1-9.-]/_/g;\n return $name;\n }\nsub url\
-2file\n {\n my ($address, $out)=(@_);\n \n \
- if (&pg_is_installed (\"wget\"))\n {\n return\
- &safe_system (\"wget $address -O$out >/dev/null 2\
->/dev/null\");\n }\n elsif (&pg_is_installed (\\
-"curl\"))\n {\n return &safe_system (\"curl $\
-address -o$out >/dev/null 2>/dev/null\");\n }\
-\n else\n {\n myexit(flus_error(\"neither \
-curl nor wget are installed. Imnpossible to fectch\
- remote file\"));\n exit ($EXIT_FAILURE);\n }\
-\n }\nsub fasta_file1_eq_fasta_file2\n {\n my\
- ($f1, $f2)=@_;\n my (%s1, %s2);\n my @names\
-;\n %s1=read_fasta_seq ($f1);\n %s2=read_fas\
-ta_seq ($f2);\n\n @names=(keys (%s1));\n \n \
- foreach $n (keys(%s1))\n {\n if ($s1{$n}{s\
-eq} ne $s2{$n}{seq}){return 0;}\n } \n \n \
- foreach $n (keys(%s2))\n {\n if ($s1{$n}{s\
-eq} ne $s2{$n}{seq}){return 0;}\n }\n retu\
-rn 1;\n }\n \n\n\nsub read_template_file\n{\n my \
-$pdb_templates = @_[0];\n open (TEMP, \"<$pdb_temp\
-lates\");\n my %temp_h;\n while (<TEMP>)\n{\n $li\
-ne = $_;\n $line =~/(\\S+)\\s(\\S+)/;\n $temp_\
-h{$1}= $2;\n}\n close(TEMP);\n return %temp_h;\n}\\
-n\nsub calc_rna_template\n{\n my ($mode, $infile, \
-$pdbfile, $outfile)=@_;\n my %s, %h ;\n my $result\
-;\n my (@profiles);\n &set_temporary_dir (\"set\",\
-$infile,\"seq.pep\");\n %s=read_fasta_seq (\"seq.p\
-ep\");\n \n %pdb_template_h = &read_template_file(\
-$pdbfile);\n my $pdb_chain;\n open (R, \">result.a\
-ln\");\n\n\n #print stdout \"\\n\";\n foreach $seq\
- (keys(%s))\n {\n if ($pdb_template_h{$seq} eq \"\
-\")\n {\n next;\n }\n open (F, \">seqfile\");\
-\n print (F \">$s{$seq}{name}\\n$s{$seq}{seq}\\n\\
-");\n close (F);\n $pdb_chain = $pdb_template_h{\
-$seq};\n $lib_name=\"$s{$seq}{name}.rfold\";\n $\
-lib_name=&clean_file_name ($lib_name);\n \n saf\
-e_system (\"secondary_struc.py seqfile $CACHE$pdb_\
-chain $lib_name\");\n \n if ( !-e $lib_name)\n \
- {\n myexit(flush_error(\"RNAplfold failed to com\
-pute the secondary structure of $s{$seq}{name}\"))\
-;\n myexit ($EXIT_FAILURE);\n }\n else\n {\n \
- print stdout \"\\tProcess: >$s{$seq}{name} _F_ $\
-lib_name\\n\";\n print R \">$s{$seq}{name} _F_ $\
-lib_name\\n\";\n }\n unshift (@profiles, $lib_na\
-me);\n }\n close (R);\n &set_temporary_dir (\"unse\
-t\",$mode, $method,\"result.aln\",$outfile, @profi\
-les);\n}\n\n\n\nsub seq2rna_pair{\n my ($mode, $pd\
-bfile1, $pdbfile2, $method, $param, $outfile)=@_;\\
-n \n if ($method eq \"runsara.py\")\n {\n open(TM\
-P,\"<$pdbfile1\");\n my $count = 0;\n my $line;\\
-n while (<TMP>)\n {\n $line = $_;\n if ($cou\
-nt ==1)\n {\n last;\n }\n $count += 1;\n \
- }\n\n \n $chain1 = substr($line,length($line)-3\
-,1);\n\n close TMP;\n open(TMP,\"<$pdbfile2\");\\
-n my $count = 0;\n while (<TMP>)\n {\n $line \
-= $_;\n if ($count ==1)\n {\n last;\n }\n\
- $count += 1;\n }\n $chain2 = substr($line,len\
-gth($line)-3,1);\n close TMP;\n\n $tmp_file=&vtm\
-pnam();\n \n safe_system(\"runsara.py $pdbfile1 $\
-chain1 $pdbfile2 $chain2 -s -o $tmp_file --limitat\
-ion 5000 > /dev/null 2> /dev/null\") == 0 or die \\
-"sara did not work $!\\n\";\n open(TMP,\"<$tmp_fi\
-le\") or die \"cannot open the sara tmp file:$!\\n\
-\";\n open(OUT,\">$outfile\") or die \"cannot ope\
-n the $outfile file:$!\\n\";\n\n my $switch = 0;\\
-n my $seqNum = 0;\n foreach my $line (<TMP>)\n \
-{\n next unless ($line=~/SARAALI/);\n if ($lin\
-e=~/>/)\n {\n $switch =0;\n print OUT \">s\
-eq$seqNum\\n\";\n $seqNum++; \n }\n if (\
-$switch < 2){\n $switch++;\n next;\n }\n \\
-n if ($line =~/REMARK\\s+SARAALI\\s+([^\\*]+)\\*\
-/)\n {\n my $string = $1;\n print OUT \"$s\
-tring\\n\";\n }\n }\n close TMP; \n close OUT\
-;\n unlink($tmp_file);\n }\n}\n\nsub seq2tblastx_\
+{\n\n $l=$_;\n if ($l=~/\\>/){print GR \"$l\";}\n \
+elsif ( $l=~/Predicted Sec. Struct./)\n {\n \
+$l=~s/Predicted Sec. Struct\\.//;\n print GR \\
+"$l\";\n }\n }\n close (GR);\n close \
+(OG);\n return;\n }\nsub seq2msa_tm_prediction\
+\n {\n my ($name, $seq, $db, $infile, $outfile\
+, $arch, $psv)=(@_);\n my (%p,%gseq,%R, $blast_\
+output, %s, $l);\n my $R2=new FileHandle;\n \
+my $db=\"uniprot\";\n my $method=\"psitm\";\n \
+ my $SERVER=\"EBI\";\n\n $blast_output=&run_bl\
+ast ($name,\"blastp\", $db, $infile, \"outfile\");\
+\n\n if (&cache_file(\"GET\",$infile,$name,$met\
+hod,$db,$outfile,$SERVER))\n {\n print \"\\tP\
+SITM: USE Cache\\n\";\n return $outfile;\n }\\
+n else\n {\n $CACHE_STATUS=\"COMPUTE CACHE\
+\";\n %p=blast_xml2profile($name,$seq,$maxid, $min\
+id,$mincov,$blast_output);\n\n\n open (F, \">tm_in\
+put\");\n for (my $a=0; $a<$p{n}; $a++)\n {\n \
+ my $s;\n\n $s=$p{$a}{seq};\n $s=uc($s);\\
+n print F \">$p{$a}{name}\\n$s\\n\";\n #pr\
+int stdout \">$p{$a}{name}\\n$s\\n\";\n }\n clos\
+e (F);\n print \"\\tPSITM: kept $p{n} Homologues \
+for Sequence $p{0}{name}\\n\";\n &safe_system (\"t\
+_coffee -other_pg fasta_seq2hmmtop_fasta.pl -in=tm\
+_input -out=$outfile -output=cons -cov=70 -trim=95\
+ -arch=$arch -psv=$psv\");\n unlink (\"tm_input\")\
+;\n &cache_file(\"SET\",$infile,$name,$method,$db,\
+$outfile,$SERVER);\n return;\n }\n }\n\n\nsu\
+b seq2msa_gor_prediction\n {\n my ($name, $seq\
+,$infile, $outfile, $gor_seq, $gor_obs)=(@_);\n \
+ my (%p,%gseq,%R, $blast_output, %s, $l);\n my \
+$R2=new FileHandle;\n my $db=\"uniprot\";\n \
+my $method=\"psigor\";\n my $SERVER=\"EBI\";\n\\
+n $blast_output=&run_blast ($name,\"blastp\", \\
+"uniprot\", $infile, \"outfile\");\n\n if (&cac\
+he_file(\"GET\",$infile,$name,$method,$db,$outfile\
+,$SERVER))\n {\n print \"\\tPSIGOR: USE Cache\
+\\n\";\n return $outfile;\n }\n else\n \
+ {\n $CACHE_STATUS=\"COMPUTE CACHE\";\n %p=blast_\
+xml2profile($name,$seq,$maxid, $minid,$mincov,$bla\
+st_output);\n\n\n open (F, \">gor_input\");\n for \
+(my $a=0; $a<$p{n}; $a++)\n {\n my $s;\n\n \
+ $s=$p{$a}{seq};\n $s=uc($s);\n print F \
+\">$p{$a}{name}\\n$s\\n\";\n #print stdout \">\
+$p{$a}{name}\\n$s\\n\";\n }\n close (F);\n print\
+ \"\\tGORTM: kept $p{n} Homologues for Sequence $\
+p{0}{name}\\n\";\n &safe_system (\"t_coffee -other\
+_pg fasta_seq2hmmtop_fasta.pl -in=gor_input -out=$\
+outfile -output=cons -cov=70 -trim=95 -gor_seq=$go\
+r_seq -gor_obs=$gor_obs -mode=gor\");\n unlink (\"\
+tm_input\");\n &cache_file(\"SET\",$infile,$name,$\
+method,$db,$outfile,$SERVER);\n return;\n }\n\
+ }\n\n\n\nsub run_blast\n {\n my ($name, $met\
+hod, $db, $infile, $outfile, $run)=(@_);\n if (\
+!$run){$run=1;}\n my $error_log=vtmpnam();\n\n \
+ if (&cache_file(\"GET\",$infile,$name,$method,$\
+db,$outfile,$SERVER) && is_valid_blast_xml ($outfi\
+le))\n {return $outfile;}\n else\n {\\
+n $CACHE_STATUS=\"COMPUTE CACHE\";\n if ( $SERVER \
+eq \"EBI_SOAP\")\n {\n &check_configuration \
+(\"EMAIL\",\"SOAP::Light\",\"INTERNET\");\n\n \
+$cl_method=$method;\n if ($cl_method =~/wu/)\n\
+ {\n $cl_method=~s/wu//;\n if ( $cl_method\
+ eq \"psiblast\")\n {\n add_warning($$,$$,\
+\"PSI BLAST cannot be used with the wuBLAST Client\
+. Use server=EBI Or server=LOCAL. blastp will be u\
+sed instead\");\n $cl_method=\"blastp\";\n \
+ }\n\n $command=\"t_coffee -other_pg wublast.pl -\
+-email $EMAIL $infile -D $db -p $cl_method --outfi\
+le $outfile -o xml>/dev/null 2>$error_log\";\n &s\
+afe_system ( $command);\n if (-e \"$outfile.xml\"\
+) {`mv $outfile.xml $outfile`;}\n }\n el\
+se\n {\n if ($cl_method eq \"psiblast\"){$c\
+l_method =\"blastp -j5\";}\n\n $command=\"t_coffe\
+e -other_pg blastpgp.pl --email $EMAIL $infile -d \
+$db --outfile $outfile -p $cl_method --mode PSI-Bl\
+ast>/dev/null 2>$error_log\";\n &safe_system ( $c\
+ommand);\n\n if (-e \"$outfile.xml\") {`mv $outfi\
+le.xml $outfile`;}\n }\n }\n elsif ($SERVE\
+R eq \"EBI_REST\" || $SERVER eq \"EBI\")\n {\n \
+ $cl_method=$method;\n &check_configuration(\
+\"EMAIL\",\"XML::Simple\", \"INTERNET\");\n if\
+ ($db eq \"uniprot\"){$db1=\"uniprotkb\";}\n e\
+lse {$db1=$db;}\n\n \n if ($cl_method =~/wu\
+/)\n {\n $cl_method=~s/wu//;\n if ( $cl_me\
+thod eq \"psiblast\"){$cl_method=\"blastp\";}\n\n \
+ $command=\"t_coffee -other_pg wublast_lwp.pl --em\
+ail $EMAIL -D $db1 -p $cl_method --outfile $outfil\
+e --align 5 --stype protein $infile>/dev/null 2>er\
+ror_log\";\n }\n else\n {\n if ( \
+$cl_method =~/psiblast/){$cl_method =\"blastp -j5\\
+";}\n $command=\"t_coffee -other_pg ncbiblast_lwp\
+.pl --email $EMAIL -D $db1 -p $cl_method --outfile\
+ $outfile --align 5 --stype protein $infile>/dev/n\
+ull 2>$error_log\";\n }\n &safe_system (\
+ $command,5);\n if (-e \"$outfile.out.xml\") {\
+`mv $outfile.out.xml $outfile`;}\n elsif (-e \\
+"$outfile.xml.xml\"){`mv $outfile.xml.xml $outfile\
+`;}\n elsif (-e \"$outfile.out..xml\") {`mv $o\
+utfile.out..xml $outfile`;}\n elsif (-e \"$out\
+file.xml..xml\"){`mv $outfile.xml..xml $outfile`;}\
+\n }\n elsif ($SERVER eq \"NCBI\")\n {\n &\
+check_configuration (\"INTERNET\");\n if ($db \
+eq \"uniprot\"){$cl_db=\"swissprot\";}\n else \
+{$cl_db=$db;}\n\n if ( $method eq \"psiblast\"\
+)\n {\n add_warning($$,$$,\"PSI BLAST canno\
+t be used with the NCBI BLAST Client. Use server=E\
+BI Or server=LOCAL. blastp will be used instead\")\
+;\n $cl_method=\"blastp\";\n }\n else\n\
+ {\n $cl_method=$method;\n }\n \
+\n &check_configuration ($cl_method); \n \
+$command=\"$cl_method -db $cl_db -query $infile -o\
+ut $outfile -outfmt 5 -remote\";\n &safe_syste\
+m ($command);\n }\n elsif ($SERVER =~/CLIENT_(.*\
+)/)\n {\n my $client=$1;\n $command=\"$c\
+lient -p $method -d $db -i $infile -o $outfile -m \
+7\";\n &safe_system ($command);\n }\n elsif \
+( $SERVER eq \"LOCAL_blastall\")\n {\n &chec\
+k_configuration (\"blastall\");\n if ($method \
+eq \"blastp\")\n {\n $command=\"blastall -d\
+ $db -i $infile -o $outfile -m7 -p blastp\";\n \
+ }\n &safe_system ($command);\n }\n elsif \
+( $SERVER eq \"LOCAL\")\n {\n\n if ($ENV{\"B\
+LAST_DB_DIR\"})\n {\n $x=$ENV{\"BLAST_DB_DI\
+R\"};\n $cl_db=\"$x$db\";\n }\n else\n \
+ {\n $cl_db=$db;\n }\n\n ##\n \
+## BLAST+ provide different binaries names and CLI\
+ options\n ## Use the 'legacy_blast.pl' to keep c\
+ompatibility with old blast commands\n ##\n $pat\
+h=`which legacy_blast.pl 2>/dev/null`; \n $path=\
+`dirname $path`; \n chomp($path);\n if ($meth\
+od eq \"blastp\")\n {\n &check_configuratio\
+n(\"legacy_blast.pl\");\n $command=\"legacy_blast\
+.pl blastpgp --path $path -d $cl_db -i $infile -o \
+$outfile -m7 -j1\";\n }\n elsif ($method\
+ eq \"psiblast\")\n {\n &check_configuratio\
+n(\"legacy_blast.pl\");\n $command=\"legacy_blast\
+.pl blastpgp --path $path -d $cl_db -i $infile -o \
+$outfile -m7 -j5\";\n }\n elsif ($method\
+ eq \"blastn\")\n {\n &check_configuration(\
+\"legacy_blast.pl\");\n $command=\"legacy_blast.p\
+l blastall --path $path -p blastn -d $cl_db -i $in\
+file -o $outfile -m7 -W6\";\n }\n &safe_\
+system ($command);\n }\n else\n {\n\n myex\
+it(add_error (EXIT_FAILURE,$$,$$,getppid(), \"BLAS\
+T_FAILURE::UnknownServer\",$CL));\n }\n\n\n #Che\
+ck that everything went well\n\n if ( !-e $outfile\
+ || !&is_valid_blast_xml($outfile))\n {\n\n \
+if ( -e $outfile)\n {\n add_warning ($$,$$,\
+\"Corrupted Blast Output (Run $run)\");\n unlink(\
+$outfile);\n }\n if ( -e $error_log)\n \
+ {\n\n my $error_msg=file2string ($error_log)\
+;\n\n if ( $error_msg =~/enter a valid email/)\n \
+ {\n myexit(add_error (EXIT_FAILURE,$$,$$,g\
+etppid(), \"BLAST_FAILURE::Invalid_or_rejected_ema\
+il::$EMAIL\", \"$command\"));\n }\n }\n \
+ if ( $run==$BLAST_MAX_NRUNS)\n {\n\n mye\
+xit(add_error (EXIT_FAILURE,$$,$$,getppid(), \"BLA\
+ST_FAILURE::UnknownReason\", \"$command\"));\n \
+ }\n else\n {\n my $out;\n if ($SERV\
+ER eq \"NCBI\") {$SERVER=\"EBI\"; }\n elsif ($SER\
+VER eq \"EBI\"){$SERVER=\"NCBI\";}\n add_warning \
+($$,$$,\"Blast for $name failed (Run: $run out of \
+$BLAST_MAX_NRUNS. Use $SERVER)\");\n $out=&run_bl\
+ast ($name, $method, $db,$infile, $outfile, $run+1\
+);\n if ($SERVER eq \"NCBI\") {$SERVER=\"EBI\"; }\
+\n elsif ($SERVER eq \"EBI\"){$SERVER=\"NCBI\";}\\
+n return $out;\n }\n }\n\n &cache_file(\"\
+SET\",$infile,$name,$method,$db,$outfile,$SERVER);\
+\n #system (\"cp $outfile ~/Dropbox/tmp/cedric.out\
+\");\n #die;\n return $outfile;\n }\n }\n\ns\
+ub cache_file\n {\n my ($cache_mode,$infile,$n\
+ame,$method,$db, $outfile,$server)=(@_);\n my $\
+cache_file;\n #Protect names so that they can b\
+e turned into legal filenames\n $name=&clean_fi\
+le_name ($name);\n\n if ($db=~/\\//)\n {\n\
+ $db=~/([^\\/]+)$/;\n $db=$1;\n }\n $cache\
+_file_sh=\"$name.$method.$db.$server.tmp\";\n $\
+cache_file=\"$CACHE/$name.$method.$db.$server.tmp\\
+";\n\n if ($infile ne \"\")\n {\n $cache_f\
+ile_infile_sh=\"$name.$method.$db.$server.infile.t\
+mp\";\n $cache_file_infile=\"$CACHE/$name.$method.\
+$db.$server.infile.tmp\";\n }\n\n if ($cac\
+he_mode eq \"GET\")\n {\n if ($CACHE eq \"\" \
+|| $CACHE eq \"no\" || $CACHE eq \"ignore\" || $C\
+ACHE eq \"local\" || $CACHE eq \"update\"){return \
+0;}\n elsif ( !-d $CACHE)\n {\n print STDERR\
+ \"ERROR: Cache Dir: $CACHE Does not Exist\";\n \
+ return 0;\n }\n else\n {\n if ( -e $cach\
+e_file && &fasta_file1_eq_fasta_file2($infile,$cac\
+he_file_infile)==1)\n {\n `cp $cache_file $\
+outfile`;\n $CACHE_STATUS=\"READ CACHE\";\n retu\
+rn 1;\n }\n }\n }\n elsif ($cache_\
+mode eq \"SET\")\n {\n if ($CACHE eq \"\" || \
+$CACHE eq \"no\" || $CACHE eq \"ignore\" || $CACH\
+E eq \"local\" || $CACHE eq \"update\"){return 0;}\
+\n elsif ( !-d $CACHE)\n {\n print STDERR \"\
+ERROR: Cache Dir: $CACHE Does not Exist\";\n r\
+eturn 0;\n }\n elsif (-e $outfile)\n {\n `\
+cp $outfile $cache_file`;\n if ($cache_file_in\
+file ne \"\"){ `cp $infile $cache_file_infile`;}\n\
+\n #functions for updating the cache\n #`t\
+_coffee -other_pg clean_cache.pl -file $cache_file\
+_sh -dir $CACHE`;\n #`t_coffee -other_pg clean\
+_cache.pl -file $cache_file_infile_sh -dir $CACHE`\
+;\n return 1;\n }\n }\n $CACHE_STATU\
+S=\"COMPUTE CACHE\";\n return 0;\n }\nsub file\
+1_eq_file2\n {\n my ($f1, $f2)=@_;\n if ( $\
+f1 eq \"\"){return 1;}\n elsif ( $f2 eq \"\"){r\
+eturn 1;}\n elsif ( !-e $f1){return 0;}\n el\
+sif ( !-e $f2){return 0;}\n elsif ($f1 eq \"\" \
+|| $f2 eq \"\" || `diff $f1 $f2` eq \"\"){return 1\
+;}\n\n return 0;\n }\nsub clean_file_name\n {\
+\n my $name=@_[0];\n\n $name=~s/[^A-Za-z1-9.\
+-]/_/g;\n return $name;\n }\nsub url2file\n {\
+\n my ($address, $out)=(@_);\n\n if (&pg_is_\
+installed (\"wget\"))\n {\n return &safe_system \
+(\"wget $address -O$out >/dev/null 2>/dev/null\");\
+\n }\n elsif (&pg_is_installed (\"curl\"))\n \
+ {\n return &safe_system (\"curl $address -o$out\
+ >/dev/null 2>/dev/null\");\n }\n else\n \
+ {\n myexit(flus_error(\"neither curl nor wget \
+are installed. Imnpossible to fectch remote file\"\
+));\n exit ($EXIT_FAILURE);\n }\n }\nsub fas\
+ta_file1_eq_fasta_file2\n {\n my ($f1, $f2)=@_\
+;\n my (%s1, %s2);\n my @names;\n %s1=rea\
+d_fasta_seq ($f1);\n %s2=read_fasta_seq ($f2);\\
+n\n @names=(keys (%s1));\n\n foreach $n (key\
+s(%s1))\n {\n if ($s1{$n}{seq} ne $s2{$n}{seq\
+}){return 0;}\n }\n\n foreach $n (keys(%s2\
+))\n {\n if ($s1{$n}{seq} ne $s2{$n}{seq}){re\
+turn 0;}\n }\n return 1;\n }\n\n\n\nsub r\
+ead_template_file\n {\n my $pdb_templates = @_\
+[0];\n my $tmp=new FileHandle;\n open ($tmp,\
+ \"<$pdb_templates\");\n my %temp_h;\n my ($\
+skip,$seq, $temp);\n\n #supports both a simple \
+[seq pdb] format and the regular fasta like templa\
+te format\n while (<$tmp>)\n {\n \n $line \
+= $_;\n if ($line=~/\\>(\\S+)\\s_._\\s(\\S+)/){$te\
+mp_h{$1}= $2;}\n elsif ($line =~/(\\S+)\\s(\\S+)/)\
+{$temp_h{$1}= $2;}\n }\n close($tmp);\n \
+ return %temp_h;\n }\n\n\n\n\n\n\nsub seq2tblastx\
+_lib\n {\n my ($mode, $infile, $outfile)=@_;\n\
+ my (%s, $method,$nseq);\n\n $method=$mode;\\
+n &set_temporary_dir (\"set\",$infile,\"infile\\
+");\n %s=read_fasta_seq(\"infile\");\n\n\n f\
+oreach $seq (keys(%s))\n {\n $slist[$s{$seq}{\
+order}]=$s{$seq}{seq};\n $sname[$s{$seq}{order}]=$\
+s{$seq}{name};\n $slen[$s{$seq}{order}]=length ($s\
+{$seq}{seq});\n }\n $nseq=$#sname+1;\n \
+open (F, \">outfile\");\n print F \"! TC_LIB_FO\
+RMAT_01\\n\";\n print F \"$nseq\\n\";\n for \
+($a=0; $a<$nseq;$a++)\n {\n print F \"$sname[\
+$a] $slen[$a] $slist[$a]\\n\"\n }\n close\
+ (F);\n &safe_system (\"formatdb -i infile -p F\
+\");\n &safe_system (\"blastall -p tblastx -i i\
+nfile -d infile -m 7 -S1>blast.output\");\n\n n\
+cbi_tblastx_xml2lib_file (\"outfile\", file2string\
+ (\"blast.output\"));\n &set_temporary_dir (\"u\
+nset\",$mode, $method, \"outfile\",$outfile);\n \
+ myexit ($EXIT_SUCCESS);\n }\nsub seq2tblastpx_\
lib\n {\n my ($mode, $infile, $outfile)=@_;\n \
- my (%s, $method,$nseq);\n\n $method=$mode;\n\
- &set_temporary_dir (\"set\",$infile,\"infile\"\
-);\n %s=read_fasta_seq(\"infile\");\n \n \
-\n foreach $seq (keys(%s))\n {\n $slist[$s\
-{$seq}{order}]=$s{$seq}{seq};\n $sname[$s{$seq}{or\
-der}]=$s{$seq}{name};\n $slen[$s{$seq}{order}]=len\
-gth ($s{$seq}{seq});\n }\n $nseq=$#sname+1\
-;\n open (F, \">outfile\");\n print F \"! TC\
-_LIB_FORMAT_01\\n\";\n print F \"$nseq\\n\";\n \
- for ($a=0; $a<$nseq;$a++)\n {\n print F \"\
-$sname[$a] $slen[$a] $slist[$a]\\n\"\n }\n \
- close (F);\n &safe_system (\"formatdb -i infi\
-le -p F\");\n &safe_system (\"blastall -p tblas\
-tx -i infile -d infile -m 7 -S1>blast.output\");\n\
- \n ncbi_tblastx_xml2lib_file (\"outfile\", \
-file2string (\"blast.output\"));\n &set_tempora\
-ry_dir (\"unset\",$mode, $method, \"outfile\",$out\
-file);\n myexit ($EXIT_SUCCESS);\n }\nsub se\
-q2tblastpx_lib\n {\n my ($mode, $infile, $outf\
-ile)=@_;\n my (%s, $method,$nseq);\n $method\
-=$mode;\n &set_temporary_dir (\"set\",$infile,\\
-"infile\");\n %s=read_fasta_seq(\"infile\");\n \
- \n foreach $seq (keys(%s))\n {\n $slist\
-[$s{$seq}{order}]=$s{$seq}{seq};\n $sname[$s{$seq}\
-{order}]=$s{$seq}{name};\n $slen[$s{$seq}{order}]=\
-length ($s{$seq}{seq});\n }\n $nseq=$#snam\
-e+1;\n open (F, \">outfile\");\n print F \"!\
- TC_LIB_FORMAT_01\\n\";\n print F \"$nseq\\n\";\
-\n for ($a=0; $a<$nseq;$a++)\n {\n print F\
- \"$sname[$a] $slen[$a] $slist[$a]\\n\"\n }\\
-n close (F);\n &safe_system(\"t_coffee -othe\
-r_pg seq_reformat -in infile -output tblastx_db1 >\
- tblastxdb\");\n &safe_system (\"formatdb -i tb\
-lastxdb -p T\");\n &safe_system (\"blastall -p \
-blastp -i tblastxdb -d tblastxdb -m7 >blast.output\
-\");\n ncbi_tblastpx_xml2lib_file (\"outfile\",\
- file2string (\"blast.output\"), %s);\n &set_te\
-mporary_dir (\"unset\",$mode, $method, \"outfile\"\
-,$outfile);\n myexit ($EXIT_SUCCESS);\n }\n\\
-n\n \n\n\n\nsub file2head\n {\n my $file =\
- shift;\n my $size = shift;\n my $f= new FileHandl\
-e;\n my $line;\n open ($f,$file);\n read ($f,$line\
-, $size);\n close ($f);\n return $line;\n }\n\
-sub file2tail\n {\n my $file = shift;\n my $s\
-ize = shift;\n my $f= new FileHandle;\n my $line;\\
-n \n open ($f,$file);\n seek ($f,$size*-1, 2);\n r\
-ead ($f,$line, $size);\n close ($f);\n return $lin\
-e;\n }\n\n\nsub vtmpnam\n {\n my $r=rand\
-(100000);\n my $f=\"file.$r.$$\";\n while (-e $f)\\
-n {\n $f=vtmpnam();\n }\n push (@TMPFILE_L\
-IST, $f);\n return $f;\n }\n\nsub myexit\n {\
-\n my $code=@_[0];\n if ($CLEAN_EXIT_STARTED\
-==1){return;}\n else {$CLEAN_EXIT_STARTED=1;}\n\
- ### ONLY BARE EXIT\n exit ($code);\n }\nsu\
-b set_error_lock\n {\n my $name = shift;\n\
- my $pid=$$;\n\n \n &lock4tc ($$,\"\
-LERROR\", \"LSET\", \"$$ -- ERROR: $name $PROGRAM\\
-\n\");\n return;\n }\nsub set_lock\n {\n \
- my $pid=shift;\n my $msg= shift;\n my $p=\
-getppid();\n &lock4tc ($pid,\"LLOCK\",\"LRESET\\
-",\"$p$msg\\n\");\n }\nsub unset_lock\n {\n \
- \n my $pid=shift;\n &lock4tc ($pid,\"LLOCK\\
-",\"LRELEASE\",\"\");\n }\nsub shift_lock\n {\n \
- my $from=shift;\n my $to=shift;\n my $fro\
-m_type=shift;\n my $to_type=shift;\n my $act\
-ion=shift;\n my $msg;\n \n if (!&lock4tc(\
-$from, $from_type, \"LCHECK\", \"\")){return 0;}\n\
- $msg=&lock4tc ($from, $from_type, \"LREAD\", \\
-"\");\n &lock4tc ($from, $from_type,\"LRELEASE\\
-", $msg);\n &lock4tc ($to, $to_type, $action, $\
-msg);\n return;\n }\nsub isshellpid\n {\n \
-my $p=shift;\n if (!lock4tc ($p, \"LLOCK\", \"L\
-CHECK\")){return 0;}\n else\n {\n my $c=lo\
-ck4tc($p, \"LLOCK\", \"LREAD\");\n if ( $c=~/-SHEL\
-L-/){return 1;}\n }\n return 0;\n }\nsub \
-isrootpid\n {\n if(lock4tc (getppid(), \"LLOCK\
-\", \"LCHECK\")){return 0;}\n else {return 1;}\\
-n }\nsub lock4tc\n {\n my ($pid,$type,$action,$\
-value)=@_;\n my $fname;\n my $host=hostname;\n\
- \n if ($type eq \"LLOCK\"){$fname=\"$LOCKDIR/\
-.$pid.$host.lock4tcoffee\";}\n elsif ( $type eq \
-\"LERROR\"){ $fname=\"$LOCKDIR/.$pid.$host.error4t\
-coffee\";}\n elsif ( $type eq \"LWARNING\"){ $fn\
-ame=\"$LOCKDIR/.$pid.$host.warning4tcoffee\";}\n \
- \n if ($debug_lock)\n {\n print STDER\
-R \"\\n\\t---lock4tc(tcg): $action => $fname =>$va\
-lue (RD: $LOCKDIR)\\n\";\n }\n\n if ($act\
-ion eq \"LCHECK\") {return -e $fname;}\n elsif (\
-$action eq \"LREAD\"){return file2string($fname);}\
-\n elsif ($action eq \"LSET\") {return string2fi\
-le ($value, $fname, \">>\");}\n elsif ($action e\
-q \"LRESET\") {return string2file ($value, $fname,\
- \">\");}\n elsif ($action eq \"LRELEASE\") \n \
- {\n if ( $debug_lock)\n {\n my $g=new\
- FileHandle;\n open ($g, \">>$fname\");\n pr\
-int $g \"\\nDestroyed by $$\\n\";\n close ($g);\
-\n safe_system (\"mv $fname $fname.old\");\n }\
-\n else\n {\n unlink ($fname);\n }\n \
- }\n return \"\";\n }\n \nsub file2string\n {\n\
- my $file=@_[0];\n my $f=new FileHandle;\n m\
-y $r;\n open ($f, \"$file\");\n while (<$f>){$\
-r.=$_;}\n close ($f);\n return $r;\n }\nsub st\
-ring2file \n {\n my ($s,$file,$mode)=@_;\n \
- my $f=new FileHandle;\n \n open ($f, \"$mo\
-de$file\");\n print $f \"$s\";\n close ($f)\
-;\n }\n\nBEGIN\n {\n srand;\n \n \
-$SIG{'SIGUP'}='signal_cleanup';\n $SIG{'SIGIN\
-T'}='signal_cleanup';\n $SIG{'SIGQUIT'}='sign\
-al_cleanup';\n $SIG{'SIGILL'}='signal_cleanup\
-';\n $SIG{'SIGTRAP'}='signal_cleanup';\n \
- $SIG{'SIGABRT'}='signal_cleanup';\n $SIG{'SI\
-GEMT'}='signal_cleanup';\n $SIG{'SIGFPE'}='si\
-gnal_cleanup';\n \n $SIG{'SIGKILL'}='sig\
-nal_cleanup';\n $SIG{'SIGPIPE'}='signal_clean\
-up';\n $SIG{'SIGSTOP'}='signal_cleanup';\n \
- $SIG{'SIGTTIN'}='signal_cleanup';\n $SIG{'\
-SIGXFSZ'}='signal_cleanup';\n $SIG{'SIGINFO'}\
-='signal_cleanup';\n \n $SIG{'SIGBUS'}='\
-signal_cleanup';\n $SIG{'SIGALRM'}='signal_cl\
-eanup';\n $SIG{'SIGTSTP'}='signal_cleanup';\n\
- $SIG{'SIGTTOU'}='signal_cleanup';\n $SI\
-G{'SIGVTALRM'}='signal_cleanup';\n $SIG{'SIGU\
-SR1'}='signal_cleanup';\n\n\n $SIG{'SIGSEGV'}\
-='signal_cleanup';\n $SIG{'SIGTERM'}='signal_\
-cleanup';\n $SIG{'SIGCONT'}='signal_cleanup';\
-\n $SIG{'SIGIO'}='signal_cleanup';\n $SI\
-G{'SIGPROF'}='signal_cleanup';\n $SIG{'SIGUSR\
-2'}='signal_cleanup';\n\n $SIG{'SIGSYS'}='sig\
-nal_cleanup';\n $SIG{'SIGURG'}='signal_cleanu\
-p';\n $SIG{'SIGCHLD'}='signal_cleanup';\n \
- $SIG{'SIGXCPU'}='signal_cleanup';\n $SIG{'S\
-IGWINCH'}='signal_cleanup';\n \n $SIG{'I\
-NT'}='signal_cleanup';\n $SIG{'TERM'}='signal\
-_cleanup';\n $SIG{'KILL'}='signal_cleanup';\n\
- $SIG{'QUIT'}='signal_cleanup';\n \n \
- our $debug_lock=$ENV{\"DEBUG_LOCK\"};\n \n \
- \n \n \n foreach my $a (@ARGV)\
-{$CL.=\" $a\";}\n if ( $debug_lock ){print ST\
-DERR \"\\n\\n\\n********** START PG: $PROGRAM ****\
-*********\\n\";}\n if ( $debug_lock ){print S\
-TDERR \"\\n\\n\\n**********(tcg) LOCKDIR: $LOCKDIR\
- $$ *************\\n\";}\n if ( $debug_lock )\
-{print STDERR \"\\n --- $$ -- $CL\\n\";}\n \n\
- \n \n \n }\nsub flush_error\n \
-{\n my $msg=shift;\n return add_error ($EXIT\
-_FAILURE,$$, $$,getppid(), $msg, $CL);\n }\nsub a\
-dd_error \n {\n my $code=shift;\n my $rpid=\
-shift;\n my $pid=shift;\n my $ppid=shift;\n \
- my $type=shift;\n my $com=shift;\n \n \
-$ERROR_DONE=1;\n lock4tc ($rpid, \"LERROR\",\"L\
-SET\",\"$pid -- ERROR: $type\\n\");\n lock4tc (\
-$$, \"LERROR\",\"LSET\", \"$pid -- COM: $com\\n\")\
-;\n lock4tc ($$, \"LERROR\",\"LSET\", \"$pid --\
- STACK: $ppid -> $pid\\n\");\n \n return $cod\
-e;\n }\nsub add_warning \n {\n my $rpid=shift\
-;\n my $pid =shift;\n my $command=shift;\n \
- my $msg=\"$$ -- WARNING: $command\\n\";\n pri\
-nt STDERR \"$msg\";\n lock4tc ($$, \"LWARNING\"\
-, \"LSET\", $msg);\n }\n\nsub signal_cleanup\n {\
-\n print dtderr \"\\n**** $$ (tcg) was killed\\\
-n\";\n &cleanup;\n exit ($EXIT_FAILURE);\n \
-}\nsub clean_dir\n {\n my $dir=@_[0];\n if \
-( !-d $dir){return ;}\n elsif (!($dir=~/tmp/)){\
-return ;}#safety check 1\n elsif (($dir=~/\\*/)\
-){return ;}#safety check 2\n else\n {\n `r\
-m -rf $dir`;\n }\n return;\n }\nsub clean\
-up\n {\n #print stderr \"\\n----tc: $$ Kills $\
-PIDCHILD\\n\";\n #kill (SIGTERM,$PIDCHILD);\n \
- my $p=getppid();\n $CLEAN_EXIT_STARTED=1;\n \
- \n \n \n if (&lock4tc($$,\"LERROR\", \"\
-LCHECK\", \"\"))\n {\n my $ppid=getppid();\n \
-if (!$ERROR_DONE) \n {\n &lock4tc($$,\"LERRO\
-R\", \"LSET\", \"$$ -- STACK: $p -> $$\\n\");\n \
- &lock4tc($$,\"LERROR\", \"LSET\", \"$$ -- COM: $\
-CL\\n\");\n }\n }\n my $warning=&lock4tc\
-($$, \"LWARNING\", \"LREAD\", \"\");\n my $erro\
-r=&lock4tc($$, \"LERROR\", \"LREAD\", \"\");\n \
- #release error and warning lock if root\n \n \
- if (isrootpid() && ($warning || $error) )\n \
- {\n \n print STDERR \"**************** Summary **\
-***********\\n$error\\n$warning\\n\";\n\n &lock4tc\
-($$,\"LERROR\",\"RELEASE\",\"\");\n &lock4tc($$,\"\
-LWARNING\",\"RELEASE\",\"\");\n } \n \n \
- \n foreach my $f (@TMPFILE_LIST)\n {\n if\
- (-e $f){unlink ($f);} \n }\n foreach my $\
-d (@TMPDIR_LIST)\n {\n clean_dir ($d);\n \
- }\n #No More Lock Release\n #&lock4tc($$,\"\
-LLOCK\",\"LRELEASE\",\"\"); #release lock \n\n \
-if ( $debug_lock ){print STDERR \"\\n\\n\\n*******\
-*** END PG: $PROGRAM ($$) *************\\n\";}\n \
- if ( $debug_lock ){print STDERR \"\\n\\n\\n*****\
-*****(tcg) LOCKDIR: $LOCKDIR $$ *************\\n\"\
-;}\n }\nEND \n {\n \n &cleanup();\n }\n \
- \nsub blast_com2new_blast_com\n {\n my $c\
-om=shift;\n if ($ENV{\"NCBI_BLAST_4_TCOFFEE\"\
-} eq \"OLD\"){return $com;}\n elsif (!&pg_is_\
-installed(\"legacy_blast.pl\")){return $com;}\n \
- else \n {\n if ($com=~/formatdb/)\n {\n \
- $com=~s/formatdb/makeblastdb/;\n $com=~\
-s/\\-i/\\-in/;\n if ($com =~/pF/){$com=~s/\\\
--pF/\\-dbtype nucl/;}\n if ($com =~/p F/){$c\
-om=~s/\\-p F/\\-dbtype nucl/;}\n $com=\"$com\
- -logfile /dev/null\";\n return $com;\n \
-}\n elsif (&is_blast_package($com))\n {\n \
- my $path;\n \n if ( $ENV{\"NCBI_BI\
-N_4_TCOFFEE\"}){$path=$ENV{\"NCBI_BLAST_4_TCOFFEE\\
-"};}\n else\n {\n $path=`which legacy_bl\
-ast.pl`;\n $path=~s/\\/legacy_blast\\.pl//;\n \
- chomp ($path);\n }\n $path=\"--path $path\
-\";\n if ( $com=~/\\>\\>/){$com=~s/\\>\\>/ $\
-path \\>\\>/;}\n elsif ( $com=~/\\>/){$com=~\
-s/\\>/ $path \\>/;}\n else {$com.=\" $path\"\
-;}\n $com=\"legacy_blast.pl $com\";\n \
-\n return $com;\n }\n }\n }\nsub safe\
-_system \n{\n my $com=shift;\n my $ntry=shift;\n\
- my $ctry=shift;\n my $pid;\n my $status;\n my\
- $ppid=getppid();\n if ($com eq \"\"){return 1;}\\
-n \n if ( ($com=~/^blast/) ||($com=~/^formatdb/)\
-){$com=&blast_com2new_blast_com($com);} \n\n if (\
-($pid = fork ()) < 0){return (-1);}\n if ($pid ==\
- 0)\n {\n set_lock($$, \" -SHELL- $com (tc\
-g)\");\n if( $debug_cmd_exec ) { printf \"exe\
-c: %s\\n\", $com; } \n exec ($com);\n }\n \
- else\n {\n lock4tc ($$, \"LLOCK\", \"LSET\
-\", \"$pid\\n\");#update parent\n $PIDCHILD=$\
-pid;\n }\n if ($debug_lock){printf STDERR \"\\\
-n\\t .... safe_system (fasta_seq2hmm) p: $$ c: $p\
-id COM: $com\\n\";}\n\n waitpid ($pid,WTERMSIG);\\
-n\n shift_lock ($pid,$$, \"LWARNING\",\"LWARNING\\
-", \"LSET\");\n\n if ($? == $EXIT_FAILURE || lock\
-4tc($pid, \"LERROR\", \"LCHECK\", \"\"))\n {\n \
- if ($ntry && $ctry <$ntry)\n {\n\n add_warn\
-ing ($$,$$,\"$com failed [retry: $ctry out of $ntr\
-y]\");\n lock4tc ($pid, \"LRELEASE\", \"LERROR\"\
-, \"\");\n #if ($com=~/EBI/){$com=~s/EBI/NCBI/;}\
-\n #elsif ($com=~/NCBI/){$com=~s/NCBI/EBI/;}\n \
- \n return safe_system ($com, $ntry, ++$ctry);\n\
- }\n elsif ($ntry == -1)\n {\n if (!shift_l\
-ock ($pid, $$, \"LERROR\", \"LWARNING\", \"LSET\")\
-)\n {\n add_warning ($$,$$,\"$com failed\
-\");\n }\n else\n {\n lock4tc ($pi\
-d, \"LRELEASE\", \"LERROR\", \"\");\n }\n re\
-turn $?;}\n else\n {\n if (!shift_lock ($pi\
-d,$$, \"LERROR\",\"LERROR\", \"LSET\"))\n {\n \
- myexit(add_error ($EXIT_FAILURE,$$,$pid,getp\
-pid(), \"UNSPECIFIED system\", $com));\n }\n }\
-\n }\n return $?;\n}\n\nsub check_configuratio\
-n \n {\n my @l=@_;\n my $v;\n fo\
-reach my $p (@l)\n {\n \n if ( $p eq \"EMAIL\
-\")\n { \n if ( !($EMAIL=~/@/))\n {\n \
-add_warning($$,$$,\"Could Not Use EMAIL\");\n mye\
-xit(add_error ($EXIT_FAILURE,$$,$$,getppid(),\"EMA\
-IL\",\"$CL\"));\n }\n }\n elsif( $p eq\
- \"INTERNET\")\n {\n if ( !&check_intern\
-et_connection())\n {\n myexit(add_error ($EXIT\
-_FAILURE,$$,$$,getppid(),\"INTERNET\",\"$CL\"));\n\
- }\n }\n elsif( $p eq \"wget\")\n {\n \
- if (!&pg_is_installed (\"wget\") && !&pg_is_i\
-nstalled (\"curl\"))\n {\n myexit(add_error ($\
-EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTALLED:wg\
-et\",\"$CL\"));\n }\n }\n elsif( !(&pg_is_i\
-nstalled ($p)))\n {\n myexit(add_error (\
-$EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTALLED:$\
-p\",\"$CL\"));\n }\n }\n return 1;\n }\
-\n\n$program=\"T-COFFEE (r550)\";\n\n","*TC_METHOD\
-_FORMAT_01\n******************generic_method.tc_me\
-thod*************\n*\n* Incorporating new me\
-thods in T-Coffee\n* Cedric Notredame 26/08/\
-08\n*\n*******************************************\
-************\n*This file is a method file\n*Copy i\
-t and adapt it to your need so that the method \n*\
-you want to use can be incorporated within T-Coffe\
-e\n***********************************************\
-********\n* USAGE \
- *\n*********************************\
-**********************\n*This file is passed to t_\
-coffee via -in:\n*\n* t_coffee -in Mgeneric_method\
-.method\n*\n* The method is passed to the shell us\
-ing the following\n*call:\n*<EXECUTABLE><PARAM1><I\
-N_FLAG><seq_file><PARAM2><OUT_FLAG><outname><PARAM\
->\n*\n*Conventions:\n*<FLAG_NAME> <TYPE> <VALUE>\
-\n*<VALUE>: no_name <=> Replaced with a space\n*<\
-VALUE>:   <=> Replaced with a space\n*\n******\
-*************************************************\\
-n* ALN_MODE \
- *\n******************************************\
-*************\n*pairwise ->all Vs all (no self )\
-[(n2-n)/2aln]\n*m_pairwise ->all Vs all (no self)[\
-n^2-n]^2\n*s_pairwise ->all Vs all (self): [n^2-n]\
-/2 + n\n*multiple ->All the sequences in one go\\
-n*\nALN_MODE pairwise\n*\n***********************\
-********************************\n* \
- OUT_MODE *\n*********\
-**********************************************\n* \
-mode for the output:\n*External methods: \n* aln -\
-> alignmnent File (Fasta or ClustalW Format)\n* li\
-b-> Lib file (TC_LIB_FORMAT_01)\n*Internal Methods\
-:\n* fL -> Internal Function returning a List (Lib\
-rairie)\n* fA -> Internal Function returning an Al\
-ignmnent\n*\nOUT_MODE aln\n**********************\
-*********************************\n* \
- SEQ_TYPE *\n********\
-***********************************************\n*\
-G: Genomic, S: Sequence, P: PDB, R: Profile\n*Exam\
-ples:\n*SEQTYPE S sequences against sequences (def\
-ault)\n*SEQTYPE S_P sequence against structure\n*S\
-EQTYPE P_P structure against structure\n*SEQTYPE P\
-S mix of sequences and structure \n*\nSEQ_TYPE S\n\
-*\n\n*********************************************\
-**********\n* COMMAND LINE \
- *\n*EXECUTABLE PARAM1 IN_FLAG OUT_\
-FLAG PARAM *\n************************\
-*******************************\n*****************\
-**************************************\n* \
- EXECUTABLE *\n***\
-**************************************************\
-**\n*name of the executable\n*passed to the shell:\
- executable\n* \nEXECUTABLE tc_generic_method.pl\n\
-*\n***********************************************\
-********\n* IN_FLAG \
- *\n********************************\
-***********************\n*IN_FLAG\n*flag indicatin\
-g the name of the in coming sequences\n*IN_FLAG S \
-no_name ->no flag\n*IN_FLAG S &bnsp-in&bnsp -> \" \
--in \"\n*\nIN_FLAG -infile=\n*\n*****************\
-**************************************\n* \
- OUT_FLAG *\n***\
+ my (%s, $method,$nseq);\n $method=$mode;\n \
+ &set_temporary_dir (\"set\",$infile,\"infile\");\
+\n %s=read_fasta_seq(\"infile\");\n\n foreac\
+h $seq (keys(%s))\n {\n $slist[$s{$seq}{order\
+}]=$s{$seq}{seq};\n $sname[$s{$seq}{order}]=$s{$se\
+q}{name};\n $slen[$s{$seq}{order}]=length ($s{$seq\
+}{seq});\n }\n $nseq=$#sname+1;\n open \
+(F, \">outfile\");\n print F \"! TC_LIB_FORMAT_\
+01\\n\";\n print F \"$nseq\\n\";\n for ($a=0\
+; $a<$nseq;$a++)\n {\n print F \"$sname[$a] $\
+slen[$a] $slist[$a]\\n\"\n }\n close (F);\
+\n &safe_system(\"t_coffee -other_pg seq_reform\
+at -in infile -output tblastx_db1 > tblastxdb\");\\
+n &safe_system (\"formatdb -i tblastxdb -p T\")\
+;\n &safe_system (\"blastall -p blastp -i tblas\
+txdb -d tblastxdb -m7 >blast.output\");\n ncbi_\
+tblastpx_xml2lib_file (\"outfile\", file2string (\\
+"blast.output\"), %s);\n &set_temporary_dir (\"\
+unset\",$mode, $method, \"outfile\",$outfile);\n \
+ myexit ($EXIT_SUCCESS);\n }\n\nsub x3dna_find\
+_pair2lib\n {\n my ($seq, $pdb, $lib, $p\
+g)=@_;\n my $outfile1=\"dssr-2ndstrs.dbn\";\n\
+ my $outfile2=\"simple.output\";\n my $f\
+= new FileHandle;\n my ($rnaSS,$pdbSS);\n \
+ my $command;\n my %s_pdb;\n my %s_seq;\
+\n \n #$pg: \"find_pair\" OR \"find_pair\
+ -p\"\n \n if (!pg_is_installed (\"find_\
+pair\"))\n {\n add_warning ($$,$$, \"x3dna/find_\
+pairs could not be used to extract RNA secondary s\
+tructures. Secondary structures will be extracted \
+by x3dna-ssr instead\");\n return x3dnassr2lib (\
+$seq, $pdb, $lib);\n }\n \n #get PDB seq\
+uence\n safe_system (\"t_coffee -other_pg ext\
+ract_from_pdb $pdb -seq >$outfile1\");\n \n \
+ #get find_pair contacts\n $command=\"$pg \
+$pdb simple.output > /dev/null 2>/dev/null\";\n \
+ safe_system ($command);\n\n if (($command=\
+~/find_pair -p/)){$outfile2=\"allpairs.ana\";}\n \
+ else {$outfile2=\"simple.output\";}\n \n \
+ if ( !-e $outfile2)\n {\n myexit(flush_erro\
+r(\"x3dna failed to compute the secondary structur\
+e file $outfile2 for $pdb\"));\n myexit ($EXIT_F\
+AILURE);\n }\n \n\n #Handle situations w\
+hen the pdb sequence differs from the RNA sequence\
+\n #my @out=file2array($outfile1);\n %s_\
+pdb=read_fasta_seq_index ($outfile1);\n %s_se\
+q=read_fasta_seq_index ($seq);\n my $rnaS=uc(\
+$s_seq{0}{seq});\n my $pdbS=uc($s_pdb{0}{seq}\
+);\n \n my $vienna;\n my @lu;\n \
+\n if ($rnaS ne $pdbS)\n {\n \n my ($rna,\
+$pdb);\n $rnaSS=$rnaS;\n $pdbSS=$pdbS;\n $rn\
+aSS=~s/T/U/g;\n $pdbSS=~s/T/U/g;\n ($rnaSS,$pd\
+bSS)=nw ($rnaS, $pdbS);\n \n my @rnaA =split (\
+//,$rnaSS);\n my @pdbA=split (//,$pdbSS);\n my\
+ $l=@rnaA;\n \n #print \"\\n--- $s_seq{0}{name\
+} $rnaSS\\n--- $s_seq{0}{name} $pdbSS\\n\\n\";\n \
+ \n for (my $b=0,my $a=0; $a<$l; $a++)\n {\n\
+ if ($rnaA[$a] ne '-' && $pdbA[$a] ne '-')\
+{$lu[++$pdb]=++$rna;}\n elsif($rnaA[$a] eq '\
+-'){$lu[++$pdb]=-1;}\n elsif($pdbA[$a] eq '-\
+'){++$rna;}\n }\n }\n else\n {\n for (m\
+y $a=0; $a<=length ($rnaS); $a++)\n {\n \
+$lu[$a]=$a;\n }\n }\n my $l=length ($rnaS\
+);\n open ($f, \">$lib\");\n print $f \"\
+! TC_LIB_FORMAT_01\\n\";\n print $f \"1\\n\";\
+\n print $f \"$s_seq{0}{name} $l $rnaS\\n\";\\
+n print $f \"!CMT: [SOURCE] >$s_seq{0}{name} \
+3D contact library Generated by $pg (x3dna)\\n\";\\
+n print $f \"#1 1\\n\";\n \n my $ne\
+;\n my @array=file2array($outfile2);\n f\
+or (my $a=0; $a<5; $a++){shift (@array);}\n w\
+hile (!($array[0]=~/####/))\n {\n my $line= shif\
+t (@array);\n my @l=($line=~/(\\d+)/g);\n \n \
+\n my $f1=$lu[$l[0]];\n my $s1=$lu[$l[1]];\n\n\
+ #print \"\\n$line\\n$l[0] --> $f1\\n$l[1] --> $\
+s1\\n\\n\"; \n \n if (!$f1 || !$s1)\n {\n \
+ print \"\\n---- $rnaSS\\n---- $pdbSS\\n$line\
+\\n[$l[0] --- $l[1]]<---->[$f1 --- $s1]\\n\";\n \
+ myexit(flush_error(\"Error while parsing s3dna\
+::find_pair output\"));\n }\n elsif ($f1==-1\
+ || $s1==-1){;}\n elsif ($f1<$s1){print $f \"$f1\
+ $s1 100\\n\";}\n else {print $f \"$s1 $f1 100\\\
+n\";$ne++;}\n }\n print $f \"! SEQ_1_TO_N\\n\\
+";\n close ($f);\n return;\n }\nsub R\
+NAplfold2lib\n {\n my ($seq, $lib)=@_;\n my\
+ $f= new FileHandle;\n \n &safe_system (\"t_\
+coffee -other_pg RNAplfold2tclib.pl -in=$seq -out=\
+$lib\");\n \n if ( !-e $lib)\n {\n myexit(f\
+lush_error(\"RNAplfold failed to compute the secon\
+dary structure of $s{$seq}{name}\"));\n myexit ($\
+EXIT_FAILURE);\n }\n open ($f, \">>$lib\"\
+);\n print $f \"!CMT: [SOURCE] 2D contact libra\
+ry Generated by RNAPlfold (Vienna Package)\\n\";\n\
+ close $f;\n return;\n }\nsub x3dnassr2lib\\
+n {\n my ($seq, $pdb, $lib)=@_;\n my \
+$outfile=\"dssr-2ndstrs.dbn\";\n my $f= new F\
+ileHandle;\n \n\n if (!pg_is_installed (\
+\"x3dna-ssr\"))\n {\n add_warning ($$,$$, \"x3dn\
+a-ssr could not be used to extract RNA secondary s\
+tructures. Secondary structures will be predicted \
+ab-initio instead with RNAPlfold\");\n return RN\
+Aplfold2lib ($seq,$lib);\n }\n \n safe_s\
+ystem (\"x3dna-ssr -i=$pdb >/dev/null 2>/dev/null\\
+");\n if ( !-e $outfile)\n {\n myexit(flush\
+_error(\"x3dna-ssr failed to compute the secondary\
+ structure file \"));\n myexit ($EXIT_FAILURE);\\
+n }\n\n #Handle situations when the pdb seque\
+nce differs from the RNA sequence\n @out=file\
+2array($outfile);\n my %s=read_fasta_seq ($se\
+q);\n my @names=keys (%s);\n my $rnaS=uc\
+($s{$names[0]}{seq});\n my $pdbS=uc($out[1]);\
+\n my $vienna;\n \n #x3dna returns \
+non legitimate nucleotides\n $pdbS=~s/[^AGCT\
+U]//g;\n \n if ($rnaS ne $pdbS)\n {\n \
+my ($rna,$pdb);\n my $rnaSS=$rnaS;\n my $pdbSS\
+=$pdbS;\n $rnaSS=~s/T/U/g;\n $pdbSS=~s/T/U/g;\\
+n ($rnaSS,$pdbSS)=nw ($rnaSS, $pdbSS);\n my @r\
+naA =split (//,$rnaSS);\n my @pdbA=split (//,$pd\
+bSS);\n my @SS=split (//, $out[2]);\n \n my \
+$l=@rnaA;\n for (my $b=0,my $a=0; $a<$l; $a++)\n\
+ {\n if ($rnaA[$a] ne '-' && $pdbA[$a]\
+ ne '-'){$vienna.=$SS[$b++];}\n elsif($rnaA[\
+$a] eq '-'){$b++;}\n elsif($pdbA[$a] eq '-')\
+{$vienna.='.';}\n }\n }\n else\n {\n $v\
+ienna=$out[2];\n }\n \n\n open ($f, \">seq\
+\");\n print $f \">$names[0]\\n$rnaS\\n\";\n \
+ close $f;\n \n open ($f, \">str\");\
+\n print $f \">$names[0]\\n$vienna\\n\";\n \
+ close $f;\n \n safe_system (\"t_coffe\
+e -other_pg seq_reformat -in seq -in2 str -output \
+vienna2tc_lib >$lib\");\n if ( !-e $lib)\n \
+ {\n myexit(flush_error(\"seq_reformat fail\
+ed to convert your secondary structure\"));\n \
+ myexit ($EXIT_FAILURE);\n }\n \n o\
+pen ($f, \">>$lib\");\n print $f \"!CMT: [SOU\
+RCE] >$names[0] 2D Contact library generated by x3\
+dna-ssr\\n\";\n #print $f \"! Vienna_Format: \
+>$names[0]\\n\";\n #print $f \"! Vienna_Forma\
+t: $vienna\\n\";\n \n close $f;\n r\
+eturn;\n }\n\n\nsub file2head\n {\n my $fi\
+le = shift;\n my $size = shift;\n my $f= new FileH\
+andle;\n my $line;\n open ($f,$file);\n read ($f,$\
+line, $size);\n close ($f);\n return $line;\n \
+ }\nsub file2tail\n {\n my $file = shift;\n m\
+y $size = shift;\n my $f= new FileHandle;\n my $li\
+ne;\n\n open ($f,$file);\n seek ($f,$size*-1, 2);\\
+n read ($f,$line, $size);\n close ($f);\n return $\
+line;\n }\n\n\nsub vtmpnam\n {\n my $r=r\
+and(100000);\n my $f=\"file.$r.$$\";\n while (-e $\
+f)\n {\n $f=vtmpnam();\n }\n push (@TMPFIL\
+E_LIST, $f);\n return $f;\n }\n\nsub myexit\n\
+ {\n my $code=@_[0];\n if ($CLEAN_EXIT_STAR\
+TED==1){return;}\n else {$CLEAN_EXIT_STARTED=1;\
+}\n ### ONLY BARE EXIT\n exit ($code);\n }\\
+nsub set_error_lock\n {\n my $name = shift\
+;\n my $pid=$$;\n\n\n &lock4tc ($$,\"LER\
+ROR\", \"LSET\", \"$$ -- ERROR: $name $PROGRAM\\n\\
+");\n return;\n }\nsub set_lock\n {\n \
+my $pid=shift;\n my $msg= shift;\n my $p=get\
+ppid();\n &lock4tc ($pid,\"LLOCK\",\"LRESET\",\\
+"$p$msg\\n\");\n }\nsub unset_lock\n {\n\n m\
+y $pid=shift;\n &lock4tc ($pid,\"LLOCK\",\"LREL\
+EASE\",\"\");\n }\nsub shift_lock\n {\n my $f\
+rom=shift;\n my $to=shift;\n my $from_type=s\
+hift;\n my $to_type=shift;\n my $action=shif\
+t;\n my $msg;\n\n if (!&lock4tc($from, $from\
+_type, \"LCHECK\", \"\")){return 0;}\n $msg=&lo\
+ck4tc ($from, $from_type, \"LREAD\", \"\");\n &\
+lock4tc ($from, $from_type,\"LRELEASE\", $msg);\n \
+ &lock4tc ($to, $to_type, $action, $msg);\n r\
+eturn;\n }\nsub isshellpid\n {\n my $p=shift;\
+\n if (!lock4tc ($p, \"LLOCK\", \"LCHECK\")){re\
+turn 0;}\n else\n {\n my $c=lock4tc($p, \"\
+LLOCK\", \"LREAD\");\n if ( $c=~/-SHELL-/){return \
+1;}\n }\n return 0;\n }\nsub isrootpid\n \
+ {\n if(lock4tc (getppid(), \"LLOCK\", \"LCHECK\
+\")){return 0;}\n else {return 1;}\n }\nsub lo\
+ck4tc\n {\n my ($pid,$type,$action,$value)=@_;\n\
+ my $fname;\n my $host=hostname;\n\n if ($ty\
+pe eq \"LLOCK\"){$fname=\"$LOCKDIR/.$pid.$host.loc\
+k4tcoffee\";}\n elsif ( $type eq \"LERROR\"){ $f\
+name=\"$LOCKDIR/.$pid.$host.error4tcoffee\";}\n \
+elsif ( $type eq \"LWARNING\"){ $fname=\"$LOCKDIR/\
+.$pid.$host.warning4tcoffee\";}\n\n if ($debug_l\
+ock)\n {\n print STDERR \"\\n\\t---lock4\
+tc(tcg): $action => $fname =>$value (RD: $LOCKDIR)\
+\\n\";\n }\n\n if ($action eq \"LCHECK\")\
+ {return -e $fname;}\n elsif ($action eq \"LREAD\
+\"){return file2string($fname);}\n elsif ($actio\
+n eq \"LSET\") {return string2file ($value, $fname\
+, \">>\");}\n elsif ($action eq \"LRESET\") {ret\
+urn string2file ($value, $fname, \">\");}\n elsi\
+f ($action eq \"LRELEASE\")\n {\n if ( $\
+debug_lock)\n {\n my $g=new FileHandle;\n o\
+pen ($g, \">>$fname\");\n print $g \"\\nDestroy\
+ed by $$\\n\";\n close ($g);\n safe_system (\
+\"mv $fname $fname.old\");\n }\n else\n {\\
+n unlink ($fname);\n }\n }\n return \"\"\
+;\n }\n\nsub file2string\n {\n my $file=@_[0];\n\
+ my $f=new FileHandle;\n my $r;\n open ($f, \
+\"$file\");\n while (<$f>){$r.=$_;}\n close ($\
+f);\n return $r;\n }\nsub file2array\n {\n my \
+$file=@_[0];\n my $f=new FileHandle;\n my @r;\\
+n open ($f, \"$file\");\n while (<$f>){@r=(@r,\
+$_);}\n close ($f);\n return @r;\n }\nsub stri\
+ng2file\n {\n my ($s,$file,$mode)=@_;\n m\
+y $f=new FileHandle;\n\n open ($f, \"$mode$file\
+\");\n print $f \"$s\";\n close ($f);\n }\\
+n\nBEGIN\n {\n srand;\n\n $SIG{'SIGUP\
+'}='signal_cleanup';\n $SIG{'SIGINT'}='signal\
+_cleanup';\n $SIG{'SIGQUIT'}='signal_cleanup'\
+;\n $SIG{'SIGILL'}='signal_cleanup';\n $\
+SIG{'SIGTRAP'}='signal_cleanup';\n $SIG{'SIGA\
+BRT'}='signal_cleanup';\n $SIG{'SIGEMT'}='sig\
+nal_cleanup';\n $SIG{'SIGFPE'}='signal_cleanu\
+p';\n\n $SIG{'SIGKILL'}='signal_cleanup';\n \
+ $SIG{'SIGPIPE'}='signal_cleanup';\n $SIG{\
+'SIGSTOP'}='signal_cleanup';\n $SIG{'SIGTTIN'\
+}='signal_cleanup';\n $SIG{'SIGXFSZ'}='signal\
+_cleanup';\n $SIG{'SIGINFO'}='signal_cleanup'\
+;\n\n $SIG{'SIGBUS'}='signal_cleanup';\n \
+ $SIG{'SIGALRM'}='signal_cleanup';\n $SIG{'SI\
+GTSTP'}='signal_cleanup';\n $SIG{'SIGTTOU'}='\
+signal_cleanup';\n $SIG{'SIGVTALRM'}='signal_\
+cleanup';\n $SIG{'SIGUSR1'}='signal_cleanup';\
+\n\n\n $SIG{'SIGSEGV'}='signal_cleanup';\n \
+ $SIG{'SIGTERM'}='signal_cleanup';\n $SIG{'\
+SIGCONT'}='signal_cleanup';\n $SIG{'SIGIO'}='\
+signal_cleanup';\n $SIG{'SIGPROF'}='signal_cl\
+eanup';\n $SIG{'SIGUSR2'}='signal_cleanup';\n\
+\n $SIG{'SIGSYS'}='signal_cleanup';\n $S\
+IG{'SIGURG'}='signal_cleanup';\n $SIG{'SIGCHL\
+D'}='signal_cleanup';\n $SIG{'SIGXCPU'}='sign\
+al_cleanup';\n $SIG{'SIGWINCH'}='signal_clean\
+up';\n\n $SIG{'INT'}='signal_cleanup';\n \
+ $SIG{'TERM'}='signal_cleanup';\n $SIG{'KILL'\
+}='signal_cleanup';\n $SIG{'QUIT'}='signal_cl\
+eanup';\n\n our $debug_lock=$ENV{\"DEBUG_LOCK\
+\"};\n\n\n\n\n foreach my $a (@ARGV){$CL.=\" \
+$a\";}\n if ( $debug_lock ){print STDERR \"\\\
+n\\n\\n********** START PG: $PROGRAM *************\
+\\n\";}\n if ( $debug_lock ){print STDERR \"\\
+\n\\n\\n**********(tcg) LOCKDIR: $LOCKDIR $$ *****\
+********\\n\";}\n if ( $debug_lock ){print ST\
+DERR \"\\n --- $$ -- $CL\\n\";}\n\n\n\n\n }\nsu\
+b flush_error\n {\n my $msg=shift;\n return\
+ add_error ($EXIT_FAILURE,$$, $$,getppid(), $msg, \
+$CL);\n }\nsub add_error\n {\n my $code=shift\
+;\n my $rpid=shift;\n my $pid=shift;\n my\
+ $ppid=shift;\n my $type=shift;\n my $com=sh\
+ift;\n\n $ERROR_DONE=1;\n lock4tc ($rpid, \"\
+LERROR\",\"LSET\",\"$pid -- ERROR: $type\\n\");\n \
+ lock4tc ($$, \"LERROR\",\"LSET\", \"$pid -- COM\
+: $com\\n\");\n lock4tc ($$, \"LERROR\",\"LSET\\
+", \"$pid -- STACK: $ppid -> $pid\\n\");\n\n re\
+turn $code;\n }\nsub add_warning\n {\n my $rp\
+id=shift;\n my $pid =shift;\n my $command=sh\
+ift;\n my $msg=\"$$ -- WARNING: $command\\n\";\\
+n print STDERR \"$msg\";\n lock4tc ($$, \"LW\
+ARNING\", \"LSET\", $msg);\n }\n\nsub signal_clea\
+nup\n {\n print dtderr \"\\n**** $$ (tcg) was \
+killed\\n\";\n &cleanup;\n exit ($EXIT_FAILU\
+RE);\n }\nsub clean_dir\n {\n my $dir=@_[0];\\
+n if ( !-d $dir){return ;}\n elsif (!($dir=~\
+/tmp/)){return ;}#safety check 1\n elsif (($dir\
+=~/\\*/)){return ;}#safety check 2\n else\n \
+ {\n `rm -rf $dir`;\n }\n return;\n }\ns\
+ub cleanup\n {\n #print stderr \"\\n----tc: $$\
+ Kills $PIDCHILD\\n\";\n #kill (SIGTERM,$PIDCHI\
+LD);\n my $p=getppid();\n $CLEAN_EXIT_STARTE\
+D=1;\n\n\n\n if (&lock4tc($$,\"LERROR\", \"LCHE\
+CK\", \"\"))\n {\n my $ppid=getppid();\n if (\
+!$ERROR_DONE)\n {\n &lock4tc($$,\"LERROR\", \
+\"LSET\", \"$$ -- STACK: $p -> $$\\n\");\n &lo\
+ck4tc($$,\"LERROR\", \"LSET\", \"$$ -- COM: $CL\\n\
+\");\n }\n }\n my $warning=&lock4tc($$, \
+\"LWARNING\", \"LREAD\", \"\");\n my $error=&lo\
+ck4tc($$, \"LERROR\", \"LREAD\", \"\");\n #rel\
+ease error and warning lock if root\n\n if (isr\
+ootpid() && ($warning || $error) )\n {\n\n pr\
+int STDERR \"**************** Summary ************\
+*\\n$error\\n$warning\\n\";\n\n &lock4tc($$,\"LERR\
+OR\",\"RELEASE\",\"\");\n &lock4tc($$,\"LWARNING\"\
+,\"RELEASE\",\"\");\n }\n\n\n foreach my $\
+f (@TMPFILE_LIST)\n {\n if (-e $f){unlink ($f\
+);}\n }\n foreach my $d (@TMPDIR_LIST)\n \
+ {\n clean_dir ($d);\n }\n #No More Loc\
+k Release\n #&lock4tc($$,\"LLOCK\",\"LRELEASE\"\
+,\"\"); #release lock\n\n if ( $debug_lock ){pr\
+int STDERR \"\\n\\n\\n********** END PG: $PROGRAM \
+($$) *************\\n\";}\n if ( $debug_lock ){\
+print STDERR \"\\n\\n\\n**********(tcg) LOCKDIR: $\
+LOCKDIR $$ *************\\n\";}\n }\nEND\n {\n\n\
+ &cleanup();\n }\n\nsub blast_com2new_blast_co\
+m\n {\n my $com=shift;\n if ($com=~/form\
+atdb/)\n {\n $com=~s/formatdb/makeblastd\
+b/;\n $com=~s/\\-i/\\-in/;\n if ($com \
+=~/pF/){$com=~s/\\-pF/\\-dbtype nucl/;}\n if\
+ ($com =~/p F/){$com=~s/\\-p F/\\-dbtype nucl/;}\n\
+ $com=\"$com -logfile /dev/null\";\n r\
+eturn $com;\n }\n else {return $com;}\n\n \
+ }\nsub safe_system\n{\n my $com=shift;\n my $nt\
+ry=shift;\n my $ctry=shift;\n my $pid;\n my $st\
+atus;\n my $ppid=getppid();\n if ($com eq \"\"){\
+return 1;}\n\n if ( ($com=~/^blast/) ||($com=~/^f\
+ormatdb/)){$com=&blast_com2new_blast_com($com);}\n\
+\n if (($pid = fork ()) < 0){return (-1);}\n if \
+($pid == 0)\n {\n set_lock($$, \" -SHELL- \
+$com (tcg)\");\n if( $debug_generic_method ) \
+{ printf \"~ exec: %s\\n\", $com; }\n exec ($\
+com);\n if( $debug_generic_method ) { printf \
+\"~ exitcode: %s\\n\", $?; }\n }\n else\n {\
+\n lock4tc ($$, \"LLOCK\", \"LSET\", \"$pid\\\
+n\");#update parent\n $PIDCHILD=$pid;\n }\\
+n if ($debug_lock){printf STDERR \"\\n\\t .... sa\
+fe_system (fasta_seq2hmm) p: $$ c: $pid COM: $com\
+\\n\";}\n\n waitpid ($pid,WTERMSIG);\n\n shift_l\
+ock ($pid,$$, \"LWARNING\",\"LWARNING\", \"LSET\")\
+;\n\n if ($? == $EXIT_FAILURE || lock4tc($pid, \"\
+LERROR\", \"LCHECK\", \"\"))\n {\n if ($nt\
+ry && $ctry <$ntry)\n {\n\n add_warning ($$,$$,\\
+"$com failed [retry: $ctry out of $ntry]\");\n l\
+ock4tc ($pid, \"LRELEASE\", \"LERROR\", \"\");\n \
+ #if ($com=~/EBI/){$com=~s/EBI/NCBI/;}\n #elsif \
+($com=~/NCBI/){$com=~s/NCBI/EBI/;}\n\n return sa\
+fe_system ($com, $ntry, ++$ctry);\n }\n elsif\
+ ($ntry == -1)\n {\n if (!shift_lock ($pid, $$, \
+\"LERROR\", \"LWARNING\", \"LSET\"))\n {\n \
+ add_warning ($$,$$,\"$com failed\");\n }\n \
+ else\n {\n lock4tc ($pid, \"LRELEASE\"\
+, \"LERROR\", \"\");\n }\n return $?;}\n \
+ else\n {\n if (!shift_lock ($pid,$$, \"LERROR\\
+",\"LERROR\", \"LSET\"))\n {\n myexit(ad\
+d_error ($EXIT_FAILURE,$$,$pid,getppid(), \"UNSPEC\
+IFIED system\", $com));\n }\n }\n }\n retu\
+rn $?;\n}\n\nsub check_configuration\n {\n \
+ my @l=@_;\n my $v;\n foreach my $p (@l)\
+\n {\n\n if ( $p eq \"EMAIL\")\n {\n \
+ if ( !($EMAIL=~/@/))\n {\n add_warning($$,$$,\"\
+Could Not Use EMAIL\");\n myexit(add_error ($EXIT\
+_FAILURE,$$,$$,getppid(),\"EMAIL\",\"$CL\"));\n \
+ }\n }\n elsif( $p eq \"INTERNET\")\n \
+ {\n if ( !&check_internet_connection())\n \
+{\n myexit(add_error ($EXIT_FAILURE,$$,$$,getpp\
+id(),\"INTERNET\",\"$CL\"));\n }\n }\n elsi\
+f( $p eq \"wget\")\n {\n if (!&pg_is_ins\
+talled (\"wget\") && !&pg_is_installed (\"curl\"))\
+\n {\n myexit(add_error ($EXIT_FAILURE,$$,$$,g\
+etppid(),\"PG_NOT_INSTALLED:wget\",\"$CL\"));\n }\
+\n }\n elsif( !(&pg_is_installed ($p)))\n \
+ {\n myexit(add_error ($EXIT_FAILURE,$$,$$,\
+getppid(),\"PG_NOT_INSTALLED:$p\",\"$CL\"));\n \
+ }\n }\n return 1;\n }\nsub nw\n {\n \
+my($A,$B)=@_;\n my ($i,$j, $s);\n my $gep=-2;\n my\
+ $match=+2;\n my $mismatch=0;\n my ($sub, $ins, $d\
+el);\n\n\n if ($A eq $B){return ($A,$B);}\n \n $A=\
+~s/[\\s\\d]//g; \n $B=~s/[\\s\\d]//g; \n\n\n my @r\
+A=split ('',$A);\n my @rB=split ('',$B);\n \n #eva\
+luate substitutions\n my $lenA=@rA;\n my $lenB=@rB\
+;\n \n for ($i=0; $i<=$lenA; $i++){$smat[$i][0]=$i\
+*$gep;$tb[$i][0 ]= 1;}\n for ($j=0; $j<=$lenB; $j+\
++){$smat[0][$j]=$j*$gep;$tb[0 ][$j]=-1;}\n \n for \
+($i=1; $i<=$lenA; $i++)\n {\n for ($j=1; $j<\
+=$lenB; $j++)\n {\n if ($rA[$i-1] eq $rB[$j\
+-1]){$s=$match;}\n else {$s=$mismatch;}\n \n $s\
+ub=$smat[$i-1][$j-1]+$s;\n $del=$smat[$i ][$j-1]\
++$gep;\n $ins=$smat[$i-1][$j ]+$gep;\n \n if \
+ ($sub>=$del && $sub>=$ins){$smat[$i][$j]=$sub;$tb\
+[$i][$j]=0;}\n elsif($del>$ins){$smat[$i][$j]=$de\
+l;$tb[$i][$j]=-1;}\n else {$smat[$i][$j]=$ins;$tb\
+[$i][$j]=1;}\n }\n }\n #print \"\\n---- SCORE=$\
+smat[$lenA][$lenB]\\n\";\n \n $i=$lenA;\n $j=$lenB\
+;\n my $aln_len=0;\n\n while (!($i==0 && $j==0))\n\
+ {\n if ($tb[$i][$j]==0)\n {\n $aA\
+[$aln_len]=$rA[--$i];\n $aB[$aln_len]=$rB[--\
+$j];\n }\n elsif ($tb[$i][$j]==-1)\n {\n\
+ $aA[$aln_len]='-';\n $aB[$aln_len]=$r\
+B[--$j];\n }\n elsif ($tb[$i][$j]==1)\n \
+{\n $aA[$aln_len]=$rA[--$i];\n $aB[$al\
+n_len]='-';\n }\n $aln_len++;\n }\n \n \n \
+@aA=reverse (@aA);\n @aB=reverse (@aB);\n my $sA=j\
+oin('',@aA);\n my $sB=join('',@aB);\n return ($sA,\
+$sB);\n }\n \n$program=\"T-COFFEE (Versi\
+on_11.00.8cbe486)\";\\n\n","use Env;\nuse FileHand\
+le;\nuse Cwd;\nuse File::Path;\nuse Sys::Hostname;\
+\nmy $f = new FileHandle;\n\nopen ($f, $ARGV[1]);\\
+n$atom=$ARGV[0];\n\n$atom=~s/PRIME/\\'/;\nwhile (<\
+$f>)\n {\n my $l=$_;\n\n $l=~s/$atom/CA /;\\
+n \n \n $l=~s/ G /GLY /g;\n $l=~s/ C\
+ /CYS /g;\n $l=~s/ T /THR /g;\n $l=~s/ A /\
+ALA /g;\n $l=~s/ U /THR /g;\n \n $l=~s/ \
+DG /GLY /g;\n $l=~s/ DC /CYS /g;\n $l=~s/ DT\
+ /THR /g;\n $l=~s/ DA /ALA /g;\n $l=~s/ DU /\
+THR /g;\n \n print $l;\n }\n\n\n\n","*TC_ME\
+THOD_FORMAT_01\n******************generic_method.t\
+c_method*************\n*\n* Incorporating ne\
+w methods in T-Coffee\n* Cedric Notredame 26\
+/08/08\n*\n***************************************\
+****************\n*This file is a method file\n*Co\
+py it and adapt it to your need so that the method\
+ \n*you want to use can be incorporated within T-C\
+offee\n*******************************************\
+************\n* USAGE \
+ *\n*****************************\
+**************************\n*This file is passed t\
+o t_coffee via -in:\n*\n* t_coffee -in Mgeneric_me\
+thod.method\n*\n* The method is passed to the shel\
+l using the following\n*call:\n*<EXECUTABLE><PARAM\
+1><IN_FLAG><seq_file><PARAM2><OUT_FLAG><outname><P\
+ARAM>\n*\n*Conventions:\n*<FLAG_NAME> <TYPE> <VA\
+LUE>\n*<VALUE>: no_name <=> Replaced with a space\
+\n*<VALUE>:   <=> Replaced with a space\n*\n**\
**************************************************\
-**\n*OUT_FLAG\n*flag indicating the name of the ou\
-t-coming data\n*same conventions as IN_FLAG\n*OUT_\
-FLAG S no_name ->no flag\n*if you want to redirect\
-, pass the parameters via PARAM1\n*set OUT_FLAG to\
- >\n*\nOUT_FLAG -outfile=\n*\n*******************\
+***\n* ALN_MODE \
+ *\n**************************************\
+*****************\n*pairwise ->all Vs all (no se\
+lf )[(n2-n)/2aln]\n*m_pairwise ->all Vs all (no se\
+lf)[n^2-n]^2\n*s_pairwise ->all Vs all (self): [n^\
+2-n]/2 + n\n*multiple ->All the sequences in one\
+ go\n*\nALN_MODE pairwise\n*\n*******************\
************************************\n* \
- PARAM_1 *\n***\
-**************************************************\
-**\n*<EXECUTABLE><PARAM1><IN_FLAG><seq_file><PARAM\
-2><OUT_FLAG><outname><PARAM>\n*Parameters sent to \
-the EXECUTABLE and specified *before* IN_FLAG \n*I\
-f there is more than 1 PARAM line, the lines are\n\
-*concatenated\n*Command_line: @EP@PARAM@-gapopen%e\
-10%s-gapext%e20\n* %s white space\n* %e equal sign\
-\n*\n*PARAM1 \n*\n*\n*\n**************************\
-*****************************\n* \
-PARAM_2 *\n**********\
-*********************************************\n*<E\
-XECUTABLE><PARAM1><IN_FLAG><seq_file><PARAM2><OUT_\
-FLAG><outname><PARAM>\n*Parameters sent to the EXE\
-CUTABLE and specified \n*after* IN_FLAG and *befor\
-e* OUT_FLAG\n*If there is more than 1 PARAM line, \
-the lines are\n*concatenated\n*\n*PARAM1 \n*\n*\n*\
+ OUT_MODE *\n*****\
**************************************************\
-****\n* PARAM \
- *\n*************************************\
-******************\n*<EXECUTABLE><PARAM1><IN_FLAG>\
-<seq_file><PARAM2><OUT_FLAG><outname><PARAM>\n*Par\
-ameters sent to the EXECUTABLE and specified *afte\
-r* OUT_FLAG\n*If there is more than 1 PARAM line, \
-the lines are\n*concatenated\n*\nPARAM -mode=seq_m\
-sa -method=clustalw\nPARAM -OUTORDER=INPUT -NEWT\
-REE=core -align -gapopen=-15\n*\n*****************\
-**************************************\n* \
- END *\n***\
+\n* mode for the output:\n*External methods: \n* a\
+ln -> alignmnent File (Fasta or ClustalW Format)\n\
+* lib-> Lib file (TC_LIB_FORMAT_01)\n*Internal Met\
+hods:\n* fL -> Internal Function returning a List \
+(Librairie)\n* fA -> Internal Function returning a\
+n Alignmnent\n*\nOUT_MODE aln\n******************\
+*************************************\n* \
+ SEQ_TYPE *\n****\
**************************************************\
-**\n","*TC_METHOD_FORMAT_01\n***************clusta\
-lw_method.tc_method*********\nEXECUTABLE clustalw\\
-nALN_MODE pairwise\nIN_FLAG -INFILE=\nOUT_FLAG \
--OUTFILE=\nOUT_MODE aln\nPARAM -gapopen=-10\nSEQ\
-_TYPE S\n****************************************\
-*********\n","$VersionTag = \
+*\n*G: Genomic, S: Sequence, P: PDB, R: Profile\n*\
+Examples:\n*SEQTYPE S sequences against sequences \
+(default)\n*SEQTYPE S_P sequence against structure\
+\n*SEQTYPE P_P structure against structure\n*SEQTY\
+PE PS mix of sequences and structure \n*\nSEQ_TYPE\
+ S\n*\n\n*****************************************\
+**************\n* COMMAND LINE \
+ *\n*EXECUTABLE PARAM1 IN_FLAG \
+OUT_FLAG PARAM *\n********************\
+***********************************\n*************\
+******************************************\n* \
+ EXECUTABLE *\\
+n*************************************************\
+******\n*name of the executable\n*passed to the sh\
+ell: executable\n* \nEXECUTABLE tc_generic_method.\
+pl\n*\n*******************************************\
+************\n* IN_FLAG \
+ *\n****************************\
+***************************\n*IN_FLAG\n*flag indic\
+ating the name of the in coming sequences\n*IN_FLA\
+G S no_name ->no flag\n*IN_FLAG S &bnsp-in&bnsp ->\
+ \" -in \"\n*\nIN_FLAG -infile=\n*\n*************\
+******************************************\n* \
+ OUT_FLAG *\\
+n*************************************************\
+******\n*OUT_FLAG\n*flag indicating the name of th\
+e out-coming data\n*same conventions as IN_FLAG\n*\
+OUT_FLAG S no_name ->no flag\n*if you want to redi\
+rect, pass the parameters via PARAM1\n*set OUT_FLA\
+G to >\n*\nOUT_FLAG -outfile=\n*\n***************\
+****************************************\n* \
+ PARAM_1 *\\
+n*************************************************\
+******\n*<EXECUTABLE><PARAM1><IN_FLAG><seq_file><P\
+ARAM2><OUT_FLAG><outname><PARAM>\n*Parameters sent\
+ to the EXECUTABLE and specified *before* IN_FLAG \
+\n*If there is more than 1 PARAM line, the lines a\
+re\n*concatenated\n*Command_line: @EP@PARAM@-gapop\
+en%e10%s-gapext%e20\n* %s white space\n* %e equal \
+sign\n*\n*PARAM1 \n*\n*\n*\n**********************\
+*********************************\n* \
+ PARAM_2 *\n******\
+*************************************************\\
+n*<EXECUTABLE><PARAM1><IN_FLAG><seq_file><PARAM2><\
+OUT_FLAG><outname><PARAM>\n*Parameters sent to the\
+ EXECUTABLE and specified \n*after* IN_FLAG and *b\
+efore* OUT_FLAG\n*If there is more than 1 PARAM li\
+ne, the lines are\n*concatenated\n*\n*PARAM1 \n*\n\
+*\n***********************************************\
+********\n* PARAM \
+ *\n*********************************\
+**********************\n*<EXECUTABLE><PARAM1><IN_F\
+LAG><seq_file><PARAM2><OUT_FLAG><outname><PARAM>\n\
+*Parameters sent to the EXECUTABLE and specified *\
+after* OUT_FLAG\n*If there is more than 1 PARAM li\
+ne, the lines are\n*concatenated\n*\nPARAM -mode=s\
+eq_msa -method=clustalw\nPARAM -OUTORDER=INPUT -\
+NEWTREE=core -align -gapopen=-15\n*\n*************\
+******************************************\n* \
+ END *\\
+n*************************************************\
+******\n","*TC_METHOD_FORMAT_01\n***************cl\
+ustalw_method.tc_method*********\nEXECUTABLE clust\
+alw\nALN_MODE pairwise\nIN_FLAG -INFILE=\nOUT_FL\
+AG -OUTFILE=\nOUT_MODE aln\nPARAM -gapopen=-10\\
+nSEQ_TYPE S\n************************************\
+*************\n","$VersionTag = \
\
\
- 2.43;\nuse Env;\nuse FileHandle;\nuse Cwd;\
-\nuse File::Path;\nuse Sys::Hostname;\nour $PIDCHI\
-LD;\nour $ERROR_DONE;\nour @TMPFILE_LIST;\nour $EX\
-IT_FAILURE=1;\nour $EXIT_SUCCESS=0;\n\nour $REFDIR\
-=getcwd;\nour $EXIT_SUCCESS=0;\nour $EXIT_FAILURE=\
-1;\n\nour $PROGRAM=\"extract_from_pdb\";\nour $CL=\
-$PROGRAM;\n\nour $CLEAN_EXIT_STARTED;\nour $debug_\
-lock=$ENV{\"DEBUG_LOCK\"};\nour $LOCKDIR=$ENV{\"LO\
-CKDIR_4_TCOFFEE\"};\nif (!$LOCKDIR){$LOCKDIR=getcw\
-d();}\nour $ERRORDIR=$ENV{\"ERRORDIR_4_TCOFFEE\"};\
-\nour $ERRORFILE=$ENV{\"ERRORFILE_4_TCOFFEE\"};\n&\
-set_lock ($$);\nif (isshellpid(getppid())){lock4tc\
-(getppid(), \"LLOCK\", \"LSET\", \"$$\\n\");}\n \
- \nour $SILENT=\" >/dev/null 2>/dev/null\";\nour\
- $INTERNET=-1;\n\n\n\n\n\n\n\nour $BLAST_MAX_NRUNS\
-=2;\nour $EXIT_SUCCESS=0;\nour $EXIT_FAILURE=1;\no\
-ur $CONFIGURATION=-1;\nour $REF_EMAIL=\"\";\nour $\
-PROGRAM=\"extract_from_pdb\";\n\n\nmy %onelett_pro\
-t=&fill_onelett_prot();\nmy %threelett_prot=&fill_\
-threelett_prot();\nmy %onelett_RNA=&fill_onelett_R\
-NA();\nmy %threelett_RNA=&fill_threelett_RNA();\nm\
-y %onelett_DNA=&fill_onelett_DNA();\nmy %threelett\
-_DNA=&fill_threelett_DNA();\n\n\n\n\n\nmy %onelett\
- = (\n'P' => \\%onelett_prot,\n'D' => \\%onelett_D\
-NA,\n'R' => \\%onelett_RNA\n);\n\n\nmy %threelett \
-= (\n'P' => \\%threelett_prot,\n'D' => \\%threelet\
-t_DNA,\n'R' => \\%threelett_RNA\n);\n\n\n\n\n\n\n\\
-nif($ARGV[0]=~/help/ ||$ARGV[0]=~/man/ || $ARGV[0]\
-=~/HELP/ || $ARGV[0]=~/Man/ || $ARGV[0] eq \"-h\" \
- || $ARGV[0] eq \"-H\" )\n{die \"SYNTAX: extract_\
-from_pdb Version $VersionTag \n Minimum: \
- [extract_from_pdb file] \n OR \n [.\
-.. | extract_from_pdb]\n Flags (Default setting o\
-n the first line)\n -version...................\
-[Returns the Version Number]\n -force...\
-..................[Forces the file to be treated l\
-ike a PDB file]\n \
- [Regenerates the header and SEQRES fields]\n \
- -force_name................[Forces the f\
-ile to be named after name]]\n -infile..\
-...file...........[Flag can be omited]\n \
- [File must be pdb or fro pgm]\n \
- [File can also be compre\
-ssed Z or gz]\n \
- [In the case of a compressed file, you can omit\
- the gz|Z extension]\n -netfile.........\
-..........[File will be fetch from the net using w\
-get]\n [wget \
-or curl must be installed]\n \
- [ftp://ftp.gnu.org/pub/gnu/wget/]\\
-n [http://cur\
-l.haxx.se/]\n \
- [Must also be used to retrieve the file from a lo\
-cal pdb copy (cf netaddress)]\n -netaddr\
-ess................[Address used for the retrievin\
-g the netfile]\n \
- [http://www.rcsb.org/pdb/cgi/export.cgi/%%.pdb\
-.gz?format=PDB&pdbId=%%&compression=gz]\n \
- [http://www.expasy.ch\
-/cgi-bin/get-pdb-entry.pl?%%]\n \
- [local -> will get the file fro\
-m pdb_dir (see pdb_dir)]\n -netcompressi\
-on............[Extension if the netfile comes comp\
-ressed]\n [gz\
-]\n -pdb_dir...................[address \
-of the repertory where the pdb is installed]\n \
- [Supports standa\
-rd ftp style installation OR every stru in DIR]\n \
- [Give the ...\
-./pdb/structure/ dir]\n \
- [If value omitted, the pg gets it from \
-the env variable PDB_DIR]\n -netcompress\
-ion_pg.........[gunzip]\n -is_pdb_name..\
-........name.[Returns 1 if the name is a PDB ID, 0\
- otherwise]\n -model_type...........name\
-.[Returns the model type if valid PDB name]\n \
- -is_released_pdb_name name.[Returns 1 if the\
- name corresponds to a released PDB file]\n \
- -get_pdb_chains.....name...[Returns the list o\
-f chains corresponding to the entry]\n -\
-get_pdb_id.........name...[Returns the PDB id with\
-in the provided pdb file]\n -get_fugue_n\
-ame.....name...[Turns a name into a name valid for\
- fugue]\n [Us\
-es the netaddress to do so]\n -chain......FIRST\
-..........[Extract the first chain only]\n \
- A B C..........[Extract Several chains if needed]\
-\n ALL............[Extract all the chains]\
- \n -ligand.....ALL............[Extract \
-the ligands in the chain (HETATM)]\n \
- <name1>,<name2>[Extract All the named lig\
-nds]\n -ligand_only...............[Extract only\
- the ligands]\n -ligand_list............\
-...[Extract the list of ligands]\n -coor.......\
-<start>..<end>.[Coordinates of the fragment to ext\
-ract]\n [Omit end to include the C\
-ter]\n -num........absolute.......[absol\
-ute: relative to the seq] \n \
- file...........[file: relative to file]\n \
- -num_out....new............[new: start 1->L]\n \
- old............[old: keep th\
-e file coordinates]\n -delete.....<start\
->..<end>.[Delete from residue start to residue end\
-]\n -atom.......CA.............[Atoms to includ\
-e, ALL for all of them]\n CA O N.........[\
-Indicate several atoms if needed]\n -code......\
-.3..............[Use the 1 letter code or the 3 le\
-tters code]\n -mode.......raw............[Outpu\
-t original pdb file]\n pdb..\
-..........[Output something that looks like pdb]\n\
- fasta..........[Output the sequences in f\
-asta format]\n simple.........[Output a fo\
-rmat easy to parse in C ]\n -seq_field.\
-.ATOM...........[Field used to extract the sequenc\
-e]\n SEQRES.........[Use the complete sequ\
-ence]\n -seq.......................[Equivalent \
-to -mode fasta]\n -model......1..............[\
-Chosen Model in an NMR file]\n -nodiagno\
-stic..............[Switches Error Messages off]\n \
- -debug.....................[Sets the DEB\
-UG ON]\n -no_remote_pdb_dir.........[Do \
-not look for a remote file]\n -cache_pdb\
-.................[Cache Value, default is $HOME/.t\
-_coffee/cache, other values: NO<=> No cache]\n\n \
- Environement Variables\n These varia\
-bles can be set from the environement\n \
-Command line values with the corresponding flag su\
-perseed evironement value\n NO_REMOTE_PD\
-B_DIR..........[Prevents the program from searchin\
-g remote file: faster]\n PDB_DIR........\
-............[Indicates where PDB file must be fetc\
-hed (localy)]\n\n PROBLEMS: please contact cedric\
-.notredame\\@europe.com\\n\";\n exit ($EXIT_SUCCE\
-SS);\n}\n\n$np=0;\n$n_para=$#ARGV;\n$model=1;\n$pd\
-b_dir=$ENV{'PDB_DIR'};if ($pdb_dir){$pdb_dir.=\"/\\
-";}\n$debug=$ENV{'DEBUG_EXTRACT_FROM_PDB'};\n\n$no\
-_remote_pdb_dir=$ENV{NO_REMOTE_PDB_DIR};\n$HOME=$E\
-NV{'HOME'};\nif ( $ENV{CACHE_4_TCOFFEE})\n{$cache=\
-$ENV{CACHE_4_TCOFFEE};}\nelse\n{\n $cache=\"$HO\
-ME/.t_coffee/cache/\";\n}\n\n \n$netaddress=\"ht\
-tp://www.rcsb.org/pdb/files/%%.pdb.gz\";\n$netcomp\
-ression_pg=\"gunzip\";\n$netcompression=\"gz\";\n\\
-nforeach ($np=0; $np<=$n_para; $np++)\n { \
-\n $value=$ARGV[$np];\n \n if ($np==0 && \
-!($value=~/^-.*/))\n { \n $pdb_file= $ARGV[$n\
-p];\n }\n elsif ( !($value=~/^-.*/))\n \
- {\n print \"@ARGV\";\n die;\n } \n \n \
- elsif ($value eq \"-nodiagnostic\"){$nodiagnostic\
-=1;}\n elsif ($value eq \"-force\")\n {\n \
-$force_pdb=1;\n }\n elsif ($value eq \"-fo\
-rce_name\")\n {\n $force_name=$ARGV[++$np];\n\
- $force_pdb=1;\n }\n \n elsif ($value e\
-q \"-is_pdb_name\")\n {\n $pdb_file= $ARGV[++\
-$np]; \n $is_pdb_name=1; \n } \n elsif ($v\
-alue eq \"-is_released_pdb_name\")\n {\n $pdb\
-_file= $ARGV[++$np]; \n $is_released_pdb_name=1;\n\
- }\n elsif ($value eq \"-model_type\")\n \
- {\n $pdb_file= $ARGV[++$np]; \n $model_type=1;\
-\n }\n elsif ($value eq \"-debug\")\n{\n $\
-debug=1;\n}\n elsif ($value eq \"-get_pdb_chain\
-s\")\n{\n $pdb_file= $ARGV[++$np];\n $get_pdb_chai\
-ns=1;\n}\n elsif ($value eq \"-get_pdb_ligands\\
-")\n{\n $get_pdb_ligands=1;\n}\n \n elsif ($\
-value eq \"-get_pdb_id\")\n{\n $pdb_file= $ARGV[++\
-$np];\n $get_pdb_id=1;\n \n}\n \n elsif ( $v\
-alue eq \"-get_fugue_name\")\n{\n $pdb_file= $ARGV\
-[++$np];\n $get_fugue_name=1;\n}\n elsif ( $val\
-ue eq \"-infile\")\n{\n $pdb_file= $ARGV[++$\
-np];\n} \n elsif ($value eq \"-netfile\")\n{\n \
-$netfile=1;\n if ( !($ARGV[$np+1]=~/^-.*/)){$pdb_f\
-ile= $ARGV[++$np];}\n}\n elsif ( $value eq \"-\
-num\")\n{\n $numbering= $ARGV[++$np];\n}\n \
- elsif ( $value eq \"-num_out\")\n{\n $num\
-bering_out= $ARGV[++$np];\n}\n elsif ( $value e\
-q \"-netaddress\")\n{\n $netadress=$ARGV[++$np];\n\
-}\n \n elsif ( $value eq \"-netcompression\\
-")\n{\n $netcompression=$ARGV[++$np];\n}\n els\
-if ( $value eq \"-pdb_dir\")\n{\n if ( !($ARGV[$n\
-p+1]=~/^-.*/)){$pdb_dir= \"$ARGV[++$np]/\";}\n}\n \
- elsif ( $value eq \"-no_remote_pdb_dir\")\n{\n\
- $no_remote_pdb_dir=1;\n if ( !($ARGV[$np+1]=~/^-.\
-*/)){$pdb_dir= \"$ARGV[++$np]/\";}\n}\n elsif (\
- $value eq \"-cache\")\n{\n $cache=$ARGV[++$np];\n\
-}\n \n elsif ($value eq \"-netcompression_pg\
-\")\n{\n $netcompression_pg=$ARGV[++$np];\n}\n \
- elsif ($value eq \"-mode\")\n{\n $MODE=$A\
-RGV[++$np];\n}\n\n elsif ( $value eq \"-model\"\
-)\n{\n $model= $ARGV[++$np];\n}\n elsif (\
-$value eq \"-seq_field\" )\n{\n $seq_field= \
-$ARGV[++$np];\n} \n elsif ($value eq \"-coor\\
-" )\n{\n $start= $ARGV[++$np];\n \n i\
-f (($ARGV[$np+1] eq \"\") ||($ARGV[$np+1]=~/^-.*/)\
-){$end=\"*\";} \n else {$end= $ARGV[++$np]\
-;} \n $coor_set=1;\n}\n elsif ($value\
- eq \"-delete\" )\n{\n $delete_start= $ARGV[\
-++$np];\n $delete_end= $ARGV[++$np];\n \
- $delete_set=1;\n}\n elsif ($value eq \"-code\\
-")\n{\n $code= $ARGV[++$np];\n}\n elsif \
-($value eq \"-no_hetatm\")\n{\n $no_hetatm=1\
-;\n}\n elsif ($value eq \"-chain\")\n{\n \
-while (!($ARGV[$np+1] eq \"\") &&!($ARGV[$np+1]=~/\
-^-.*/))\n{\n ++$np;\n @c_chain=(@chain\
-, $ARGV[$np]);\n $hc_chain{$ARGV[$np]}=$#c_\
-chain+1;\n} \n}\n elsif ($value eq \"\
--atom\")\n{\n\n while (!($ARGV[$np+1] eq \"\\
-") && !($ARGV[$np+1]=~/^-.*/))\n{\n ++$np;\n\
- $atom[$n_atom++]= $ARGV[$np];\n $ato\
-m_list{$ARGV[$np]}=1; \n} \n \n}\n \
-elsif ( $value eq \"-unfold\")\n{\n $unfold=1;\n}\\
-n elsif ($value eq \"-seq\" ||$value eq \"-fast\
-a\" )\n{\n $MODE=\"fasta\";\n}\n elsif ( \
-$value eq \"-version\")\n{\n print STDERR \"\\nex\
-tract_from_pdb: Version $VersionTag\\n\";\n &myexi\
-t ($EXIT_SUCCESS);\n}\n elsif ( $value eq \"-li\
-gand\")\n{\n while (!($ARGV[$np+1] eq \"\") && !($\
-ARGV[$np+1]=~/^-.*/))\n{\n ++$np;\n $ligan\
-d=1;\n $ligand_list{$ARGV[$np]}=1; \n} \\
-n $hc_chain{'LIGAND'}=1;\n}\n elsif ( $value eq\
- \"-ligand_only\")\n{\n $ligand_only=1;\n}\n}\nif \
-( $debug)\n{\n print STDERR \"\\n[DEBUG:extract\
-_from_pdb] NO_REMOTE_PDB_DIR: $no_remote_pdb_dir\\\
-n\";\n print STDERR \"\\n[DEBUG:extract_from_pd\
-b] PDB_DIR: $pdb_dir\\n\";\n}\n\n\nif ( $is_pdb_na\
-me)\n {\n if (&remote_is_pdb_name($pdb_file))\\
-n {\n print \"1\";\n }\n else\n \
-{\n print \"0\";\n }\n exit ($EXIT_SUCCESS\
-);\n }\n\nif ( $is_released_pdb_name)\n {\n \\
-n if (&is_released($pdb_file))\n {\n print\
- \"1\";\n }\n else\n {\n print \"0\";\
-\n }\n exit ($EXIT_SUCCESS);\n }\nif ($mo\
-del_type)\n {\n \n printf \"%s\", &pdb2model\
-_type($pdb_file);\n exit ($EXIT_SUCCESS);\n \
-\n }\n \n\nif (!$force_name)\n{\n $pdb_file\
-=~/([^\\/]*)$/;\n $force_name=$1;\n}\n\n$local_\
-pdb_file=$pdb_file;\n\nif ( $debug){print STDERR \\
-"\\n[DEBUG: extract_from_pdb] Scan For $local_pdb_\
-file\\n\";}\n\n$mem=$no_remote_pdb_dir;\n$no_remot\
-e_pdb_dir=1;\n$tmp_pdb_file=get_pdb_file ($local_p\
-db_file);\n\nif ( !-e $tmp_pdb_file || $tmp_pdb_fi\
-le eq \"\")\n {\n $local_pdb_file=$pdb_file;\n\
- ($local_pdb_file, $suffix_chain)=&pdb_name2nam\
-e_and_chain($local_pdb_file);\n\n if ($local_pd\
-b_file)\n {\n if ( $debug){print STDERR \"\\n\
-Split $pdb_file into $local_pdb_file and $suffix_c\
-hain \\n\";}\n $tmp_pdb_file=get_pdb_file ($local_\
-pdb_file);\n if ( $tmp_pdb_file ne \"\")\n {\n \
- @c_chain=();\n @c_chain=($suffix_chain);\n \
- %hc_chain=();\n $hc_chain{$suffix_chain}=1\
-;\n }\n }\n }\n\n$no_remote_pdb_dir=$mem;\\
-nif ($no_remote_pdb_dir==0)\n {\n \n if ( !\
--e $tmp_pdb_file || $tmp_pdb_file eq \"\")\n \
-{\n \n $local_pdb_file=$pdb_file;\n ($local_pdb_fi\
-le, $suffix_chain)=&pdb_name2name_and_chain($local\
-_pdb_file);\n if ($local_pdb_file)\n {\n \n \
- if ( $debug){print STDERR \"\\nSplit $pdb_file\
- into $local_pdb_file and $suffix_chain \\n\";}\n \
- \n $tmp_pdb_file=get_pdb_file ($local_pdb_\
-file); \n \n if ( $tmp_pdb_file ne \"\"\
-)\n {\n @c_chain=();\n @c_chain=($suffix_c\
-hain);\n %hc_chain=();\n $hc_chain{$suffix_chain\
-}=1;\n }\n }\n }\n }\n\nif ( $debug)\
-{print STDERR \"\\n$pdb_file copied into ##$tmp_pd\
-b_file##\\n\";}\n\nif ( !-e $tmp_pdb_file || $tmp_\
-pdb_file eq \"\")\n{\n if ($is_pdb_name)\n{\n \
-print \"0\\n\"; exit ($EXIT_SUCCESS);\n}\n else\n{\
-\n \n print \"\\nEXTRACT_FROM_PDB: NO RESULT \
-for $pdb_file\\n\";\n &myexit ($EXIT_SUCCESS);\
- \n}\n}\n\n\n\n\n%molecule_type=&pdbfile2chaintype\
-($tmp_pdb_file);\nif ( $debug){print STDERR \"\\n\\
-\tSequence Type determined\\n\";}\n\n$pdb_id=&get_\
-pdb_id ($tmp_pdb_file);\nif ( $debug){print STDERR\
- \"\\n\\tID: $pdb_id (for $tmp_pdb_file)\\n\";}\n\\
-nif ( $pdb_id eq \"\"){$pdb_id=$force_name;}\n\n@f\
-_chain=&get_chain_list ($tmp_pdb_file);\nif ( $deb\
-ug){print STDERR \"\\n\\tChain_list:@f_chain\\n\";\
-}\n\nif ( $get_pdb_chains)\n{\n print \"@f_chai\
-n\\n\";\n &myexit ($EXIT_SUCCESS);\n}\nif ( $ge\
-t_pdb_ligands)\n{\n %complete_ligand_list=&get_\
-ligand_list ($tmp_pdb_file);\n print $complete_\
-ligand_list{\"result\"};\n &myexit ($EXIT_SUCCE\
-SS);\n}\n\nelsif ( $get_pdb_id ||$get_fugue_name )\
-\n{\n if (@c_chain && $c_chain[0] eq \"FIRST\
-\"){$pdb_id=$pdb_id.$f_chain[0];}\n elsif (@c_c\
-hain && $c_chain[0] ne \" \"){$pdb_id=$pdb_id.$c_c\
-hain[0];}\n \n print \"$pdb_id\\n\";\n &m\
-yexit ($EXIT_SUCCESS);\n \n}\nelsif ( $is_pdb_n\
-ame)\n{\n printf \"1\\n\";\n &myexit ($EXIT_\
-SUCCESS);\n}\n\n\n\n$structure_file=vtmpnam();\n\n\
-if ( $debug){print STDERR \"\\n\\tCheck_point #1: \
-$tmp_pdb_file $structure_file\\n\";}\n\n$INFILE=v\
-fopen (\"$tmp_pdb_file\", \"r\"); \n$TMP=vfopen (\\
-"$structure_file\", \"w\");\n\n$print_model=1;\n$i\
-n_model=0;\n\nif ( $debug){print STDERR \"\\n\\tCh\
-eck_point #2\\n\";}\nwhile ( <$INFILE>)\n{\n my $\
-first_model=0;\n $line=$_;\n\n if ( !$first_mode\
-l && ($line =~/^MODEL\\s*(\\d*)/))\n {\n $\
-first_model=$1;\n if ($model==1){$model=$firs\
-t_model;}\n }\n \n if (($line =~/^MODEL\\s*(\\
-\d*)/))\n {\n if ($1==$model)\n {\n $in_\
-model=1;\n $print_model=1;\n $is_nmr=1;\n }\n \
- elsif ( $in_model==0)\n {\n $print_model=0;\
-\n }\n elsif ( $in_model==1)\n {\n last;\n \
-}\n }\n if ($print_model){print $TMP $line;} \
-\n}\nclose ($TMP);\nclose ($INFILE);\n\nif ( $debu\
-g){print STDERR \"\\n\\tCheck_point #3\\n\";} \n\n\
- if ($numbering eq \"\"){$numbering=\"absolute\";\
-}\n if ($numbering_out eq \"\"){$numbering_out=\"\
-new\";}\n\n if ( $delete_set && $coor_set) {die \\
-"-delete and -coor are mutually exclusive, sorry\\\
-n\";}\n if ( $n_atom==0){$atom_list[$n_atom++]=\"\
-ALL\";$atom_list{$atom_list[0]}=1;}\n if ( $seq_f\
-ield eq \"\"){$seq_field=\"ATOM\";}\n \n if ( $M\
-ODE eq \"\"){$MODE=\"pdb\";}\n elsif ( $MODE eq \\
-"simple\" && $code==0){$code=1;}\n\n if ( $code==\
-0){$code=3;}\n\n\nif ($f_chain[0] eq \" \"){$hc_ch\
-ain{' '}=1;$c_chain[0]=\" \";}\nelsif (!@c_chain){\
-$hc_chain{FIRST}=1;$c_chain[0]=\"FIRST\";}#make su\
-re the first chain is taken by default\n\nif ($\
-hc_chain{ALL}) \n{\n @c_chain=@f_chain;\n \
- foreach $e (@c_chain){$hc_chain{$e}=1;}\n}\nelsi\
-f($hc_chain{FIRST})\n{\n @c_chain=($f_chain[0]);\n\
- $hc_chain{$f_chain[0]}=1;\n}\n\n\n$MAIN_HOM_CODE=\
-&get_main_hom_code ($structure_file);\n$INFILE=vfo\
-pen ($structure_file, \"r\");\n\n\nif ( $MODE eq \\
-"raw_pdb\" || $MODE eq \"raw\")\n{\n while (<$I\
-NFILE>)\n{ print \"$_\";}\n close ( $INFILE);\n\
- &myexit($EXIT_SUCCESS);\n} \nif ( $MODE eq \
-\"raw4fugue\" )\n{\n while (<$INFILE>)\n{ \n $l\
-=$_;\n if ($l=~/^SEQRES/)\n{\n \n $c= subs\
-tr($l,11,1);\n if ($hc_chain {$c}){print \"$l\\
-";}\n}\n elsif ( $l=~/^ATOM/)\n{\n $c=substr($\
-l,21,1);\n if ($hc_chain {$c}){print \"$l\";}\\
-n}\n}\n close ( $INFILE);\n &myexit($EXIT_SU\
-CCESS);\n} \n\nif ( $MODE eq \"pdb\")\n{\n\n \
- $read_header=0;\n while (<$INFILE>) \n{\n \
-$line=$_;\n if ($line =~ /^HEADER/){print \\
-"$line\";$read_header=1;}\n}\n close ($INFILE);\
-\n\n if (!$read_header)\n{\n print \"HEADER \
-UNKNOWN 00-JAN-00 \
- $force_name\\n\";\n}\n\n $INFILE=vfopen ($str\
-ucture_file, \"r\");\n \n print \"COMPND 1\
- CHAIN:\";\n $last=pop(@c_chain);\n foreach \
-$c ( @c_chain){ print \" $c,\";}\n if ( $last e\
-q \" \"){print \" NULL;\\n\";}\n else \n{\n \
- print \" $last;\\n\";\n}\n @c_chain=(@c_chain\
-, $last);\n \n print \"REMARK Output of the \
-program extract_from_pdb (Version $VersionTag)\\n\\
-";\n print \"REMARK Legal PDB format not Guaran\
-teed\\n\";\n print \"REMARK This format is not \
-meant to be used in place of the PDB format\\n\";\\
-n print \"REMARK The header refers to the origi\
-nal entry\\n\";\n print \"REMARK The sequence f\
-rom the original file has been taken in the field:\
- $seq_field\\n\";\n print \"REMARK extract_from\
-_pdb, 2001, 2002, 2003, 2004, 2005 2006 (c) CNRS a\
-nd Cedric Notredame\\n\"; \n if ( $coor_set)\\
-n{\n print \"REMARK Partial chain: Start $st\
-art End $end\\n\";\n}\n if ( $is_nmr)\n{\n \
- print \"REMARK NMR structure: MODEL $model\\n\";\
-\n}\n \n if ( $n_atom!=0)\n{\n print \"\
-REMARK Contains Coordinates of: \";\n foreac\
-h $a (@atom){print \"$a \";}\n print \"\\n\"\
-;\n} \n}\n\n\n\n\nmy $residue_index = -999;\nmy $\
-old_c = \"TemporaryChain\";\n\nwhile (<$INFILE>) \\
-n{\n $line=$_;\n\n\n if ($line =~ /^SEQRES/)\n{\n\\
-n @field=/(\\S*)\\s*/g;\n\n $c= substr($_,11,1);\
-\n\n \n $l=$#field;\n for ($a=4; $a<$#field ;)\\
-n{\n if (!$onelett{$molecule_type{$c}}->{$field[\
-$a]})\n{\n splice @field, $a, 1;\n}\n else \n\
-{\n $a++;\n}\n}\n \n if ( $c ne $in_chain)\n{\\
-n $pdb_chain_list[$n_pdb_chains]=$c;\n $pdb_ch\
-ain_len [$n_pdb_chains]=$len;\n $in_chain=$c;\n \
- $n_pdb_chains++;\n}\n \n for ( $a=4; $a<$#field\
-;$a++)\n{\n @{$complete_seq{$c}}->[$complete_seq\
-_len{$c}++]=$field[$a];\n}\n}\n elsif ( $line=~\
-/^ATOM/ || ($line=~/^HETATM/ && &is_aa(substr($lin\
-e,17,3),substr($line,21,1)) && !$no_hetatm))\n{\n\\
-n \n $RAW_AT_ID=$AT_ID=substr($line,12,4);\n $\
-RES_ID=&is_aa(substr($line,17,3),substr($line,21,1\
-));\n $CHAIN=substr($line,21,1);\n\n $RES_NO=su\
-bstr($line,22,4);\n $HOM_CODE=substr ($line, 26, 1\
-);\n $TEMP=substr($line,60,6);\n \n $TEMP=~s/\\s//\
-g;\n $AT_ID=~s/\\s//g;\n $RES_ID=~s/\\s//g;\
-\n $RES_NO=~s/\\s//g;\n \n if ( $HOM_CODE \
-ne $MAIN_HOM_CODE){next;}\n elsif ( $already_read2\
-{$CHAIN}{$RES_ID}{$AT_ID}{$RES_NO}){next;}\n else{\
-$already_read2{$CHAIN}{$RES_ID}{$AT_ID}{$RES_NO}=1\
-;}\n \n \n if ($coor_set && $numbering eq \"file\"\
- && $residue_index ne $RES_NO)\n{\n \n if \
-( $RES_NO<=$start){$real_start{$CHAIN}++;}\n i\
-f ( $RES_NO<=$end){$real_end{$CHAIN}++;}\n}\n elsi\
-f ($numbering eq \"absolute\")\n{\n $real_star\
-t{$CHAIN}=$start;\n $real_end{$CHAIN}=$end;\n}\
-\n\n $KEY=\"ALL\";\n if ( $CHAIN ne \
-$in_atom_chain)\n{\n \n $pdb_atom_chain_list\
-[$n_pdb_atom_chains]=$c;\n $pdb_atom_chain_len [\
-$n_pdb_atom_chains]=$len;\n $in_atom_chain=$c;\n\
- $n_pdb_atom_chains++;\n}\n \n if ( $residue_ind\
-ex ne $RES_NO)\n{\n $residue_index = $RES_NO;\
-\n @{$atom_seq{$CHAIN}}->[$atom_seq_len{$CHAI\
-N}++]=$RES_ID;;\n}\n}\n\n}\nclose ($INFILE);\n\n\n\
-\n\n\n\n$INFILE=vfopen ($structure_file, \"r\");\n\
-foreach $c (@c_chain)\n{\n\n if ( $seq_field eq\
- \"SEQRES\"){@pdb_seq=@{$complete_seq{$c}};}\n els\
-if ( $seq_field eq \"ATOM\") {@pdb_seq=@{$atom_se\
-q{$c}};}\n \n\n $full_length=$l=$#pdb_seq+1;\n \n\
- if ( $real_end{$c}==\"*\"){$real_end{$c}=$full_le\
-ngth;}\n if ( $coor_set)\n{ \n\n if ( $real_\
-end{$c} < $l){splice @pdb_seq, $real_end{$c}, $l;}\
-\n if ( $real_start{$c} < $l){splice @pdb_seq, \
-0, $real_start{$c}-1;} \n $l=$#pdb_seq;\n\
-}\n\n elsif ( $delete_set)\n{\n splice @pdb_seq\
-, $delete_start, $delete_end-$delete_start+1;\n \
- $l=$#pdb_seq;\n}\n \n $new_fasta_name=\"$pdb_id$c\
-\";\n if ( $coor_set)\n{\n if ( $n_pdb_chains==\
-0){$new_fasta_name=\"$new_fasta_name$c\";}\n $n\
-ew_fasta_name= $new_fasta_name.\"\\_$start\\_$end\\
-";\n}\n \n if ( $MODE eq \"pdb\")\n{\n $nl=1\
-;\n $n=0;\n \n foreach $res ( @pdb_seq)\n\
- {\n if ( !$n)\n {\n \n printf \"SEQRES %3d \
-%1s %4d \", $nl,$c, $l;\n $nl++;\n }\n $re\
-s=~s/\\s//g;\n \n if ($code==1){ printf \
-\"%3s \",$onelett{$molecule_type{$c}}->{$res};}\n \
- elsif ($code==3){ printf \"%3s \",$res};\n \
- \n $n++; \n if ( $n==13){$n=0;pri\
-nt \"\\n\";}\n}\n if ( $n!=0){print \"\\n\"; $n=\
-0;}\n}\n elsif ( $MODE eq \"simple\")\n{\n print\
- \"# SIMPLE_PDB_FORMAT\\n\";\n if ( $new_fasta_n\
-ame eq \" \"){$new_fasta_name=\"dummy_name\";}\n \
- print \">$new_fasta_name\\n\";\n\n foreach $res\
- ( @pdb_seq)\n{\n print \"$onelett{$molecule\
-_type{$c}}->{$res}\";\n}\n print \"\\n\";\n}\n e\
-lsif ( $MODE eq \"fasta\")\n{\n $n=0;\n print \
-\">$new_fasta_name\\n\";\n \n foreach $res ( @\
-pdb_seq)\n{\n\n print \"$onelett{$molecule_t\
-ype{$c}}->{$res}\";\n $n++;\n i\
-f ( $n==60){print \"\\n\"; $n=0;}\n}\n print \"\\
-\n\"; \n}\n}\n\nif ( $MODE eq \"fasta\")\n{\n \
-&myexit($EXIT_SUCCESS);\n \n}\n\n \n $charcount\
-=0;\n $inchain=\"BEGIN\";\n $n=0;\n while (<$IN\
-FILE>) \n{\n $line=$_;\n \n if ($line =~\
-/^ATOM/ || ($line=~/^HETATM/))\n{\n $line_header\
-=\"UNKNWN\";\n $RES_ID=substr($line,17,3);\n $chai\
-n = substr($line,21,1);\n\n if ($line =~/^ATOM/)\n\
-{\n $line_header=\"ATOM\";\n $RES_ID=(&is_\
-aa($RES_ID,$chain))?&is_aa($RES_ID,$chain):$RES_ID\
-;\n}\n elsif ($line=~/^HETATM/ && ($ligand_list {$\
-RES_ID} ||$ligand_list {'ALL'} || !&is_aa($RES_ID,\
-$chain)))\n{\n $line_header=\"HETATM\";\n}\n e\
-lsif ($line=~/^HETATM/ && (&is_aa($RES_ID,$chain) \
-&& !$no_hetatm))\n{\n $line_header=\"ATOM\";\n\
- $RES_ID=&is_aa($RES_ID,$chain);\n}\n else\n{\\
-n next;\n}\n\n \n\n $X=substr($line,30,8); \
- \n $Y=substr($line,38,8);\n $Z=substr($line,46,8)\
-;\n $TEMP=substr($line,60,6);\n \n $RAW_AT_ID=$AT_\
-ID=substr($line,12,4);\n $CHAIN=substr($line,21,1)\
-;\n $RES_NO=substr($line,22,4);\n $HOM_CODE=substr\
- ($line, 26, 1);\n \n $X=~s/\\s//g;\n $Y=~s/\\s//g\
-;\n $Z=~s/\\s//g;\n $TEMP=~s/\\s//g;\n \n $AT_ID=~\
-s/\\s//g;\n $RES_ID=~s/\\s//g;\n $RES_NO=~s/\\s//g\
-;\n\n \n if ( $HOM_CODE ne $MAIN_HOM_CODE){next;}\\
-n elsif ( $already_read{$CHAIN}{$RES_ID}{$AT_ID}{$\
-RES_NO}){next;}\n else{$already_read{$CHAIN}{$RES_\
-ID}{$AT_ID}{$RES_NO}=1;}\n \n $KEY=\"ALL\";\n\n \
- if ( $RES_NO ==0){$start_at_zero=1;}\n\n $RES_\
-NO+=$start_at_zero; \n \n if ( $current_chain n\
-e $CHAIN)\n{\n $current_chain=$CHAIN;\n $p\
-os=$current_residue=0;\n $offset=($coor_set)?(\
-$real_start{$CHAIN}-1):0;\n if ( $seq_field\
- eq \"SEQRES\"){@ref_seq=@{$complete_seq{$CHAIN}};\
-}\n elsif ( $seq_field eq \"ATOM\") {@ref_seq\
-=@{$atom_seq{$CHAIN}};}\n}\n \n if ($current_resid\
-ue != $RES_NO)\n{\n $current_residue=$RES_NO;\\
-n if ( $seq_field eq \"SEQRES\"){$pos=$curr\
-ent_residue;}\n elsif ( $seq_field eq \"ATOM\"\
-){$pos++;}\n}\n \n \n if ($n_atom==0 || $atom_list\
-{$AT_ID}==1 || $atom_list{$KEY}==1)\n{ \n \n \
- $do_it=(!@c_chain || $hc_chain{$CHAIN} ||$hc_c\
-hain{'LIGAND'} );\n \n $do_it= ($do_it==1)\
- && ($coor_set==0 ||($pos>=$real_start{$CHAIN} && \
-$pos<=$real_end{$CHAIN}));\n $do_it= ($do_it==\
-1) && ($delete_set==0 || $pos<$delete_start ||$pos\
->$delete_end );\n if ($ligand==0 && $line_head\
-er eq \"HETATM\" ){$do_it=0;}\n if ($ligand_on\
-ly==1 && $line_header eq \"ATOM\" ){$do_it=0;}\n \
- if ($ligand==1 && $line_header eq \"HETATM\" &&\
- $ligand_list{$RES_ID}==0 && $ligand_list{\"ALL\"}\
-==0){$do_it=0;} \n \n \n if ( $do_it)\\
-n{\n $n++;\n $out_pos=$pos;\n \n if ( $d\
-elete_set)\n{\n if ( $out_pos< $delete_start){;\
-}\n else {$offset=$delete_end-$delete_start;}\n\
-} \n \n if ( $numbering_out eq\
- \"new\"){$out_pos-=$offset;}\n elsif ( $nu\
-mbering_out eq \"old\"){$out_pos=$RES_NO;}\n \
- \n \n \n if ( $code==1){$RES\
-_ID=$onelett{$molecule_type{$c}}->{$RES_ID};}\n \
- \n if ($unfold)\n{\n $unfolded_x+=5;\\
-n $X=$unfolded_x;\n $Y=0;\n $Z=0;\n \
- $float=1;\n}\n else\n{\n $float=3;\n}\
-\n\n if ( $MODE eq \"pdb\")\n{\n printf\
- \"%-6s%5d %-4s %3s %s%4d %8.3f%8.3f%8.3f 1.00\
- %5.2f\\n\",$line_header, $n, $RAW_AT_ID,$RES_ID,$\
-CHAIN,$out_pos, $X, $Y, $Z,$TEMP; \n}\n \
-elsif ( $MODE eq \"simple\")\n{\n if ( $RES_I\
-D eq \"\"){$RES_ID=\"X\";}\n printf \"%-6s %5s \
-%s %2s %4d %8.3f %8.3f %8.3f\\n\",$line_header,\
- $AT_ID, $RES_ID,($CHAIN eq\"\" || $CHAIN eq \" \"\
-)?\"A\":$CHAIN,$out_pos, $X, $Y, $Z,$TEMP;\n}\n\n}\
-\n}\n}\n}\nprint \"\\n\";\nclose($INFILE);\n\n\nif\
- ( $error ne \"\") \n{$error=$error.\"\\nDiagnosti\
-c: SEQRES and the residues in ATOM are probably\
- Incompatible\\n\";\n $error=$error. \"Recomen\
-dation: Rerun with '-fix 1' in order to ignore the\
- SEQRES sequences\\n\";\n}\nif (!$nodiagnostic){pr\
-int STDERR $error;}\n&myexit ( $EXIT_SUCCESS);\n\n\
-sub is_released \n {\n my ($r);\n my $in=@_\
-[0];\n my $name=&remote_is_pdb_name ($in);\n \
- my $hold=&remote_is_on_hold($in);\n \n $r=(\
-$name && !$hold)?1:0;\n return $r;\n }\nsub re\
-mote_is_pdb_name \n{\n my $in=@_[0];\n my ($\
-ref_file, $pdb);\n my ($value,$value1,$value2);\
-\n\n if ( $in=~/[^\\w\\d\\:\\_]/){return 0;}\n \
- $ref_file=\"$cache/pdb_entry_type.txt\";\n \\
-n if ( !-e $ref_file || (-M $ref_file)>2 || -z \
-$ref_file)\n {\n &url2file(\"ftp://ftp.wwpdb.\
-org/pub/pdb/derived_data/pdb_entry_type.txt\", $re\
-f_file);\n }\n $pdb=substr ($in,0, 4);\n \
- chomp(($value1=`grep -c $pdb $ref_file`));\n \
-$pdb=lc($pdb);\n chomp(($value2=`grep -c $pdb $\
-ref_file`));\n $value=($value1 || $value2)?1:0;\
-\n $value=($value>0)?1:0;\n \n return $va\
-lue;\n }\n\nsub pdb2model_type\n{\n my $in=@_[\
-0];\n my ($ref_file, $pdb);\n my ($value, $r\
-et);\n\n if ( $in=~/[^\\w\\d\\:\\_]/){return 0;\
-}\n $ref_file=\"$cache/pdb_entry_type.txt\";\n \
- \n if ( !-e $ref_file || (-M $ref_file)>2 ||\
- -z $ref_file)\n {\n &url2file(\"ftp://ftp.ww\
-pdb.org/pub/pdb/derived_data/pdb_entry_type.txt\",\
- $ref_file);\n }\n $pdb=substr ($in,0, 4);\
-\n $pdb=lc($pdb);\n \n chomp(($value=`gre\
-p $pdb $ref_file`));\n \n $value=~/^\\S+\\s+\
-\\S+\\s+(\\S+)/;\n $ret=$1;\n if ( $ret eq\"\
-\"){return \"UNKNOWN\";}\n \n return $ret;\n\
- }\nsub remote_is_on_hold\n {\n my $in=@_[0];\
-\n my ($ref_file, $pdb);\n my ($value1, $val\
-ue2,$value);\n \n if ( $in=~/[^\\w\\d\\:\\_]\
-/){return 0;}\n $ref_file=\"$cache/unreleased.x\
-ml\";\n \n if ( !-e $ref_file || (-M $ref_fi\
-le)>2 || -z $ref_file)\n {\n &url2file(\"http\
-://www.rcsb.org/pdb/rest/getUnreleased\",$ref_file\
-);\n }\n \n $pdb=substr ($in,0, 4);\n \
- chomp(($value1=`grep -c $pdb $ref_file`));\n \
-$pdb=lc($pdb);\n chomp(($value2=`grep -c $pdb $\
-ref_file`));\n $value=($value1 || $value2)?1:0;\
-\n $value=($value>0)?1:0;\n return $value;\n\
- }\nsub is_pdb_file\n{\n my @arg=@_;\n\n if\
- ( !-e $arg[0]){return 0;}\n \n $F=vfopen ($\
-arg[0], \"r\");\n while ( <$F>)\n{\n if (/^HEAD\
-ER/)\n{\n close $F;\n return 1;\n}\n elsif\
- ( /^SEQRES/)\n{\n close $F;\n return 1;\n\
-}\n elsif ( /^ATOM/)\n{\n close $F;\n retu\
-rn 1;\n}\n}\n return 0;\n}\nsub get_pdb_id\n{\n\
- my $header_file=@_[0];\n my $id;\n my $F\
-= new FileHandle;\n \n \n $F=vfopen (\"$h\
-eader_file\", \"r\");\n\n while ( <$F>)\n \
-{\n if ( /HEADER/)\n {\n if ($debug){print \\
-"$_\";}\n $id=substr($_,62,4 );\n return $\
-id;\n }\n }\n close ($F);\n \n ret\
-urn \"\";\n}\n\nsub get_ligand_list\n{\n my $pd\
-b_file=@_[0];\n my $chain;\n my $ligand;\n \
- my %complete_ligand_list;\n \n\n $F=vfopen\
- ($pdb_file, \"r\");\n while ( <$F>)\n{\n if ( \
-/^HETATM/)\n{\n $line=$_;\n $chain=substr(\
-$line,21,1);\n $ligand=substr($line,17,3);\n \
- \n if (!$complete_ligand_list{$chain}{$liga\
-nd})\n{\n \n $complete_ligand_list{\"result\"}.=\
-\"CHAIN $chain LIGAND $ligand\\n\";\n $complete_l\
-igand_list{$chain}{$ligand}=1;\n}\n}\n}\n close\
- ($F);\n return %complete_ligand_list;\n}\n\nsu\
-b get_chain_list \n{\n my $header_file;\n my\
- @chain_list;\n my @list;\n my $n_chains;\n \
- my %chain_hasch;\n my $pdb_file=@_[0];\n \
-my $c;\n my %hasch;\n my $chain;\n \n \n\
- $F=vfopen ($pdb_file, \"r\");\n while ( <$F\
->)\n{\n\n\n if (/SEQRES\\s+\\d+\\s+(\\S+)/)\n {\\
-n $chain = substr($_,11,1);$chain=~s/\\s//g;if\
- ( $chain eq \"\"){$chain=\" \";}\n if (!$hasc\
-h{$chain}){$hasch{$chain}=1;push @chain_list, $cha\
-in;}\n }\n if (/^ATOM/ || /^HETATM/)\n {\n \
- $chain = substr($_,21,1); $chain=~s/\\s//g;if ( $\
-chain eq \"\"){$chain=\" \";}\n if (!$hasch{$c\
-hain}){$hasch{$chain}=1;push @chain_list, $chain;}\
-\n }\n }\n\n\nclose ($F);\nif (!@chain_list\
-)\n {\n @chain_list=(\"A\");\n }\n\n\nreturn \
-@chain_list;\n}\n\nsub token_is_in_list\n{\n\n \
-my @list=@_;\n my $a;\n \n for ($a=1; $a<\
-=$#list; $a++)\n{\n if ( $list[$a] eq $list[0]){re\
-turn $a;}\n}\n}\n\nsub pdb_name2name_and_chain \n{\
-\n my $pdb_file=@_[0];\n my $pdb_file_in;\n \
- my @array;\n my $chain;\n my $c;\n\n $\
-pdb_file_in=$pdb_file;\n\n $pdb_file=~/^(.{4})/\
-;$pdb_id=$1;\n @array=($pdb_file=~/([\\w])/g);\\
-n \n \n $chain=uc ($array[4]);\n $chain=($\
-chain eq \"\")?\"FIRST\":$chain;\n \n return\
- ( $pdb_id, $chain);\n\n if ( $#array==3){retur\
-n ($pdb_id, \"FIRST\");}\n elsif ( $#array<4){ \
-return ($pdb_id, \"\");}\n else {return ( $pdb_\
-id, $chain);}\n \n \n \n}\nsub get_main\
-_hom_code \n{\n my $pdb_file=@_[0];\n my %ho\
-m, $n, $best, $best_h;\n open (F, $pdb_file);\n\
- while (<F>)\n{\n if ( $_=~/^ATOM/)\n{\n $h\
-=substr ($_,26, 1);\n $n=++$hom{$h};\n if \
-($n>$best)\n{\n $best=$n;\n $best_h=$h;\n}\n}\n}\
-\n close (F);\n return $best_h;\n}\n\n\nsub \
-get_pdb_file \n{\n my ($pdb_file_in)=(@_);\n \
- my $result;\n my @letter;\n my @chain;\n \
- my $v;\n my $pdb_file=$pdb_file_in;\n\n $pd\
-b_file=($pdb_file_in=~/\\S+_S_(\\S+)/)?$1:$pdb_fil\
-e_in;\n \n if ($no_remote_pdb_dir==0)\n \
- {\n $no_remote_pdb_dir=1;\n $result=get_pdb_file3\
- ($pdb_file);\n $no_remote_pdb_dir=0;\n if ( $resu\
-lt){return $result;}\n else\n {\n \n lc \
-($pdb_file);\n $result=get_pdb_file3($pdb_file\
-);\n return $result;\n }\n }\n else\
-\n {\n return get_pdb_file3 ($pdb_file);\n \
- }\n \n }\n\nsub get_pdb_file3 \n{\n my $\
-pdb_file_in=@_[0];\n my $result;\n my @lette\
-r;\n my @chain;\n my $lcfile;\n my $ucfil\
-e;\n my $pdb_file=$pdb_file_in;\n \n $lcf\
-ile=lc $pdb_file;\n $ucfile=uc $pdb_file;\n\n \
- if ( ($result=get_pdb_file2 ($pdb_file))){return\
- $result;}\n \n\n if ($lcfile ne $pdb_file &\
-& ($result=get_pdb_file2 ($lcfile))){return $resul\
-t;}\n if ($ucfile ne $pdb_file && ($result=get_\
-pdb_file2 ($ucfile))){return $result;}\n \n \\
-n \n return \"\";\n}\nsub get_pdb_file2\n{\n\
- my $pdb_file=@_[0];\n my $return_value;\n \
- \n $return_value=\"\";\n \n if ( ($resu\
-lt=get_pdb_file1 ($pdb_file))){$return_value=$resu\
-lt;}\n elsif ( !($pdb_file=~/\\.pdb/) && !($pdb\
-_file=~/\\.PDB/))\n{\n if ( ($result=get_pdb_file1\
- (\"$pdb_file.pdb\"))){$return_value=$result;}\n e\
-lsif ( ($result=get_pdb_file1 (\"$pdb_file.PDB\"))\
+ 2.43;\nuse Env;\nuse FileHandle;\nuse \
+Cwd;\nuse File::Path;\nuse Sys::Hostname;\nour $PI\
+DCHILD;\nour $ERROR_DONE;\nour @TMPFILE_LIST;\nour\
+ $EXIT_FAILURE=1;\nour $EXIT_SUCCESS=0;\n\nour $RE\
+FDIR=getcwd;\nour $EXIT_SUCCESS=0;\nour $EXIT_FAIL\
+URE=1;\n\nour $PROGRAM=\"extract_from_pdb\";\nour \
+$CL=$PROGRAM;\n\nour $CLEAN_EXIT_STARTED;\nour $de\
+bug_lock=$ENV{\"DEBUG_LOCK\"};\nour $LOCKDIR=$ENV{\
+\"LOCKDIR_4_TCOFFEE\"};\nif (!$LOCKDIR){$LOCKDIR=g\
+etcwd();}\nour $ERRORDIR=$ENV{\"ERRORDIR_4_TCOFFEE\
+\"};\nour $ERRORFILE=$ENV{\"ERRORFILE_4_TCOFFEE\"}\
+;\n&set_lock ($$);\nif (isshellpid(getppid())){loc\
+k4tc(getppid(), \"LLOCK\", \"LSET\", \"$$\\n\");}\\
+n \nour $SILENT=\" >/dev/null 2>/dev/null\";\\
+nour $INTERNET=-1;\n\n\n\n\n\n\n\nour $BLAST_MAX_N\
+RUNS=2;\nour $EXIT_SUCCESS=0;\nour $EXIT_FAILURE=1\
+;\nour $CONFIGURATION=-1;\nour $REF_EMAIL=\"\";\no\
+ur $PROGRAM=\"extract_from_pdb\";\n\n\nmy %onelett\
+_prot=&fill_onelett_prot();\nmy %threelett_prot=&f\
+ill_threelett_prot();\nmy %onelett_RNA=&fill_onele\
+tt_RNA();\nmy %threelett_RNA=&fill_threelett_RNA()\
+;\nmy %onelett_DNA=&fill_onelett_DNA();\nmy %three\
+lett_DNA=&fill_threelett_DNA();\n\n\n\n\n\nmy %one\
+lett = (\n'P' => \\%onelett_prot,\n'D' => \\%onele\
+tt_DNA,\n'R' => \\%onelett_RNA\n);\n\n\nmy %threel\
+ett = (\n'P' => \\%threelett_prot,\n'D' => \\%thre\
+elett_DNA,\n'R' => \\%threelett_RNA\n);\n\n\n\n\n\\
+n\n\nif($ARGV[0]=~/help/ ||$ARGV[0]=~/man/ || $ARG\
+V[0]=~/HELP/ || $ARGV[0]=~/Man/ || $ARGV[0] eq \"-\
+h\" || $ARGV[0] eq \"-H\" )\n{die \"SYNTAX: extr\
+act_from_pdb Version $VersionTag \n Minimum: \
+ [extract_from_pdb file] \n OR \n \
+ [... | extract_from_pdb]\n Flags (Default setti\
+ng on the first line)\n -version...............\
+....[Returns the Version Number]\n -forc\
+e.....................[Forces the file to be treat\
+ed like a PDB file]\n \
+ [Regenerates the header and SEQRES fields\
+]\n -force_name................[Forces t\
+he file to be named after name]]\n -infi\
+le.....file...........[Flag can be omited]\n \
+ [File must be pdb or fro pgm]\n \
+ [File can also be co\
+mpressed Z or gz]\n \
+ [In the case of a compressed file, you can \
+omit the gz|Z extension]\n -netfile.....\
+..............[File will be fetch from the net usi\
+ng wget]\n [w\
+get or curl must be installed]\n \
+ [ftp://ftp.gnu.org/pub/gnu/wge\
+t/]\n [http:/\
+/curl.haxx.se/]\n \
+ [Must also be used to retrieve the file from \
+a local pdb copy (cf netaddress)]\n -net\
+address................[Address used for the retri\
+eving the netfile]\n \
+ [http://www.rcsb.org/pdb/cgi/export.cgi/%%\
+.pdb.gz?format=PDB&pdbId=%%&compression=gz]\n \
+ [http://www.expas\
+y.ch/cgi-bin/get-pdb-entry.pl?%%]\n \
+ [local -> will get the file\
+ from pdb_dir (see pdb_dir)]\n -netcompr\
+ession............[Extension if the netfile comes \
+compressed]\n \
+ [gz]\n -pdb_dir...................[addr\
+ess of the repertory where the pdb is installed]\n\
+ [Supports st\
+andard ftp style installation OR every stru in DIR\
+]\n [Give the\
+ ..../pdb/structure/ dir]\n \
+ [If value omitted, the pg gets it f\
+rom the env variable PDB_DIR]\n -netcomp\
+ression_pg.........[gunzip]\n -is_pdb_na\
+me..........name.[Returns 1 if the name is a PDB I\
+D, 0 otherwise]\n -model_type...........\
+name.[Returns the model type if valid PDB name]\n \
+ -is_released_pdb_name name.[Returns 1 if\
+ the name corresponds to a released PDB file]\n \
+ -get_pdb_chains.....name...[Returns the li\
+st of chains corresponding to the entry]\n \
+ -get_pdb_id.........name...[Returns the PDB id \
+within the provided pdb file]\n -get_fug\
+ue_name.....name...[Turns a name into a name valid\
+ for fugue]\n \
+ [Uses the netaddress to do so]\n -chain......F\
+IRST..........[Extract the first chain only]\n \
+ A B C..........[Extract Several chains if nee\
+ded]\n ALL............[Extract all the cha\
+ins] \n -ligand.....ALL............[Extr\
+act the ligands in the chain (HETATM)]\n \
+ <name1>,<name2>[Extract All the named\
+ lignds]\n -ligand_only...............[Extract \
+only the ligands]\n -ligand_list........\
+.......[Extract the list of ligands]\n -coor...\
+....<start>..<end>.[Coordinates of the fragment to\
+ extract]\n [Omit end to include t\
+he Cter]\n -num........absolute.......[a\
+bsolute: relative to the seq] \n \
+ file...........[file: relative to file]\n \
+ -num_out....new............[new: start 1->L\
+]\n old............[old: kee\
+p the file coordinates]\n -delete.....<s\
+tart>..<end>.[Delete from residue start to residue\
+ end]\n -atom.......CA.............[Atoms to in\
+clude, ALL for all of them]\n CA O N......\
+...[Indicate several atoms if needed]\n -code..\
+.....3..............[Use the 1 letter code or the \
+3 letters code]\n -mode.......raw............[O\
+utput original pdb file]\n p\
+db............[Output something that looks like pd\
+b]\n fasta..........[Output the sequences \
+in fasta format]\n simple.........[Output \
+a format easy to parse in C ]\n -seq_fi\
+eld..ATOM...........[Field used to extract the seq\
+uence]\n SEQRES.........[Use the complete \
+sequence]\n -seq.......................[Equival\
+ent to -mode fasta]\n -model......1...........\
+...[Chosen Model in an NMR file]\n -nodi\
+agnostic..............[Switches Error Messages off\
+]\n -debug.....................[Sets the\
+ DEBUG ON]\n -no_remote_pdb_dir.........\
+[Do not look for a remote file]\n -cache\
+_pdb.................[Cache Value, default is $HOM\
+E/.t_coffee/cache, other values: NO<=> No cache]\n\
+\n Environement Variables\n These v\
+ariables can be set from the environement\n \
+ Command line values with the corresponding fla\
+g superseed evironement value\n NO_REMOT\
+E_PDB_DIR..........[Prevents the program from sear\
+ching remote file: faster]\n PDB_DIR....\
+................[Indicates where PDB file must be \
+fetched (localy)]\n\n PROBLEMS: please contact ce\
+dric.notredame\\@europe.com\\n\";\n exit ($EXIT_S\
+UCCESS);\n}\n\n$np=0;\n$n_para=$#ARGV;\n$model=1;\\
+n$pdb_dir=$ENV{'PDB_DIR'};if ($pdb_dir){$pdb_dir.=\
+\"/\";}\n$debug=$ENV{'DEBUG_EXTRACT_FROM_PDB'};\n\\
+n$no_remote_pdb_dir=$ENV{NO_REMOTE_PDB_DIR};\n$HOM\
+E=$ENV{'HOME'};\nif ( $ENV{CACHE_4_TCOFFEE})\n{$ca\
+che=$ENV{CACHE_4_TCOFFEE};}\nelse\n{\n $cache=\\
+"$HOME/.t_coffee/cache/\";\n}\n\n \n$netaddress=\
+\"http://www.rcsb.org/pdb/files/%%.pdb.gz\";\n$net\
+compression_pg=\"gunzip\";\n$netcompression=\"gz\"\
+;\n\nforeach ($np=0; $np<=$n_para; $np++)\n { \
+ \n $value=$ARGV[$np];\n \n if ($np==0\
+ && !($value=~/^-.*/))\n { \n $pdb_file= $ARG\
+V[$np];\n }\n elsif ( !($value=~/^-.*/))\n\
+ {\n print \"@ARGV\";\n die;\n } \n \\
+n elsif ($value eq \"-nodiagnostic\"){$nodiagno\
+stic=1;}\n elsif ($value eq \"-force\")\n \
+{\n $force_pdb=1;\n }\n elsif ($value eq \\
+"-force_name\")\n {\n $force_name=$ARGV[++$np\
+];\n $force_pdb=1;\n }\n \n elsif ($val\
+ue eq \"-is_pdb_name\")\n {\n $pdb_file= $ARG\
+V[++$np]; \n $is_pdb_name=1; \n } \n elsif\
+ ($value eq \"-is_released_pdb_name\")\n {\n \
+$pdb_file= $ARGV[++$np]; \n $is_released_pdb_name=\
+1;\n }\n elsif ($value eq \"-model_type\")\
+\n {\n $pdb_file= $ARGV[++$np]; \n $model_typ\
+e=1;\n }\n elsif ($value eq \"-debug\")\n{\
+\n $debug=1;\n}\n elsif ($value eq \"-get_pdb_c\
+hains\")\n{\n $pdb_file= $ARGV[++$np];\n $get_pdb_\
+chains=1;\n}\n elsif ($value eq \"-get_pdb_liga\
+nds\")\n{\n $get_pdb_ligands=1;\n}\n \n elsi\
+f ($value eq \"-get_pdb_id\")\n{\n $pdb_file= $ARG\
+V[++$np];\n $get_pdb_id=1;\n \n}\n \n elsif \
+( $value eq \"-get_fugue_name\")\n{\n $pdb_file= $\
+ARGV[++$np];\n $get_fugue_name=1;\n}\n elsif ( \
+$value eq \"-infile\")\n{\n $pdb_file= $ARGV\
+[++$np];\n} \n elsif ($value eq \"-netfile\")\n\
+{\n $netfile=1;\n if ( !($ARGV[$np+1]=~/^-.*/)){$p\
+db_file= $ARGV[++$np];}\n}\n elsif ( $value eq\
+ \"-num\")\n{\n $numbering= $ARGV[++$np];\n}\
+\n elsif ( $value eq \"-num_out\")\n{\n \
+$numbering_out= $ARGV[++$np];\n}\n elsif ( $val\
+ue eq \"-netaddress\")\n{\n $netadress=$ARGV[++$np\
+];\n}\n \n elsif ( $value eq \"-netcompress\
+ion\")\n{\n $netcompression=$ARGV[++$np];\n}\n \
+ elsif ( $value eq \"-pdb_dir\")\n{\n if ( !($ARG\
+V[$np+1]=~/^-.*/)){$pdb_dir= \"$ARGV[++$np]/\";}\n\
+}\n elsif ( $value eq \"-no_remote_pdb_dir\")\\
+n{\n $no_remote_pdb_dir=1;\n if ( !($ARGV[$np+1]=~\
+/^-.*/)){$pdb_dir= \"$ARGV[++$np]/\";}\n}\n els\
+if ( $value eq \"-cache\")\n{\n $cache=$ARGV[++$np\
+];\n}\n \n elsif ($value eq \"-netcompressio\
+n_pg\")\n{\n $netcompression_pg=$ARGV[++$np];\n}\
+\n elsif ($value eq \"-mode\")\n{\n $MOD\
+E=$ARGV[++$np];\n}\n\n elsif ( $value eq \"-mod\
+el\")\n{\n $model= $ARGV[++$np];\n}\n els\
+if ($value eq \"-seq_field\" )\n{\n $seq_fie\
+ld= $ARGV[++$np];\n} \n elsif ($value eq \"-c\
+oor\" )\n{\n $start= $ARGV[++$np];\n \n \
+ if (($ARGV[$np+1] eq \"\") ||($ARGV[$np+1]=~/^-\
+.*/)){$end=\"*\";} \n else {$end= $ARGV[++\
+$np];} \n $coor_set=1;\n}\n elsif ($v\
+alue eq \"-delete\" )\n{\n $delete_start= $A\
+RGV[++$np];\n $delete_end= $ARGV[++$np];\n \
+ $delete_set=1;\n}\n elsif ($value eq \"-c\
+ode\")\n{\n $code= $ARGV[++$np];\n}\n els\
+if ($value eq \"-no_hetatm\")\n{\n $no_heta\
+tm=1;\n}\n elsif ($value eq \"-chain\")\n{\n \
+ while (!($ARGV[$np+1] eq \"\") &&!($ARGV[$np+1\
+]=~/^-.*/))\n{\n ++$np;\n @c_chain=(@c\
+hain, $ARGV[$np]);\n $hc_chain{$ARGV[$np]}=\
+$#c_chain+1;\n} \n}\n elsif ($value e\
+q \"-atom\")\n{\n\n while (!($ARGV[$np+1] eq\
+ \"\") && !($ARGV[$np+1]=~/^-.*/))\n{\n ++$n\
+p;\n $atom[$n_atom++]= $ARGV[$np];\n \
+$atom_list{$ARGV[$np]}=1; \n} \n \n}\n\
+ elsif ( $value eq \"-unfold\")\n{\n $unfold=1;\
+\n}\n elsif ($value eq \"-seq\" ||$value eq \"-\
+fasta\" )\n{\n $MODE=\"fasta\";\n}\n elsi\
+f ( $value eq \"-version\")\n{\n print STDERR \"\\
+\nextract_from_pdb: Version $VersionTag\\n\";\n &m\
+yexit ($EXIT_SUCCESS);\n}\n elsif ( $value eq \\
+"-ligand\")\n{\n while (!($ARGV[$np+1] eq \"\") &&\
+ !($ARGV[$np+1]=~/^-.*/))\n{\n ++$np;\n $l\
+igand=1;\n $ligand_list{$ARGV[$np]}=1; \\
+n} \n $hc_chain{'LIGAND'}=1;\n}\n elsif ( $valu\
+e eq \"-ligand_only\")\n{\n $ligand_only=1;\n}\n}\\
+nif ( $debug)\n{\n print STDERR \"\\n[DEBUG:ext\
+ract_from_pdb] NO_REMOTE_PDB_DIR: $no_remote_pdb_d\
+ir\\n\";\n print STDERR \"\\n[DEBUG:extract_fro\
+m_pdb] PDB_DIR: $pdb_dir\\n\";\n}\n\n\nif ( $is_pd\
+b_name)\n {\n if (&remote_is_pdb_name($pdb_fil\
+e))\n {\n print \"1\";\n }\n else\n \
+ {\n print \"0\";\n }\n exit ($EXIT_SUC\
+CESS);\n }\n\nif ( $is_released_pdb_name)\n {\n \
+ \n if (&is_released($pdb_file))\n {\n p\
+rint \"1\";\n }\n else\n {\n print \"\
+0\";\n }\n exit ($EXIT_SUCCESS);\n }\nif \
+($model_type)\n {\n \n printf \"%s\", &pdb2m\
+odel_type($pdb_file);\n exit ($EXIT_SUCCESS);\n\
+ \n }\n \n\nif (!$force_name)\n{\n $pdb_\
+file=~/([^\\/]*)$/;\n $force_name=$1;\n}\n\n$lo\
+cal_pdb_file=$pdb_file;\n\nif ( $debug){print STDE\
+RR \"\\n[DEBUG: extract_from_pdb] Scan For $local_\
+pdb_file\\n\";}\n\n$mem=$no_remote_pdb_dir;\n$no_r\
+emote_pdb_dir=1;\n$tmp_pdb_file=get_pdb_file ($loc\
+al_pdb_file);\n\nif ( !-e $tmp_pdb_file || $tmp_pd\
+b_file eq \"\")\n {\n $local_pdb_file=$pdb_fil\
+e;\n ($local_pdb_file, $suffix_chain)=&pdb_name\
+2name_and_chain($local_pdb_file);\n\n if ($loca\
+l_pdb_file)\n {\n if ( $debug){print STDERR \\
+"\\nSplit $pdb_file into $local_pdb_file and $suff\
+ix_chain \\n\";}\n $tmp_pdb_file=get_pdb_file ($lo\
+cal_pdb_file);\n if ( $tmp_pdb_file ne \"\")\n {\
+\n @c_chain=();\n @c_chain=($suffix_chain)\
+;\n %hc_chain=();\n $hc_chain{$suffix_chai\
+n}=1;\n }\n }\n }\n\n$no_remote_pdb_dir=$m\
+em;\nif ($no_remote_pdb_dir==0)\n {\n \n if\
+ ( !-e $tmp_pdb_file || $tmp_pdb_file eq \"\")\n \
+ {\n \n $local_pdb_file=$pdb_file;\n ($local_pd\
+b_file, $suffix_chain)=&pdb_name2name_and_chain($l\
+ocal_pdb_file);\n if ($local_pdb_file)\n {\n \
+ \n if ( $debug){print STDERR \"\\nSplit $pdb_\
+file into $local_pdb_file and $suffix_chain \\n\";\
+}\n \n $tmp_pdb_file=get_pdb_file ($local_\
+pdb_file); \n \n if ( $tmp_pdb_file ne \
+\"\")\n {\n @c_chain=();\n @c_chain=($suff\
+ix_chain);\n %hc_chain=();\n $hc_chain{$suffix_c\
+hain}=1;\n }\n }\n }\n }\n\nif ( $de\
+bug){print STDERR \"\\n$pdb_file copied into ##$tm\
+p_pdb_file##\\n\";}\n\nif ( !-e $tmp_pdb_file || $\
+tmp_pdb_file eq \"\")\n{\n if ($is_pdb_name)\n{\n \
+ print \"0\\n\"; exit ($EXIT_SUCCESS);\n}\n els\
+e\n{\n \n print \"\\nEXTRACT_FROM_PDB: NO RES\
+ULT for $pdb_file\\n\";\n &myexit ($EXIT_SUCCE\
+SS); \n}\n}\n\n\n\n\n%molecule_type=&pdbfile2chain\
+type($tmp_pdb_file);\nif ( $debug){print STDERR \"\
+\\n\\tSequence Type determined\\n\";}\n\n$pdb_id=&\
+get_pdb_id ($tmp_pdb_file);\nif ( $debug){print ST\
+DERR \"\\n\\tID: $pdb_id (for $tmp_pdb_file)\\n\";\
+}\n\nif ( $pdb_id eq \"\"){$pdb_id=$force_name;}\n\
+\n@f_chain=&get_chain_list ($tmp_pdb_file);\nif ( \
+$debug){print STDERR \"\\n\\tChain_list:@f_chain\\\
+n\";}\n\nif ( $get_pdb_chains)\n{\n print \"@f_\
+chain\\n\";\n &myexit ($EXIT_SUCCESS);\n}\nif (\
+ $get_pdb_ligands)\n{\n %complete_ligand_list=&\
+get_ligand_list ($tmp_pdb_file);\n print $compl\
+ete_ligand_list{\"result\"};\n &myexit ($EXIT_S\
+UCCESS);\n}\n\nelsif ( $get_pdb_id ||$get_fugue_na\
+me )\n{\n if (@c_chain && $c_chain[0] eq \"F\
+IRST\"){$pdb_id=$pdb_id.$f_chain[0];}\n elsif (\
+@c_chain && $c_chain[0] ne \" \"){$pdb_id=$pdb_id.\
+$c_chain[0];}\n \n print \"$pdb_id\\n\";\n \
+ &myexit ($EXIT_SUCCESS);\n \n}\nelsif ( $is_p\
+db_name)\n{\n printf \"1\\n\";\n &myexit ($E\
+XIT_SUCCESS);\n}\n\n\n\n$structure_file=vtmpnam();\
+\n\nif ( $debug){print STDERR \"\\n\\tCheck_point \
+#1: $tmp_pdb_file $structure_file\\n\";}\n\n$INFI\
+LE=vfopen (\"$tmp_pdb_file\", \"r\"); \nmy $TMP=vf\
+open (\"$structure_file\", \"w\");\n\n$print_model\
+=1;\n$in_model=0;\n\nif ( $debug){print STDERR \"\\
+\n\\tCheck_point #2\\n\";}\nwhile ( <$INFILE>)\n{\\
+n my $first_model=0;\n $line=$_;\n\n if ( !$fir\
+st_model && ($line =~/^MODEL\\s*(\\d*)/))\n {\n\
+ $first_model=$1;\n if ($model==1){$mode\
+l=$first_model;}\n }\n \n if (($line =~/^MODE\
+L\\s*(\\d*)/))\n {\n if ($1==$model)\n {\n\
+ $in_model=1;\n $print_model=1;\n $is_nmr=1;\
+\n }\n elsif ( $in_model==0)\n {\n $print_m\
+odel=0;\n }\n elsif ( $in_model==1)\n {\n l\
+ast;\n }\n }\n if ($print_model){print $TMP $l\
+ine;} \n}\nclose ($TMP);\nclose ($INFILE);\n\nif \
+( $debug){print STDERR \"\\n\\tCheck_point #3\\n\"\
+;} \n\n if ($numbering eq \"\"){$numbering=\"abso\
+lute\";}\n if ($numbering_out eq \"\"){$numbering\
+_out=\"new\";}\n\n if ( $delete_set && $coor_set)\
+ {die \"-delete and -coor are mutually exclusive, \
+sorry\\n\";}\n if ( $n_atom==0){$atom_list[$n_ato\
+m++]=\"ALL\";$atom_list{$atom_list[0]}=1;}\n if (\
+ $seq_field eq \"\"){$seq_field=\"ATOM\";}\n \n \
+if ( $MODE eq \"\"){$MODE=\"pdb\";}\n elsif ( $MO\
+DE eq \"simple\" && $code==0){$code=1;}\n\n if ( \
+$code==0){$code=3;}\n\n\nif ($f_chain[0] eq \" \")\
+{$hc_chain{' '}=1;$c_chain[0]=\" \";}\nelsif (!@c_\
+chain){$hc_chain{FIRST}=1;$c_chain[0]=\"FIRST\";}#\
+make sure the first chain is taken by default\n\ni\
+f ($hc_chain{ALL}) \n{\n @c_chain=@f_chain\
+;\n foreach $e (@c_chain){$hc_chain{$e}=1;}\n\
+}\nelsif($hc_chain{FIRST})\n{\n @c_chain=($f_chain\
+[0]);\n $hc_chain{$f_chain[0]}=1;\n}\n\n\n$MAIN_HO\
+M_CODE=&get_main_hom_code ($structure_file);\n$INF\
+ILE=vfopen ($structure_file, \"r\");\n\n\nif ( $MO\
+DE eq \"raw_pdb\" || $MODE eq \"raw\")\n{\n whi\
+le (<$INFILE>)\n{ print \"$_\";}\n close ( $INF\
+ILE);\n &myexit($EXIT_SUCCESS);\n} \nif ( $M\
+ODE eq \"raw4fugue\" )\n{\n while (<$INFILE>)\n\
+{ \n $l=$_;\n if ($l=~/^SEQRES/)\n{\n \n $\
+c= substr($l,11,1);\n if ($hc_chain {$c}){prin\
+t \"$l\";}\n}\n elsif ( $l=~/^ATOM/)\n{\n $c=s\
+ubstr($l,21,1);\n if ($hc_chain {$c}){print \"\
+$l\";}\n}\n}\n close ( $INFILE);\n &myexit($\
+EXIT_SUCCESS);\n} \n\nif ( $MODE eq \"pdb\")\n{\
+\n\n $read_header=0;\n while (<$INFILE>) \n{\
+\n $line=$_;\n if ($line =~ /^HEADER/){\
+print \"$line\";$read_header=1;}\n}\n close ($I\
+NFILE);\n\n if (!$read_header)\n{\n print \"HEA\
+DER UNKNOWN 00-\
+JAN-00 $force_name\\n\";\n}\n\n $INFILE=vfope\
+n ($structure_file, \"r\");\n \n print \"COM\
+PND 1 CHAIN:\";\n $last=pop(@c_chain);\n f\
+oreach $c ( @c_chain){ print \" $c,\";}\n if ( \
+$last eq \" \"){print \" NULL;\\n\";}\n else \n\
+{\n print \" $last;\\n\";\n}\n @c_chain=(@\
+c_chain, $last);\n \n print \"REMARK Output \
+of the program extract_from_pdb (Version $VersionT\
+ag)\\n\";\n print \"REMARK Legal PDB format not\
+ Guaranteed\\n\";\n print \"REMARK This format \
+is not meant to be used in place of the PDB format\
+\\n\";\n print \"REMARK The header refers to th\
+e original entry\\n\";\n print \"REMARK The seq\
+uence from the original file has been taken in the\
+ field: $seq_field\\n\";\n print \"REMARK extra\
+ct_from_pdb, 2001, 2002, 2003, 2004, 2005 2006 (c)\
+ CNRS and Cedric Notredame\\n\"; \n if ( $coo\
+r_set)\n{\n print \"REMARK Partial chain: St\
+art $start End $end\\n\";\n}\n if ( $is_nmr)\n{\
+\n print \"REMARK NMR structure: MODEL $mode\
+l\\n\";\n}\n \n if ( $n_atom!=0)\n{\n p\
+rint \"REMARK Contains Coordinates of: \";\n \
+ foreach $a (@atom){print \"$a \";}\n print \
+\"\\n\";\n} \n}\n\n\n\n\nmy $residue_index = -999\
+;\nmy $old_c = \"TemporaryChain\";\n\nwhile (<$INF\
+ILE>) \n{\n $line=$_;\n\n\n if ($line =~ /^SEQRES/\
+)\n{\n\n @field=/(\\S*)\\s*/g;\n\n $c= substr($_\
+,11,1);\n\n \n $l=$#field;\n for ($a=4; $a<$#fi\
+eld ;)\n{\n if (!$onelett{$molecule_type{$c}}->{\
+$field[$a]})\n{\n splice @field, $a, 1;\n}\n \
+else \n{\n $a++;\n}\n}\n \n if ( $c ne $in_cha\
+in)\n{\n $pdb_chain_list[$n_pdb_chains]=$c;\n \
+$pdb_chain_len [$n_pdb_chains]=$len;\n $in_chain\
+=$c;\n $n_pdb_chains++;\n}\n \n for ( $a=4; $a<\
+$#field;$a++)\n{\n $complete_seq{$c}[$complete_s\
+eq_len{$c}++]=$field[$a];\n}\n}\n elsif ( $line\
+=~/^ATOM/ || ($line=~/^HETATM/ && &is_aa(substr($l\
+ine,17,3),substr($line,21,1)) && !$no_hetatm))\n{\\
+n\n \n $RAW_AT_ID=$AT_ID=substr($line,12,4);\n\
+ $RES_ID=&is_aa(substr($line,17,3),substr($line,21\
+,1));\n $CHAIN=substr($line,21,1);\n\n $RES_NO=\
+substr($line,22,4);\n $HOM_CODE=substr ($line, 26,\
+ 1);\n $TEMP=substr($line,60,6);\n \n $TEMP=~s/\\s\
+//g;\n $AT_ID=~s/\\s//g;\n $RES_ID=~s/\\s//\
+g;\n $RES_NO=~s/\\s//g;\n \n if ( $HOM_COD\
+E ne $MAIN_HOM_CODE){next;}\n elsif ( $already_rea\
+d2{$CHAIN}{$RES_ID}{$AT_ID}{$RES_NO}){next;}\n els\
+e{$already_read2{$CHAIN}{$RES_ID}{$AT_ID}{$RES_NO}\
+=1;}\n \n \n if ($coor_set && $numbering eq \"file\
+\" && $residue_index ne $RES_NO)\n{\n \n i\
+f ( $RES_NO<=$start){$real_start{$CHAIN}++;}\n \
+ if ( $RES_NO<=$end){$real_end{$CHAIN}++;}\n}\n el\
+sif ($numbering eq \"absolute\")\n{\n $real_st\
+art{$CHAIN}=$start;\n $real_end{$CHAIN}=$end;\\
+n}\n\n $KEY=\"ALL\";\n if ( $CHAIN n\
+e $in_atom_chain)\n{\n \n $pdb_atom_chain_li\
+st[$n_pdb_atom_chains]=$c;\n $pdb_atom_chain_len\
+ [$n_pdb_atom_chains]=$len;\n $in_atom_chain=$c;\
+\n $n_pdb_atom_chains++;\n}\n \n if ( $residue_i\
+ndex ne $RES_NO)\n{\n $residue_index = $RES_N\
+O;\n $atom_seq{$CHAIN}[$atom_seq_len{$CHAIN}+\
++]=$RES_ID;;\n}\n}\n\n}\nclose ($INFILE);\n\n\n\n\\
+n\n\n$INFILE=vfopen ($structure_file, \"r\");\nfor\
+each $c (@c_chain)\n{\n\n if ( $seq_field eq \"\
+SEQRES\"){@pdb_seq=@{$complete_seq{$c}};}\n elsif \
+( $seq_field eq \"ATOM\") {@pdb_seq=@{$atom_seq{$\
+c}};}\n \n\n $full_length=$l=$#pdb_seq+1;\n \n if\
+ ( $real_end{$c}==\"*\"){$real_end{$c}=$full_lengt\
+h;}\n if ( $coor_set)\n{ \n\n if ( $real_end\
+{$c} < $l){splice @pdb_seq, $real_end{$c}, $l;}\n \
+ if ( $real_start{$c} < $l){splice @pdb_seq, 0, \
+$real_start{$c}-1;} \n $l=$#pdb_seq;\n}\n\
+\n elsif ( $delete_set)\n{\n splice @pdb_seq, $\
+delete_start, $delete_end-$delete_start+1;\n $l\
+=$#pdb_seq;\n}\n \n $new_fasta_name=\"$pdb_id$c\";\
+\n if ( $coor_set)\n{\n if ( $n_pdb_chains==0){\
+$new_fasta_name=\"$new_fasta_name$c\";}\n $new_\
+fasta_name= $new_fasta_name.\"\\_$start\\_$end\";\\
+n}\n \n if ( $MODE eq \"pdb\")\n{\n $nl=1;\n\
+ $n=0;\n \n foreach $res ( @pdb_seq)\n {\
+\n if ( !$n)\n {\n \n printf \"SEQRES %3d %1s\
+ %4d \", $nl,$c, $l;\n $nl++;\n }\n $res=~\
+s/\\s//g;\n \n if ($code==1){ printf \"%\
+3s \",$onelett{$molecule_type{$c}}->{$res};}\n \
+ elsif ($code==3){ printf \"%3s \",$res};\n \
+ \n $n++; \n if ( $n==13){$n=0;print \
+\"\\n\";}\n}\n if ( $n!=0){print \"\\n\"; $n=0;}\
+\n}\n elsif ( $MODE eq \"simple\")\n{\n print \"\
+# SIMPLE_PDB_FORMAT\\n\";\n if ( $new_fasta_name\
+ eq \" \"){$new_fasta_name=\"dummy_name\";}\n pr\
+int \">$new_fasta_name\\n\";\n\n foreach $res ( \
+@pdb_seq)\n{\n print \"$onelett{$molecule_ty\
+pe{$c}}->{$res}\";\n}\n print \"\\n\";\n}\n elsi\
+f ( $MODE eq \"fasta\")\n{\n $n=0;\n print \">\
+$new_fasta_name\\n\";\n \n foreach $res ( @pdb\
+_seq)\n{\n\n print \"$onelett{$molecule_type\
+{$c}}->{$res}\";\n $n++;\n if (\
+ $n==60){print \"\\n\"; $n=0;}\n}\n print \"\\n\\
+"; \n}\n}\n\nif ( $MODE eq \"fasta\")\n{\n &my\
+exit($EXIT_SUCCESS);\n \n}\n\n \n $charcount=0;\
+\n $inchain=\"BEGIN\";\n $n=0;\n while (<$INFIL\
+E>) \n{\n $line=$_;\n \n if ($line =~/^A\
+TOM/ || ($line=~/^HETATM/))\n{\n $line_header=\"\
+UNKNWN\";\n $RES_ID=substr($line,17,3);\n $chain =\
+ substr($line,21,1);\n\n if ($line =~/^ATOM/)\n{\n\
+ $line_header=\"ATOM\";\n $RES_ID=(&is_aa(\
+$RES_ID,$chain))?&is_aa($RES_ID,$chain):$RES_ID;\n\
+}\n elsif ($line=~/^HETATM/ && ($ligand_list {$RES\
+_ID} ||$ligand_list {'ALL'} || !&is_aa($RES_ID,$ch\
+ain)))\n{\n $line_header=\"HETATM\";\n}\n elsi\
+f ($line=~/^HETATM/ && (&is_aa($RES_ID,$chain) && \
+!$no_hetatm))\n{\n $line_header=\"ATOM\";\n \
+ $RES_ID=&is_aa($RES_ID,$chain);\n}\n else\n{\n \
+ next;\n}\n\n \n\n $X=substr($line,30,8); \n\
+ $Y=substr($line,38,8);\n $Z=substr($line,46,8);\n\
+ $TEMP=substr($line,60,6);\n \n $RAW_AT_ID=$AT_ID=\
+substr($line,12,4);\n $CHAIN=substr($line,21,1);\n\
+ $RES_NO=substr($line,22,4);\n $HOM_CODE=substr ($\
+line, 26, 1);\n \n $X=~s/\\s//g;\n $Y=~s/\\s//g;\n\
+ $Z=~s/\\s//g;\n $TEMP=~s/\\s//g;\n \n $AT_ID=~s/\\
+\s//g;\n $RES_ID=~s/\\s//g;\n $RES_NO=~s/\\s//g;\n\
+\n \n if ( $HOM_CODE ne $MAIN_HOM_CODE){next;}\n e\
+lsif ( $already_read{$CHAIN}{$RES_ID}{$AT_ID}{$RES\
+_NO}){next;}\n else{$already_read{$CHAIN}{$RES_ID}\
+{$AT_ID}{$RES_NO}=1;}\n \n $KEY=\"ALL\";\n\n \
+ if ( $RES_NO ==0){$start_at_zero=1;}\n\n $RES_NO+\
+=$start_at_zero; \n \n if ( $current_chain ne $\
+CHAIN)\n{\n $current_chain=$CHAIN;\n $pos=\
+$current_residue=0;\n $offset=($coor_set)?($re\
+al_start{$CHAIN}-1):0;\n if ( $seq_field eq\
+ \"SEQRES\"){@ref_seq=@{$complete_seq{$CHAIN}};}\n\
+ elsif ( $seq_field eq \"ATOM\") {@ref_seq=@{\
+$atom_seq{$CHAIN}};}\n}\n \n if ($current_residue \
+!= $RES_NO)\n{\n $current_residue=$RES_NO;\n \
+ if ( $seq_field eq \"SEQRES\"){$pos=$current\
+_residue;}\n elsif ( $seq_field eq \"ATOM\"){$\
+pos++;}\n}\n \n \n if ($n_atom==0 || $atom_list{$A\
+T_ID}==1 || $atom_list{$KEY}==1)\n{ \n \n \
+ $do_it=(!@c_chain || $hc_chain{$CHAIN} ||$hc_chai\
+n{'LIGAND'} );\n \n $do_it= ($do_it==1) &&\
+ ($coor_set==0 ||($pos>=$real_start{$CHAIN} && $po\
+s<=$real_end{$CHAIN}));\n $do_it= ($do_it==1) \
+&& ($delete_set==0 || $pos<$delete_start ||$pos>$d\
+elete_end );\n if ($ligand==0 && $line_header \
+eq \"HETATM\" ){$do_it=0;}\n if ($ligand_only=\
+=1 && $line_header eq \"ATOM\" ){$do_it=0;}\n \
+if ($ligand==1 && $line_header eq \"HETATM\" && $l\
+igand_list{$RES_ID}==0 && $ligand_list{\"ALL\"}==0\
+){$do_it=0;} \n \n \n if ( $do_it)\n{\\
+n $n++;\n $out_pos=$pos;\n \n if ( $dele\
+te_set)\n{\n if ( $out_pos< $delete_start){;}\n\
+ else {$offset=$delete_end-$delete_start;}\n} \
+ \n \n if ( $numbering_out eq \"\
+new\"){$out_pos-=$offset;}\n elsif ( $numbe\
+ring_out eq \"old\"){$out_pos=$RES_NO;}\n \\
+n \n \n if ( $code==1){$RES_ID\
+=$onelett{$molecule_type{$c}}->{$RES_ID};}\n \\
+n if ($unfold)\n{\n $unfolded_x+=5;\n \
+ $X=$unfolded_x;\n $Y=0;\n $Z=0;\n $\
+float=1;\n}\n else\n{\n $float=3;\n}\n\\
+n if ( $MODE eq \"pdb\")\n{\n printf \"\
+%-6s%5d %-4s %3s %s%4d %8.3f%8.3f%8.3f 1.00 %5\
+.2f\\n\",$line_header, $n, $RAW_AT_ID,$RES_ID,$CHA\
+IN,$out_pos, $X, $Y, $Z,$TEMP; \n}\n els\
+if ( $MODE eq \"simple\")\n{\n if ( $RES_ID e\
+q \"\"){$RES_ID=\"X\";}\n printf \"%-6s %5s %s \
+%2s %4d %8.3f %8.3f %8.3f\\n\",$line_header, $A\
+T_ID, $RES_ID,($CHAIN eq\"\" || $CHAIN eq \" \")?\\
+"A\":$CHAIN,$out_pos, $X, $Y, $Z,$TEMP;\n}\n\n}\n}\
+\n}\n}\nprint \"\\n\";\nclose($INFILE);\n\n\nif ( \
+$error ne \"\") \n{$error=$error.\"\\nDiagnostic: \
+ SEQRES and the residues in ATOM are probably In\
+compatible\\n\";\n $error=$error. \"Recomendat\
+ion: Rerun with '-fix 1' in order to ignore the SE\
+QRES sequences\\n\";\n}\nif (!$nodiagnostic){print\
+ STDERR $error;}\n&myexit ( $EXIT_SUCCESS);\n\nsub\
+ is_released \n {\n my ($r);\n my $in=@_[0]\
+;\n my $name=&remote_is_pdb_name ($in);\n my\
+ $hold=&remote_is_on_hold($in);\n \n $r=($na\
+me && !$hold)?1:0;\n return $r;\n }\nsub remot\
+e_is_pdb_name \n{\n my $in=@_[0];\n my ($ref\
+_file, $pdb);\n my ($value,$value1,$value2);\n \
+ my $max=2;\n \n $ref_file=\"$cache/pdb_en\
+try_type.txt\";\n \n if ( $in=~/[^\\w\\d\\:\\
+\_]/){return 0;}\n elsif ($no_remote_pdb_dir==1\
+)\n {\n my $pdbdir=$ENV{'PDB_DIR'};\n \n my $\
+r1=\"$pdbdir/derived_data/pdb_entry_type.txt\";\n \
+my $r2=$ref_file;\n if (-e $r1){$ref_file=$r1;}\
+\n elsif (-e $r2){$ref_file=$r2;}\n else\n {\n \
+ my $p=substr ($in,0, 4);\n add_warning (\"C\
+annot find pdb_entry_type.txt; $p is assumed to b\
+e valid; add ftp://ftp.wwpdb.org/pub/pdb/derived_d\
+ata/pdb_entry_type.txt in $cache to check name sta\
+tus\");\n }\n }\n elsif ( !-e $ref_file \
+|| (-M $ref_file)>$max || -z $ref_file)\n {\n\
+ &url2file(\"ftp://ftp.wwpdb.org/pub/pdb/derived_d\
+ata/pdb_entry_type.txt\", $ref_file);\n }\n \
+ $pdb=substr ($in,0, 4);\n chomp(($value1=`gre\
+p -c $pdb $ref_file`));\n $pdb=lc($pdb);\n c\
+homp(($value2=`grep -c $pdb $ref_file`));\n $va\
+lue=($value1 || $value2)?1:0;\n $value=($value>\
+0)?1:0;\n \n return $value;\n }\n\nsub pdb2\
+model_type\n{\n my $in=@_[0];\n my ($ref_fil\
+e, $pdb);\n my ($value, $ret);\n\n if ( $in=\
+~/[^\\w\\d\\:\\_]/){return 0;}\n $ref_file=\"$c\
+ache/pdb_entry_type.txt\";\n \n if ( !-e $re\
+f_file || (-M $ref_file)>2 || -z $ref_file)\n \
+ {\n &url2file(\"ftp://ftp.wwpdb.org/pub/pdb/deriv\
+ed_data/pdb_entry_type.txt\", $ref_file);\n }\
+\n $pdb=substr ($in,0, 4);\n $pdb=lc($pdb);\\
+n \n chomp(($value=`grep $pdb $ref_file`));\\
+n \n $value=~/^\\S+\\s+\\S+\\s+(\\S+)/;\n \
+ $ret=$1;\n if ( $ret eq\"\"){return \"UNKNOWN\\
+";}\n \n return $ret;\n }\nsub remote_is_on\
+_hold\n {\n my $in=@_[0];\n my ($ref_file, \
+$pdb);\n my ($value1, $value2,$value);\n \n \
+ if ($no_rmote_pdb==1){return 0;}\n elsif ( $\
+in=~/[^\\w\\d\\:\\_]/){return 0;}\n $ref_file=\\
+"$cache/unreleased.xml\";\n \n if ( !-e $ref\
+_file || (-M $ref_file)>2 || -z $ref_file)\n \
+{\n &url2file(\"http://www.rcsb.org/pdb/rest/getUn\
+released\",$ref_file);\n }\n \n $pdb=su\
+bstr ($in,0, 4);\n chomp(($value1=`grep -c $pdb\
+ $ref_file`));\n $pdb=lc($pdb);\n chomp(($va\
+lue2=`grep -c $pdb $ref_file`));\n $value=($val\
+ue1 || $value2)?1:0;\n $value=($value>0)?1:0;\n\
+ return $value;\n }\nsub is_pdb_file\n{\n m\
+y @arg=@_;\n\n if ( !-e $arg[0]){return 0;}\n \
+ \n $F=vfopen ($arg[0], \"r\");\n while ( <\
+$F>)\n{\n if (/^HEADER/)\n{\n close $F;\n \
+return 1;\n}\n elsif ( /^SEQRES/)\n{\n close $\
+F;\n return 1;\n}\n elsif ( /^ATOM/)\n{\n \
+close $F;\n return 1;\n}\n}\n return 0;\n}\\
+nsub get_pdb_id\n{\n my $header_file=@_[0];\n \
+ my $id;\n my $F= new FileHandle;\n \n \\
+n $F=vfopen (\"$header_file\", \"r\");\n\n w\
+hile ( <$F>)\n {\n if ( /HEADER/)\n {\n \
+ if ($debug){print \"$_\";}\n $id=substr($_,62\
+,4 );\n return $id;\n }\n }\n close \
+($F);\n \n return \"\";\n}\n\nsub get_ligand\
+_list\n{\n my $pdb_file=@_[0];\n my $chain;\\
+n my $ligand;\n my %complete_ligand_list;\n \
+ \n\n $F=vfopen ($pdb_file, \"r\");\n whil\
+e ( <$F>)\n{\n if ( /^HETATM/)\n{\n $line=$_;\\
+n $chain=substr($line,21,1);\n $ligand=sub\
+str($line,17,3);\n \n if (!$complete_ligan\
+d_list{$chain}{$ligand})\n{\n \n $complete_ligan\
+d_list{\"result\"}.=\"CHAIN $chain LIGAND $ligand\\
+\n\";\n $complete_ligand_list{$chain}{$ligand}=1;\
+\n}\n}\n}\n close ($F);\n return %complete_l\
+igand_list;\n}\n\nsub get_chain_list \n{\n my $\
+header_file;\n my @chain_list;\n my @list;\n\
+ my $n_chains;\n my %chain_hasch;\n my $p\
+db_file=@_[0];\n my $c;\n my %hasch;\n my\
+ $chain;\n \n \n $F=vfopen ($pdb_file, \"r\\
+");\n while ( <$F>)\n{\n\n\n if (/SEQRES\\s+\\d\
++\\s+(\\S+)/)\n {\n $chain = substr($_,11,1)\
+;$chain=~s/\\s//g;if ( $chain eq \"\"){$chain=\" \\
+";}\n if (!$hasch{$chain}){$hasch{$chain}=1;pu\
+sh @chain_list, $chain;}\n }\n if (/^ATOM/ || /^\
+HETATM/)\n {\n $chain = substr($_,21,1); $ch\
+ain=~s/\\s//g;if ( $chain eq \"\"){$chain=\" \";}\\
+n if (!$hasch{$chain}){$hasch{$chain}=1;push @\
+chain_list, $chain;}\n }\n }\n\n\nclose ($F\
+);\nif (!@chain_list)\n {\n @chain_list=(\"A\"\
+);\n }\n\n\nreturn @chain_list;\n}\n\nsub token_i\
+s_in_list\n{\n\n my @list=@_;\n my $a;\n \
+\n for ($a=1; $a<=$#list; $a++)\n{\n if ( $list\
+[$a] eq $list[0]){return $a;}\n}\n}\n\nsub pdb_nam\
+e2name_and_chain \n{\n my $pdb_file=@_[0];\n \
+ my $pdb_file_in;\n my @array;\n my $chain;\\
+n my $c;\n\n $pdb_file_in=$pdb_file;\n\n \
+$pdb_file=~/^(.{4})/;$pdb_id=$1;\n @array=($pdb\
+_file=~/([\\w])/g);\n \n \n $chain=uc ($array\
+[4]);\n $chain=($chain eq \"\")?\"FIRST\":$chai\
+n;\n \n return ( $pdb_id, $chain);\n\n if\
+ ( $#array==3){return ($pdb_id, \"FIRST\");}\n \
+elsif ( $#array<4){ return ($pdb_id, \"\");}\n \
+else {return ( $pdb_id, $chain);}\n \n \n \
+ \n}\nsub get_main_hom_code \n{\n my $pdb_fil\
+e=@_[0];\n my %hom, $n, $best, $best_h;\n op\
+en (F, $pdb_file);\n while (<F>)\n{\n if ( $_=~\
+/^ATOM/)\n{\n $h=substr ($_,26, 1);\n $n=+\
++$hom{$h};\n if ($n>$best)\n{\n $best=$n;\n \
+$best_h=$h;\n}\n}\n}\n close (F);\n return $\
+best_h;\n}\n\n\nsub get_pdb_file \n{\n my ($pdb\
+_file_in)=(@_);\n my $result;\n my @letter;\\
+n my @chain;\n my $v;\n my $pdb_file=$pdb\
+_file_in;\n\n $pdb_file=($pdb_file_in=~/\\S+_S_\
+(\\S+)/)?$1:$pdb_file_in;\n \n if ($no_remot\
+e_pdb_dir==0)\n {\n $no_remote_pdb_dir=1;\n $\
+result=get_pdb_file3 ($pdb_file);\n $no_remote_pdb\
+_dir=0;\n if ( $result){return $result;}\n else\n \
+ {\n \n lc ($pdb_file);\n $result=get\
+_pdb_file3($pdb_file);\n return $result;\n \
+}\n }\n else\n {\n return get_pdb_fil\
+e3 ($pdb_file);\n }\n \n }\n\nsub get_pdb\
+_file3 \n{\n my $pdb_file_in=@_[0];\n my $re\
+sult;\n my @letter;\n my @chain;\n my $lc\
+file;\n my $ucfile;\n my $pdb_file=$pdb_file\
+_in;\n \n $lcfile=lc $pdb_file;\n $ucfile\
+=uc $pdb_file;\n\n if ( ($result=get_pdb_file2 \
+($pdb_file))){return $result;}\n \n\n if ($l\
+cfile ne $pdb_file && ($result=get_pdb_file2 ($lcf\
+ile))){return $result;}\n if ($ucfile ne $pdb_f\
+ile && ($result=get_pdb_file2 ($ucfile))){return $\
+result;}\n \n \n \n return \"\";\n}\nsu\
+b get_pdb_file2\n{\n my $pdb_file=@_[0];\n m\
+y $return_value;\n \n $return_value=\"\";\n \
+ \n if ( ($result=get_pdb_file1 ($pdb_file)))\
+{$return_value=$result;}\n elsif ( !($pdb_file=\
+~/\\.pdb/) && !($pdb_file=~/\\.PDB/))\n{\n if ( ($\
+result=get_pdb_file1 (\"$pdb_file.pdb\"))){$return\
+_value=$result;}\n elsif ( ($result=get_pdb_file1 \
+(\"$pdb_file.PDB\"))){$return_value=$result;}\n\n \
+elsif ( ($result=get_pdb_file1 (\"pdb$pdb_file.pdb\
+\"))){$return_value=$result;} \n elsif ( ($result=\
+get_pdb_file1 (\"pdb$pdb_file.PDB\"))){$return_val\
+ue=$result;}\n elsif ( ($result=get_pdb_file1 (\"P\
+DB$pdb_file.PDB\"))){$return_value=$result;}\n els\
+if ( ($result=get_pdb_file1 (\"PDB$pdb_file.pdb\")\
+)){$return_value=$result;}\n \n \n elsif ( ($resul\
+t=get_pdb_file1 (\"$pdb_file.ent\"))){$return_valu\
+e=$result;}\n elsif ( ($result=get_pdb_file1 (\"pd\
+b$pdb_file.ent\"))){$return_value=$result;}\n elsi\
+f ( ($result=get_pdb_file1 (\"PDB$pdb_file.ent\"))\
){$return_value=$result;}\n\n elsif ( ($result=get\
-_pdb_file1 (\"pdb$pdb_file.pdb\"))){$return_value=\
-$result;} \n elsif ( ($result=get_pdb_file1 (\"pdb\
-$pdb_file.PDB\"))){$return_value=$result;}\n elsif\
- ( ($result=get_pdb_file1 (\"PDB$pdb_file.PDB\")))\
-{$return_value=$result;}\n elsif ( ($result=get_pd\
-b_file1 (\"PDB$pdb_file.pdb\"))){$return_value=$re\
-sult;}\n \n \n elsif ( ($result=get_pdb_file1 (\"$\
-pdb_file.ent\"))){$return_value=$result;}\n elsif \
-( ($result=get_pdb_file1 (\"pdb$pdb_file.ent\"))){\
-$return_value=$result;}\n elsif ( ($result=get_pdb\
-_file1 (\"PDB$pdb_file.ent\"))){$return_value=$res\
-ult;}\n\n elsif ( ($result=get_pdb_file1 (\"$pdb_f\
-ile.ENT\"))){$return_value=$result;}\n elsif ( ($r\
-esult=get_pdb_file1 (\"pdb$pdb_file.ENT\"))){$retu\
-rn_value=$result;}\n elsif ( ($result=get_pdb_file\
-1 (\"PDB$pdb_file.ENT\"))){$return_value=$result;}\
-\n \n \n \n}\n return $return_value;\n}\n \n\
-sub get_pdb_file1\n{\n my ($pdb_file)=(@_);\n \
- my $return_value;\n \n\n $return_value=\"\\
-";\n if ( ($result=get_pdb_file0 ($pdb_file))){\
+_pdb_file1 (\"$pdb_file.ENT\"))){$return_value=$re\
+sult;}\n elsif ( ($result=get_pdb_file1 (\"pdb$pdb\
+_file.ENT\"))){$return_value=$result;}\n elsif ( (\
+$result=get_pdb_file1 (\"PDB$pdb_file.ENT\"))){$re\
+turn_value=$result;}\n \n \n \n}\n return $retu\
+rn_value;\n}\n \nsub get_pdb_file1\n{\n my (\
+$pdb_file)=(@_);\n my $return_value;\n \n\n \
+ $return_value=\"\";\n if ( ($result=get_pdb_\
+file0 ($pdb_file))){$return_value=$result;}\n e\
+lsif ( ($result=get_pdb_file0 (\"$pdb_file.Z\"))){\
$return_value=$result;}\n elsif ( ($result=get_\
-pdb_file0 (\"$pdb_file.Z\"))){$return_value=$resul\
-t;}\n elsif ( ($result=get_pdb_file0 (\"$pdb_fi\
-le.gz\"))){$return_value=$result;}\n elsif ( ($\
-result=get_pdb_file0 (\"$pdb_file.GZ\"))){$return_\
-value=$result;}\n return $return_value;\n}\nsub\
- get_pdb_file0 \n{ \n my ($pdb_file, $attempt)=\
-(@_);\n my $pdb_file=@_[0];\n my $tmp_pdb_fi\
-le; \n my $return_value;\n\n if ( !$attem\
-pt){$attempt=1;}\n \n $local_pdb_file=\"$pdb\
-_file\";\n if ( $local_pdb_file eq \"\")\n{\n $\
-tmp_pdb_file=vtmpnam();\n open F, \">$tmp_pdb_file\
-\";\n \n while (<STDIN>){print F \"$_\";}\n close \
-(F);\n \n if (-e $tmp_pdb_file && &is_pdb_file ( $\
-local_pdb_file))\n{return $tmp_pdb_file;}\n}\n\n \
- $local_pdb_file=\"$pdb_file\";\n &debug_print\
- (\"\\nTry access local file: $local_pdb_file\");\\
-n \n $local_pdb_file=&check_pdb_file4compres\
-sion ($local_pdb_file);\n if ( -e $local_pdb_fi\
-le && (&is_pdb_file ($local_pdb_file) || $force_pd\
-b))\n{\n &debug_print ( \"\\n\\tIs in Current Dir\\
-");\n $tmp_pdb_file=vtmpnam();\n `cp $local_pdb_fi\
-le $tmp_pdb_file`;\n return $tmp_pdb_file;\n}\n \
- else\n{\n &debug_print (\"\\n\\tFile Not in Curre\
-nt Dir\");\n}\n\n if ($pdb_file=~/^pdb/||$pdb_f\
-ile=~/^PDB/){$pdb_div=substr ($pdb_file, 4, 2);}\n\
- else\n{\n $pdb_div=substr ($pdb_file, 1, 2);\
-\n}\n $local_pdb_file=\"$pdb_dir/$pdb_div/$pdb_\
-file\";\n $local_pdb_file=&check_pdb_file4compr\
-ession ( $local_pdb_file);\n &debug_print (\"\\\
-nTry access file From PDB_DIR: $local_pdb_file\");\
-\n if ($pdb_dir && -e $local_pdb_file && &is_pd\
-b_file ($local_pdb_file))\n{\n &debug_print ( \"\\\
-n\\tIs in Local PDB DIR\");\n $tmp_pdb_file=vtmpna\
-m();\n `cp $local_pdb_file $tmp_pdb_file`;\n retur\
-n $tmp_pdb_file;\n}\n\n $local_pdb_file=\"$pdb_\
-dir/$pdb_file\";\n $local_pdb_file=&check_pdb_f\
-ile4compression ( $local_pdb_file);\n &debug_pr\
-int (\"\\nTry access file From PDB_DIR: local_pdb_\
-file\");\n if ($pdb_dir && -e $local_pdb_file &\
-& &is_pdb_file ($local_pdb_file))\n{\n &debug_prin\
-t ( \"\\n\\tIs in Local PDB DIR\");\n $tmp_pdb_fil\
-e=vtmpnam();\n `cp $local_pdb_file $tmp_pdb_file`;\
-\n return $tmp_pdb_file;\n}\n\n $local_pdb_file\
-=\"$pdb_dir$pdb_file\";\n $local_pdb_file=&chec\
-k_pdb_file4compression ( $local_pdb_file);\n &d\
-ebug_print (\"\\nTry access file From PDB_DIR: $lo\
-cal_pdb_file\");\n if ($pdb_dir && -e $local_pd\
-b_file && &is_pdb_file ($local_pdb_file))\n{\n &de\
-bug_print ( \"\\n\\tIs in Local PDB DIR\");\n $tmp\
-_pdb_file=vtmpnam();\n `cp $local_pdb_file $tmp_pd\
-b_file`;\n return $tmp_pdb_file;\n}\n else\n{&d\
-ebug_print ( \"\\n\\tNot In Local Pdb Dir\");}\n\n\
- if ($cache ne \"NO\" && $cache ne \"no\")\n{\n\
-\n $local_pdb_file=\"$cache/$pdb_file\";\n $local_\
-pdb_file=&check_pdb_file4compression ( $local_pdb_\
-file);\n &debug_print(\"\\nTry access file From Ca\
-che: $local_pdb_file\");\n if (-e $local_pdb_file \
-&& &is_pdb_file ($local_pdb_file))\n{\n &debug\
-_print ( \"\\n\\tIs in T-Coffee Cache\");\n $t\
-mp_pdb_file=vtmpnam();\n `cp $local_pdb_file $\
-tmp_pdb_file`;\n return $tmp_pdb_file;\n}\n el\
-se{&debug_print ( \"\\n\\tNot in Cache Dir\");}\n}\
-\n\nif (!$no_remote_pdb_dir) \n {\n my $value=\
-&is_released ($pdb_file);\n my $return_value=\"\
-\";\n if ($value==1)\n {\n \n &debug_print\
- (\"\\n*******************************************\
-**********\\nTry Remote Access for $pdb_file\");\n\
- $tmp_pdb_file=vtmpnam();\n $netcommand=$netaddres\
-s;\n $netcommand=~s/%%/$pdb_file/g;\n &url2file(\"\
-$netcommand\", \"$tmp_pdb_file.$netcompression\");\
-\n &debug_print(\"\\nREMOTE: $netcommand\\n\");\n \
-\n $compressed_tmp_file_name=\"$tmp_pdb_file.$netc\
-ompression\";\n \n if ($netcompression && -B $comp\
-ressed_tmp_file_name)\n {\n my $r;\n &de\
-bug_print (\"\\n\\tFile Found Remotely\");\n i\
-f (($r=safe_system ( \"$netcompression_pg $compres\
-sed_tmp_file_name\")!=$EXIT_SUCCESS) && $attempts<\
-5)\n {\n &debug_print (\"\\n\\tProper Downl\
-oad Failed Try again\");\n unlink $compressed_tmp\
-_file_name;\n print \"\\nFailed to Download $comp\
-ressed_tmp_file_name. New Attempt $attempt/5\\n\";\
-\n return &get_pdb_file0($pdb_file, $attempt+1);\\
-n }\n elsif ($r== $EXIT_SUCCESS)\n \
- {\n &debug_print (\"\\n\\tProper Download Succee\
-ded \");\n $return_value=$tmp_pdb_file;\n }\
-\n else\n {\n &debug_print (\"\\n\\tPro\
-per Download Failed \");\n &debug_print (\"\\nFil\
-e Not Found Remotely\");\n unlink $compressed_tmp\
-_file_name;\n }\n }\n else\n {\n\n &\
-debug_print (\"\\nFile Not Found Remotely\");\n \
- unlink $compressed_tmp_file_name;\n }\n #Updat\
-e cache if required\n if ($cache ne \"no\" && $cac\
-he ne \"update\" && -e $return_value)\n {\n \
-`cp $return_value $cache/$pdb_file.pdb`;\n #`t\
-_coffee -other_pg clean_cache.pl -file $pdb_file.p\
-db -dir $cache`;\n }\n }\n &debug_print \
-(\"\\nRemote Download Finished\");\n return $re\
-turn_value;\n }\nreturn \"\";\n}\n\nsub check_pdb\
-_file4compression \n{\n my $file=@_[0];\n my\
- $tmp;\n my $r;\n \n $tmp=&vtmpnam();\n \
- if (-e $tmp){unlink $tmp;}\n \n $file=~s/\\
-\/\\//\\//g;\n if (-B $file && ($file=~/\\.Z\
-/)) {`cp $file $tmp.Z`;`rm $tmp`;`gunzip $tmp.Z $S\
-ILENT`;$r=$tmp;}\n elsif (-B $file && ($file=~/\
-\\.gz/)){`cp $file $tmp.gz`;`gunzip $tmp.gz $SILEN\
-T`;return $r=$tmp;}\n elsif (-B $file ){`cp $fi\
-le $tmp.gz`;`gunzip $tmp.gz $SILENT`;$r=$tmp;}\n \
- elsif ( -e $file ) {$r= $file;}\n elsif ( -e \
-\"$file.gz\" ){ `cp $file.gz $tmp.gz`;`gunzip \
-$tmp.gz $SILENT`;$r=$tmp;} \n elsif ( -e \"$\
-file.Z\") {`cp $file.Z $tmp.Z`; `gunzip $tmp.Z $S\
-ILENT`;$r=$tmp;}\n else {$r= $file;}\n\n if\
- ( -e \"$tmp.Z\"){unlink \"$tmp.Z\";}\n if ( -e\
- \"$tmp.gz\"){unlink \"$tmp.gz\";}\n \n retu\
-rn $r;\n \n}\n\n\n\n\n\n \n\n\n\n\n\n\n\nsub\
- vfopen \n{\n my $file=@_[0];\n my $mode=@_[\
-1];\n my $tmp;\n my $F = new FileHandle;\n \
- \n \n $tmp=$file;\n \n \n if ( $mode\
- eq \"r\" && !-e $file){ myexit(flush_error (\"Can\
-not open file $file\"));}\n elsif ($mode eq \"w\
-\"){$tmp=\">$file\";}\n elsif ($mode eq \"a\"){\
-$tmp=\">>$file\";}\n \n \n open ($F,$tmp)\
-;\n return $F;\n}\nsub debug_print\n{\n my $\
-message =@_[0];\n if ($debug){print STDERR \"NO\
-_REMOTE_PDB_DIR: $no_remote_pdb_dir - $message [DE\
-BUG:extract_from_pdb]\";}\n return;\n}\nsub is_\
-aa \n{\n my ($aa, $chain) =@_;\n\n my $one;\\
-n my $trhee;\n \n if ( $onelett{$molecule\
-_type{$chain}}->{$aa} eq 'X' || !$onelett{$molecul\
-e_type{$chain}}->{$aa} ){return '';}\n else\n \
- {\n $one=$onelett{$molecule_type{$chain}}->{$a\
-a};\n\n $three=$threelett{$molecule_type{$chain}}-\
->{$one};\n \n\n return $three;\n }\n }\n\n\n\
-\n\n\nsub url2file\n{\n my ($address, $out, $wg\
-et_arg, $curl_arg)=(@_);\n my ($pg, $flag, $r, \
-$arg, $count);\n \n if (!$CONFIGURATION){&ch\
-eck_configuration (\"wget\", \"INTERNET\", \"gzip\\
-");$CONFIGURATION=1;}\n \n if (&pg_is_instal\
-led (\"wget\")) {$pg=\"wget\"; $flag=\"-O\";$arg\
-=$wget_arg;}\n elsif (&pg_is_installed (\"curl\\
-")){$pg=\"curl\"; $flag=\"-o\";$arg=$curl_arg;}\n \
- return safe_system (\"$pg $flag$out $address >/\
-dev/null 2>/dev/null\");\n\n}\n\n\n\n\nsub pdbfile\
-2chaintype\n {\n my $file=@_[0];\n my %ct;\\
-n my $F;\n \n $F=vfopen ($file, \"r\");\n\
- while (<$F>)\n {\n my $line=$_;\n if ($li\
-ne =~/^ATOM/)\n {\n my $C=substr($line,21,1)\
-;\n if (!$ct{$C})\n { \n my $r=substr($\
-line,17,3);\n $r=~s/\\s+//;\n if (length ($r)==1\
-){$ct{$C}=\"R\";}\n elsif (length ($r)==2){$ct{$C\
-}=\"D\";}\n elsif (length ($r)==3){$ct{$C}=\"P\";\
-}\n else \n {\n myexit(flush_error(\"ERRO\
-R: Could not read RES_ID field in file $file\"));\\
-n }\n }\n }\n }\n close ($F);\n\
- return %ct;\n }\n \n \n\n\n\nsub fill_th\
-reelett_RNA\n{\n\n my %threelett=(\n 'A', ' A',\n\
- 'T', ' T',\n 'U', ' U',\n 'C', ' C',\n 'G', ' \
- G',\n 'I', ' I', #Inosine\n );\n \n return %thre\
-elett;\n\n}\n\n\nsub fill_onelett_RNA\n{\n my %o\
-nelett=(\n ' A' => 'A',\n ' T' => 'T',\n ' U' =\
-> 'U',\n ' C' => 'C',\n ' G' => 'G',\n 'CSL' => \
-'X',\n 'UMS' => 'X',\n ' I' => 'I',\n 'A' => 'A',\
-\n 'T' => 'T',\n 'U' => 'U',\n 'C' => 'C',\n 'G' =\
-> 'G',\n 'I' => 'I',\n );\n\n return %onelett;\n\n\
-}\n\n\nsub fill_onelett_DNA\n{\n my %onelett=(\n\
- ' DA', 'A',\n ' DT', 'T',\n ' DC', 'C',\n ' DG', \
-'G',\n 'DA', 'A',\n 'DT', 'T',\n 'DC', 'C',\n 'DG'\
-, 'G',\n );\n\n return %onelett;\n\n}\n\nsub fill_\
-threelett_DNA\n{\n\n my %threelett=(\n 'A', ' DA',\
-\n 'T', ' DT',\n 'C', ' DC',\n 'G', ' DG',\n );\n\\
-n return %threelett;\n\n}\n\n\n\n\nsub fill_threel\
-ett_prot\n{ \n my %threelett;\n\n %threelett=(\\
-n'A', 'ALA',\n'C', 'CYS',\n'D', 'ASP',\n'E', 'GLU'\
-,\n'F', 'PHE',\n'G', 'GLY',\n'H', 'HIS',\n'I', 'IL\
-E',\n'K', 'LYS',\n'L', 'LEU',\n'N', 'ASN',\n'M', '\
-MET',\n'P', 'PRO',\n'Q', 'GLN',\n'R', 'ARG',\n'S',\
- 'SER',\n'T', 'THR',\n'V', 'VAL',\n'W', 'TRP',\n'Y\
-', 'TYR',\n);\n\nreturn %threelett;\n\n\n}\n\nsub \
-fill_onelett_prot\n{\n my %onelett;\n \n \
-%onelett=(\n\n'10A', 'X',\n'11O', 'X',\n'12A', 'X'\
-,\n'13P', 'X',\n'13R', 'X',\n'13S', 'X',\n'14W', '\
-X',\n'15P', 'X',\n'16A', 'X',\n'16G', 'X',\n'1AN',\
- 'X',\n'1AP', 'X',\n'1AR', 'X',\n'1BH', 'X',\n'1BO\
-', 'X',\n'1C5', 'X',\n'1CU', 'X',\n'1DA', 'X',\n'1\
-GL', 'X',\n'1GN', 'X',\n'1IN', 'X',\n'1LU', 'L',\n\
-'1MA', 'X',\n'1MC', 'X',\n'1MG', 'X',\n'1MZ', 'X',\
-\n'1NA', 'X',\n'1NB', 'X',\n'1NI', 'X',\n'1PA', 'A\
-',\n'1PC', 'X',\n'1PE', 'X',\n'1PG', 'X',\n'1PI', \
-'A',\n'1PM', 'X',\n'1PN', 'X',\n'1PU', 'X',\n'1PY'\
-, 'X',\n'1UN', 'X',\n'24T', 'X',\n'25T', 'X',\n'26\
-P', 'X',\n'2AB', 'X',\n'2AM', 'X',\n'2AN', 'X',\n'\
-2AP', 'X',\n'2AR', 'X',\n'2AS', 'D',\n'2BL', 'X',\\
-n'2BM', 'X',\n'2CP', 'X',\n'2DA', 'X',\n'2DG', 'X'\
-,\n'2DP', 'X',\n'2DT', 'X',\n'2EP', 'X',\n'2EZ', '\
-X',\n'2FG', 'X',\n'2FL', 'X',\n'2FP', 'X',\n'2FU',\
- 'X',\n'2GL', 'X',\n'2GP', 'X',\n'2HP', 'X',\n'2IB\
-', 'X',\n'2IP', 'X',\n'2LU', 'L',\n'2MA', 'X',\n'2\
-MD', 'X',\n'2ME', 'X',\n'2MG', 'X',\n'2ML', 'L',\n\
-'2MO', 'X',\n'2MR', 'R',\n'2MU', 'X',\n'2MZ', 'X',\
-\n'2NO', 'X',\n'2NP', 'X',\n'2OG', 'X',\n'2PA', 'X\
-',\n'2PC', 'X',\n'2PE', 'X',\n'2PG', 'X',\n'2PH', \
-'X',\n'2PI', 'X',\n'2PL', 'X',\n'2PP', 'X',\n'2PU'\
-, 'X',\n'2SI', 'X',\n'2TB', 'X',\n'34C', 'X',\n'35\
-G', 'X',\n'3AA', 'X',\n'3AD', 'X',\n'3AH', 'H',\n'\
-3AN', 'X',\n'3AP', 'X',\n'3AT', 'X',\n'3BT', 'X',\\
-n'3CH', 'X',\n'3CN', 'X',\n'3CO', 'X',\n'3CP', 'X'\
-,\n'3DR', 'X',\n'3EP', 'X',\n'3FM', 'X',\n'3GA', '\
-X',\n'3GP', 'X',\n'3HB', 'X',\n'3HC', 'X',\n'3HP',\
- 'X',\n'3IB', 'X',\n'3ID', 'X',\n'3IN', 'X',\n'3MA\
-', 'X',\n'3MB', 'X',\n'3MC', 'X',\n'3MD', 'D',\n'3\
-MF', 'X',\n'3MP', 'X',\n'3MT', 'X',\n'3OL', 'X',\n\
-'3PA', 'X',\n'3PG', 'X',\n'3PO', 'X',\n'3PP', 'X',\
-\n'3PY', 'X',\n'49A', 'X',\n'4AB', 'X',\n'4AM', 'X\
-',\n'4AN', 'X',\n'4AP', 'X',\n'4BA', 'X',\n'4BT', \
-'X',\n'4CA', 'X',\n'4CO', 'X',\n'4HP', 'X',\n'4IP'\
-, 'X',\n'4MO', 'X',\n'4MV', 'X',\n'4MZ', 'X',\n'4N\
-C', 'X',\n'4NP', 'X',\n'4OX', 'X',\n'4PB', 'X',\n'\
-4PN', 'X',\n'4PP', 'X',\n'4SC', 'X',\n'4SU', 'X',\\
-n'4TB', 'X',\n'55C', 'X',\n'5AD', 'X',\n'5AN', 'X'\
-,\n'5AT', 'X',\n'5CM', 'X',\n'5GP', 'X',\n'5HP', '\
-E',\n'5HT', 'X',\n'5IT', 'X',\n'5IU', 'X',\n'5MB',\
- 'X',\n'5MC', 'X',\n'5MD', 'X',\n'5MP', 'X',\n'5MU\
-', 'X',\n'5NC', 'X',\n'5OB', 'X',\n'5PA', 'X',\n'5\
-PV', 'X',\n'6AB', 'X',\n'6CT', 'X',\n'6HA', 'X',\n\
-'6HC', 'X',\n'6HG', 'X',\n'6HT', 'X',\n'6IN', 'X',\
-\n'6MO', 'X',\n'6MP', 'X',\n'6PG', 'X',\n'6WO', 'X\
-',\n'70U', 'X',\n'7DG', 'X',\n'7HP', 'X',\n'7I2', \
-'X',\n'7MG', 'X',\n'7MQ', 'X',\n'7NI', 'X',\n'87Y'\
-, 'X',\n'8AD', 'X',\n'8BR', 'X',\n'8IG', 'X',\n'8I\
-N', 'X',\n'8OG', 'X',\n'95A', 'X',\n'9AD', 'X',\n'\
-9AM', 'X',\n'9AP', 'X',\n'9DG', 'X',\n'9DI', 'X',\\
-n'9HX', 'X',\n'9OH', 'X',\n'9TA', 'X',\n'A12', 'X'\
-,\n'A15', 'X',\n'A23', 'X',\n'A24', 'X',\n'A26', '\
-X',\n'A2G', 'X',\n'A2P', 'X',\n'A32', 'X',\n'A3P',\
- 'X',\n'A4P', 'X',\n'A5P', 'X',\n'A70', 'X',\n'A76\
-', 'X',\n'A77', 'X',\n'A78', 'X',\n'A79', 'X',\n'A\
-80', 'X',\n'A85', 'X',\n'A88', 'X',\n'A9A', 'X',\n\
-'AA3', 'X',\n'AA4', 'X',\n'AA6', 'X',\n'AAA', 'X',\
-\n'AAB', 'X',\n'AAC', 'X',\n'AAE', 'X',\n'AAG', 'R\
-',\n'AAH', 'X',\n'AAM', 'X',\n'AAN', 'X',\n'AAP', \
-'X',\n'AAR', 'R',\n'AAS', 'X',\n'AAT', 'X',\n'ABA'\
-, 'X',\n'ABC', 'X',\n'ABD', 'X',\n'ABE', 'X',\n'AB\
-H', 'X',\n'ABI', 'X',\n'ABK', 'X',\n'ABM', 'X',\n'\
-ABN', 'X',\n'ABP', 'X',\n'ABR', 'X',\n'ABS', 'X',\\
-n'ABU', 'X',\n'AC1', 'X',\n'AC2', 'X',\n'ACA', 'X'\
-,\n'ACB', 'D',\n'ACC', 'C',\n'ACD', 'X',\n'ACE', '\
-X',\n'ACH', 'X',\n'ACI', 'X',\n'ACL', 'R',\n'ACM',\
- 'X',\n'ACN', 'X',\n'ACO', 'X',\n'ACP', 'X',\n'ACQ\
-', 'X',\n'ACR', 'X',\n'ACS', 'X',\n'ACT', 'X',\n'A\
-CV', 'V',\n'ACX', 'X',\n'ACY', 'X',\n'AD2', 'X',\n\
-'AD3', 'X',\n'ADC', 'X',\n'ADD', 'X',\n'ADE', 'X',\
-\n'ADH', 'X',\n'ADI', 'X',\n'ADM', 'X',\n'ADN', 'X\
-',\n'ADP', 'X',\n'ADQ', 'X',\n'ADR', 'X',\n'ADS', \
-'X',\n'ADT', 'X',\n'ADU', 'X',\n'ADW', 'X',\n'ADX'\
-, 'X',\n'AE2', 'X',\n'AEA', 'X',\n'AEB', 'X',\n'AE\
-I', 'D',\n'AEN', 'X',\n'AET', 'T',\n'AF1', 'X',\n'\
-AF3', 'X',\n'AFA', 'D',\n'AFP', 'X',\n'AG7', 'X',\\
-n'AGB', 'X',\n'AGF', 'X',\n'AGL', 'X',\n'AGM', 'R'\
-,\n'AGN', 'X',\n'AGP', 'X',\n'AGS', 'X',\n'AGU', '\
-X',\n'AH0', 'X',\n'AH1', 'X',\n'AHA', 'X',\n'AHB',\
- 'D',\n'AHC', 'X',\n'AHF', 'X',\n'AHG', 'X',\n'AHH\
-', 'X',\n'AHM', 'X',\n'AHO', 'X',\n'AHP', 'X',\n'A\
-HS', 'X',\n'AHT', 'Y',\n'AHU', 'X',\n'AHX', 'X',\n\
-'AI1', 'X',\n'AI2', 'X',\n'AIB', 'X',\n'AIC', 'X',\
-\n'AIM', 'X',\n'AIP', 'X',\n'AIQ', 'X',\n'AIR', 'X\
-',\n'AJ3', 'X',\n'AKB', 'X',\n'AKG', 'X',\n'AKR', \
-'X',\n'AL1', 'X',\n'AL2', 'X',\n'AL3', 'X',\n'AL4'\
-, 'X',\n'AL5', 'X',\n'AL6', 'X',\n'AL7', 'X',\n'AL\
-8', 'X',\n'AL9', 'X',\n'ALA', 'A',\n'ALB', 'X',\n'\
-ALC', 'X',\n'ALD', 'L',\n'ALE', 'X',\n'ALF', 'X',\\
-n'ALG', 'X',\n'ALL', 'X',\n'ALM', 'A',\n'ALN', 'A'\
-,\n'ALO', 'T',\n'ALP', 'X',\n'ALQ', 'X',\n'ALR', '\
-X',\n'ALS', 'X',\n'ALT', 'A',\n'ALY', 'K',\n'ALZ',\
- 'X',\n'AMA', 'X',\n'AMB', 'X',\n'AMC', 'X',\n'AMD\
-', 'X',\n'AMG', 'X',\n'AMH', 'X',\n'AMI', 'X',\n'A\
-ML', 'X',\n'AMN', 'X',\n'AMO', 'X',\n'AMP', 'X',\n\
-'AMQ', 'X',\n'AMR', 'X',\n'AMS', 'X',\n'AMT', 'X',\
-\n'AMU', 'X',\n'AMW', 'X',\n'AMX', 'X',\n'AMY', 'X\
-',\n'ANA', 'X',\n'ANB', 'X',\n'ANC', 'X',\n'AND', \
-'X',\n'ANE', 'X',\n'ANI', 'X',\n'ANL', 'X',\n'ANO'\
-, 'X',\n'ANP', 'X',\n'ANS', 'X',\n'ANT', 'X',\n'AO\
-E', 'X',\n'AOP', 'X',\n'AP1', 'X',\n'AP2', 'X',\n'\
-AP3', 'X',\n'AP4', 'X',\n'AP5', 'X',\n'AP6', 'X',\\
-n'APA', 'X',\n'APB', 'X',\n'APC', 'X',\n'APE', 'F'\
-,\n'APF', 'X',\n'APG', 'X',\n'APH', 'A',\n'API', '\
-X',\n'APL', 'X',\n'APM', 'X',\n'APN', 'G',\n'APP',\
- 'X',\n'APQ', 'X',\n'APR', 'X',\n'APS', 'X',\n'APT\
-', 'X',\n'APU', 'X',\n'APX', 'X',\n'APY', 'X',\n'A\
-PZ', 'X',\n'AQS', 'X',\n'AR1', 'X',\n'AR2', 'X',\n\
-'ARA', 'X',\n'ARB', 'X',\n'ARC', 'X',\n'ARD', 'X',\
-\n'ARG', 'R',\n'ARH', 'X',\n'ARI', 'X',\n'ARM', 'R\
-',\n'ARN', 'X',\n'ARO', 'R',\n'ARP', 'X',\n'ARQ', \
-'X',\n'ARS', 'X',\n'AS1', 'R',\n'AS2', 'X',\n'ASA'\
-, 'D',\n'ASB', 'D',\n'ASC', 'X',\n'ASD', 'X',\n'AS\
-E', 'X',\n'ASF', 'X',\n'ASI', 'X',\n'ASK', 'D',\n'\
-ASL', 'X',\n'ASM', 'N',\n'ASO', 'X',\n'ASP', 'D',\\
-n'ASQ', 'X',\n'ASU', 'X',\n'ATA', 'X',\n'ATC', 'X'\
-,\n'ATD', 'X',\n'ATF', 'X',\n'ATG', 'X',\n'ATH', '\
-X',\n'ATM', 'X',\n'ATO', 'X',\n'ATP', 'X',\n'ATQ',\
- 'X',\n'ATR', 'X',\n'ATT', 'X',\n'ATY', 'X',\n'ATZ\
-', 'X',\n'AUC', 'X',\n'AUR', 'X',\n'AVG', 'X',\n'A\
-XP', 'X',\n'AYA', 'A',\n'AZ2', 'X',\n'AZA', 'X',\n\
-'AZC', 'X',\n'AZD', 'X',\n'AZE', 'X',\n'AZI', 'X',\
-\n'AZL', 'X',\n'AZM', 'X',\n'AZR', 'X',\n'AZT', 'X\
-',\n'B12', 'X',\n'B1F', 'F',\n'B2A', 'A',\n'B2F', \
-'F',\n'B2I', 'I',\n'B2V', 'V',\n'B3I', 'X',\n'B3P'\
-, 'X',\n'B7G', 'X',\n'B96', 'X',\n'B9A', 'X',\n'BA\
-1', 'X',\n'BAA', 'X',\n'BAB', 'X',\n'BAC', 'X',\n'\
-BAF', 'X',\n'BAH', 'X',\n'BAI', 'X',\n'BAK', 'X',\\
-n'BAL', 'A',\n'BAM', 'X',\n'BAO', 'X',\n'BAP', 'X'\
-,\n'BAR', 'X',\n'BAS', 'X',\n'BAT', 'F',\n'BAY', '\
-X',\n'BAZ', 'X',\n'BB1', 'X',\n'BB2', 'X',\n'BBA',\
- 'X',\n'BBH', 'X',\n'BBS', 'X',\n'BBT', 'X',\n'BBZ\
-', 'X',\n'BCA', 'X',\n'BCB', 'X',\n'BCC', 'X',\n'B\
-CD', 'X',\n'BCL', 'X',\n'BCN', 'X',\n'BCR', 'X',\n\
-'BCS', 'C',\n'BCT', 'X',\n'BCY', 'X',\n'BCZ', 'X',\
-\n'BDA', 'X',\n'BDG', 'X',\n'BDK', 'X',\n'BDM', 'X\
-',\n'BDN', 'X',\n'BDS', 'X',\n'BE1', 'X',\n'BE2', \
-'X',\n'BEA', 'X',\n'BEF', 'X',\n'BEN', 'X',\n'BEO'\
-, 'X',\n'BEP', 'X',\n'BER', 'X',\n'BES', 'X',\n'BE\
-T', 'X',\n'BEZ', 'X',\n'BF2', 'X',\n'BFA', 'X',\n'\
-BFD', 'X',\n'BFP', 'X',\n'BFS', 'X',\n'BFU', 'X',\\
-n'BG6', 'X',\n'BGF', 'X',\n'BGG', 'X',\n'BGL', 'X'\
-,\n'BGN', 'X',\n'BGP', 'X',\n'BGX', 'X',\n'BH4', '\
-X',\n'BHA', 'X',\n'BHC', 'X',\n'BHD', 'D',\n'BHO',\
- 'X',\n'BHS', 'X',\n'BIC', 'X',\n'BIN', 'X',\n'BIO\
-', 'X',\n'BIP', 'X',\n'BIS', 'X',\n'BIZ', 'X',\n'B\
-JH', 'X',\n'BJI', 'X',\n'BJP', 'X',\n'BLA', 'X',\n\
-'BLB', 'X',\n'BLE', 'L',\n'BLG', 'P',\n'BLI', 'X',\
-\n'BLM', 'X',\n'BLV', 'X',\n'BLY', 'K',\n'BM1', 'X\
-',\n'BM2', 'X',\n'BM5', 'X',\n'BM9', 'X',\n'BMA', \
-'X',\n'BMD', 'X',\n'BME', 'X',\n'BMP', 'X',\n'BMQ'\
-, 'X',\n'BMS', 'X',\n'BMT', 'T',\n'BMU', 'X',\n'BM\
-Y', 'X',\n'BMZ', 'X',\n'BNA', 'X',\n'BNG', 'X',\n'\
-BNI', 'X',\n'BNN', 'F',\n'BNO', 'L',\n'BNS', 'X',\\
-n'BNZ', 'X',\n'BO3', 'X',\n'BO4', 'X',\n'BOC', 'X'\
-,\n'BOG', 'X',\n'BOM', 'X',\n'BOT', 'X',\n'BOX', '\
-X',\n'BOZ', 'X',\n'BPA', 'X',\n'BPB', 'X',\n'BPD',\
- 'X',\n'BPG', 'X',\n'BPH', 'X',\n'BPI', 'X',\n'BPJ\
-', 'X',\n'BPM', 'X',\n'BPN', 'X',\n'BPO', 'X',\n'B\
-PP', 'X',\n'BPT', 'X',\n'BPY', 'X',\n'BRB', 'X',\n\
-'BRC', 'X',\n'BRE', 'X',\n'BRI', 'X',\n'BRL', 'X',\
-\n'BRM', 'X',\n'BRN', 'X',\n'BRO', 'X',\n'BRS', 'X\
-',\n'BRU', 'X',\n'BRZ', 'X',\n'BSB', 'X',\n'BSI', \
-'X',\n'BSP', 'X',\n'BT1', 'X',\n'BT2', 'X',\n'BT3'\
-, 'X',\n'BTA', 'L',\n'BTB', 'X',\n'BTC', 'C',\n'BT\
-D', 'X',\n'BTN', 'X',\n'BTP', 'X',\n'BTR', 'W',\n'\
-BU1', 'X',\n'BUA', 'X',\n'BUB', 'X',\n'BUC', 'X',\\
-n'BUG', 'X',\n'BUL', 'X',\n'BUM', 'X',\n'BUQ', 'X'\
-,\n'BUT', 'X',\n'BVD', 'X',\n'BX3', 'X',\n'BYS', '\
-X',\n'BZ1', 'X',\n'BZA', 'X',\n'BZB', 'X',\n'BZC',\
- 'X',\n'BZD', 'X',\n'BZF', 'X',\n'BZI', 'X',\n'BZM\
-', 'X',\n'BZO', 'X',\n'BZP', 'X',\n'BZQ', 'X',\n'B\
-ZS', 'X',\n'BZT', 'X',\n'C02', 'X',\n'C11', 'X',\n\
-'C1O', 'X',\n'C20', 'X',\n'C24', 'X',\n'C2F', 'X',\
-\n'C2O', 'X',\n'C2P', 'X',\n'C3M', 'X',\n'C3P', 'X\
-',\n'C3X', 'X',\n'C48', 'X',\n'C4M', 'X',\n'C4X', \
-'X',\n'C5C', 'X',\n'C5M', 'X',\n'C5P', 'X',\n'C5X'\
-, 'X',\n'C60', 'X',\n'C6C', 'X',\n'C6M', 'X',\n'C7\
-8', 'X',\n'C8E', 'X',\n'CA3', 'X',\n'CA5', 'X',\n'\
-CAA', 'X',\n'CAB', 'X',\n'CAC', 'X',\n'CAD', 'X',\\
-n'CAF', 'C',\n'CAG', 'X',\n'CAH', 'X',\n'CAL', 'X'\
-,\n'CAM', 'X',\n'CAN', 'X',\n'CAO', 'X',\n'CAP', '\
-X',\n'CAQ', 'X',\n'CAR', 'X',\n'CAS', 'C',\n'CAT',\
- 'X',\n'CAV', 'X',\n'CAY', 'C',\n'CAZ', 'X',\n'CB3\
-', 'X',\n'CB4', 'X',\n'CBA', 'X',\n'CBD', 'X',\n'C\
-BG', 'X',\n'CBI', 'X',\n'CBL', 'X',\n'CBM', 'X',\n\
-'CBN', 'X',\n'CBO', 'X',\n'CBP', 'X',\n'CBS', 'X',\
-\n'CBX', 'X',\n'CBZ', 'X',\n'CC0', 'X',\n'CC1', 'X\
-',\n'CCC', 'X',\n'CCH', 'X',\n'CCI', 'X',\n'CCM', \
-'X',\n'CCN', 'X',\n'CCO', 'X',\n'CCP', 'X',\n'CCR'\
-, 'X',\n'CCS', 'C',\n'CCV', 'X',\n'CCY', 'X',\n'CD\
-1', 'X',\n'CDC', 'X',\n'CDE', 'X',\n'CDF', 'X',\n'\
-CDI', 'X',\n'CDL', 'X',\n'CDM', 'X',\n'CDP', 'X',\\
-n'CDR', 'X',\n'CDU', 'X',\n'CE1', 'X',\n'CEA', 'C'\
-,\n'CEB', 'X',\n'CEC', 'X',\n'CED', 'X',\n'CEF', '\
-X',\n'CEH', 'X',\n'CEM', 'X',\n'CEO', 'X',\n'CEP',\
- 'X',\n'CEQ', 'X',\n'CER', 'X',\n'CES', 'G',\n'CET\
-', 'X',\n'CFC', 'X',\n'CFF', 'X',\n'CFM', 'X',\n'C\
-FO', 'X',\n'CFP', 'X',\n'CFS', 'X',\n'CFX', 'X',\n\
-'CGN', 'X',\n'CGP', 'X',\n'CGS', 'X',\n'CGU', 'E',\
-\n'CH2', 'X',\n'CH3', 'X',\n'CHA', 'X',\n'CHB', 'X\
-',\n'CHD', 'X',\n'CHF', 'X',\n'CHG', 'G',\n'CHI', \
-'X',\n'CHN', 'X',\n'CHO', 'X',\n'CHP', 'G',\n'CHR'\
-, 'X',\n'CHS', 'F',\n'CHT', 'X',\n'CHX', 'X',\n'CI\
-C', 'X',\n'CIN', 'X',\n'CIP', 'X',\n'CIR', 'X',\n'\
-CIT', 'X',\n'CIU', 'X',\n'CKI', 'X',\n'CL1', 'X',\\
-n'CL2', 'X',\n'CLA', 'X',\n'CLB', 'A',\n'CLC', 'S'\
-,\n'CLD', 'A',\n'CLE', 'L',\n'CLF', 'X',\n'CLK', '\
-S',\n'CLL', 'X',\n'CLM', 'X',\n'CLN', 'X',\n'CLO',\
- 'X',\n'CLP', 'X',\n'CLQ', 'X',\n'CLR', 'X',\n'CLS\
-', 'X',\n'CLT', 'X',\n'CLX', 'X',\n'CLY', 'X',\n'C\
-MA', 'R',\n'CMC', 'X',\n'CMD', 'X',\n'CME', 'C',\n\
-'CMG', 'X',\n'CMK', 'X',\n'CMN', 'X',\n'CMO', 'X',\
-\n'CMP', 'X',\n'CMR', 'X',\n'CMS', 'X',\n'CMT', 'C\
-',\n'CMX', 'X',\n'CNA', 'X',\n'CNC', 'X',\n'CND', \
-'X',\n'CNH', 'X',\n'CNM', 'X',\n'CNN', 'X',\n'CNO'\
-, 'X',\n'CNP', 'X',\n'CO2', 'X',\n'CO3', 'X',\n'CO\
-5', 'X',\n'CO8', 'X',\n'COA', 'X',\n'COB', 'X',\n'\
-COC', 'X',\n'COD', 'X',\n'COE', 'X',\n'COF', 'X',\\
-n'COH', 'X',\n'COI', 'X',\n'COJ', 'X',\n'COL', 'X'\
-,\n'COM', 'X',\n'CON', 'X',\n'COP', 'X',\n'COR', '\
-X',\n'COS', 'X',\n'COT', 'X',\n'COY', 'X',\n'CP1',\
- 'G',\n'CP2', 'X',\n'CP4', 'X',\n'CPA', 'X',\n'CPB\
-', 'X',\n'CPC', 'X',\n'CPD', 'X',\n'CPG', 'X',\n'C\
-PH', 'X',\n'CPI', 'X',\n'CPM', 'X',\n'CPN', 'G',\n\
-'CPO', 'X',\n'CPP', 'X',\n'CPQ', 'X',\n'CPR', 'X',\
-\n'CPS', 'X',\n'CPT', 'X',\n'CPU', 'X',\n'CPV', 'X\
-',\n'CPY', 'X',\n'CR1', 'X',\n'CR6', 'X',\n'CRA', \
-'X',\n'CRB', 'X',\n'CRC', 'X',\n'CRG', 'X',\n'CRH'\
-, 'X',\n'CRO', 'T',\n'CRP', 'X',\n'CRQ', 'X',\n'CR\
-S', 'X',\n'CRT', 'X',\n'CRY', 'X',\n'CSA', 'C',\n'\
-CSB', 'X',\n'CSD', 'C',\n'CSE', 'C',\n'CSH', 'X',\\
-n'CSI', 'X',\n'CSN', 'X',\n'CSO', 'C',\n'CSP', 'C'\
-,\n'CSR', 'C',\n'CSS', 'C',\n'CST', 'X',\n'CSW', '\
-C',\n'CSX', 'C',\n'CSY', 'X',\n'CSZ', 'C',\n'CT3',\
- 'X',\n'CTA', 'X',\n'CTB', 'X',\n'CTC', 'X',\n'CTD\
-', 'X',\n'CTH', 'T',\n'CTO', 'X',\n'CTP', 'X',\n'C\
-TR', 'X',\n'CTS', 'X',\n'CTT', 'X',\n'CTY', 'X',\n\
-'CTZ', 'X',\n'CU1', 'X',\n'CUA', 'X',\n'CUC', 'X',\
-\n'CUL', 'X',\n'CUO', 'X',\n'CUZ', 'X',\n'CVI', 'X\
-',\n'CXF', 'X',\n'CXL', 'X',\n'CXM', 'M',\n'CXN', \
-'X',\n'CXP', 'X',\n'CXS', 'X',\n'CY1', 'C',\n'CY3'\
-, 'X',\n'CYB', 'X',\n'CYC', 'X',\n'CYF', 'C',\n'CY\
-G', 'C',\n'CYH', 'X',\n'CYL', 'X',\n'CYM', 'C',\n'\
-CYN', 'X',\n'CYO', 'X',\n'CYP', 'X',\n'CYQ', 'C',\\
-n'CYS', 'C',\n'CYU', 'X',\n'CYY', 'X',\n'CYZ', 'X'\
-,\n'CZH', 'X',\n'CZZ', 'C',\n'D12', 'X',\n'D13', '\
-X',\n'D16', 'X',\n'D18', 'X',\n'D19', 'X',\n'D1P',\
- 'X',\n'D24', 'X',\n'D34', 'X',\n'D35', 'X',\n'D4D\
-', 'X',\n'D4T', 'X',\n'D6G', 'X',\n'DA2', 'R',\n'D\
-A3', 'X',\n'DA6', 'X',\n'DA7', 'X',\n'DAA', 'X',\n\
-'DAB', 'X',\n'DAC', 'X',\n'DAD', 'X',\n'DAE', 'X',\
-\n'DAF', 'X',\n'DAG', 'X',\n'DAH', 'A',\n'DAJ', 'X\
-',\n'DAK', 'X',\n'DAL', 'A',\n'DAM', 'A',\n'DAN', \
-'X',\n'DAO', 'X',\n'DAP', 'X',\n'DAQ', 'X',\n'DAR'\
-, 'R',\n'DAS', 'D',\n'DAT', 'X',\n'DAU', 'X',\n'DA\
-V', 'X',\n'DBA', 'X',\n'DBD', 'X',\n'DBF', 'X',\n'\
-DBG', 'X',\n'DBI', 'X',\n'DBV', 'X',\n'DBY', 'Y',\\
-n'DCA', 'X',\n'DCB', 'X',\n'DCE', 'X',\n'DCF', 'X'\
-,\n'DCG', 'X',\n'DCH', 'X',\n'DCI', 'I',\n'DCL', '\
-X',\n'DCM', 'X',\n'DCP', 'X',\n'DCS', 'X',\n'DCT',\
- 'X',\n'DCY', 'C',\n'DCZ', 'X',\n'DDA', 'X',\n'DDB\
-', 'X',\n'DDC', 'X',\n'DDF', 'X',\n'DDG', 'X',\n'D\
-DH', 'X',\n'DDL', 'X',\n'DDM', 'X',\n'DDO', 'L',\n\
-'DDP', 'X',\n'DDQ', 'X',\n'DDT', 'Y',\n'DDU', 'X',\
-\n'DEA', 'X',\n'DEB', 'X',\n'DEC', 'X',\n'DEF', 'X\
-',\n'DEL', 'X',\n'DEM', 'X',\n'DEN', 'X',\n'DEP', \
-'X',\n'DEQ', 'X',\n'DES', 'X',\n'DET', 'X',\n'DFC'\
-, 'X',\n'DFG', 'X',\n'DFI', 'X',\n'DFL', 'X',\n'DF\
-O', 'X',\n'DFP', 'X',\n'DFR', 'X',\n'DFT', 'X',\n'\
-DFV', 'X',\n'DFX', 'X',\n'DG2', 'X',\n'DG3', 'X',\\
-n'DG6', 'X',\n'DGA', 'X',\n'DGD', 'X',\n'DGG', 'X'\
-,\n'DGL', 'E',\n'DGN', 'Q',\n'DGP', 'X',\n'DGT', '\
-X',\n'DGX', 'X',\n'DH2', 'X',\n'DHA', 'A',\n'DHB',\
- 'X',\n'DHC', 'X',\n'DHD', 'X',\n'DHE', 'X',\n'DHF\
-', 'X',\n'DHG', 'X',\n'DHI', 'H',\n'DHL', 'X',\n'D\
-HM', 'X',\n'DHN', 'V',\n'DHP', 'X',\n'DHQ', 'X',\n\
-'DHR', 'X',\n'DHS', 'X',\n'DHT', 'X',\n'DHU', 'X',\
-\n'DHY', 'X',\n'DHZ', 'X',\n'DI2', 'X',\n'DI3', 'G\
-',\n'DI4', 'X',\n'DI5', 'X',\n'DIA', 'X',\n'DIC', \
-'X',\n'DIF', 'X',\n'DIG', 'X',\n'DII', 'X',\n'DIL'\
-, 'I',\n'DIM', 'X',\n'DIO', 'X',\n'DIP', 'X',\n'DI\
-Q', 'X',\n'DIS', 'X',\n'DIT', 'X',\n'DIV', 'V',\n'\
-DIX', 'X',\n'DIY', 'X',\n'DKA', 'X',\n'DLA', 'X',\\
-n'DLE', 'L',\n'DLF', 'X',\n'DLS', 'K',\n'DLY', 'K'\
-,\n'DM1', 'X',\n'DM2', 'X',\n'DM3', 'X',\n'DM4', '\
-X',\n'DM5', 'X',\n'DM6', 'X',\n'DM7', 'X',\n'DM8',\
- 'X',\n'DM9', 'X',\n'DMA', 'X',\n'DMB', 'X',\n'DMC\
-', 'X',\n'DMD', 'X',\n'DME', 'X',\n'DMF', 'X',\n'D\
-MG', 'G',\n'DMH', 'N',\n'DMI', 'X',\n'DMJ', 'X',\n\
-'DML', 'X',\n'DMM', 'X',\n'DMN', 'X',\n'DMO', 'X',\
-\n'DMP', 'X',\n'DMQ', 'X',\n'DMR', 'X',\n'DMS', 'X\
-',\n'DMT', 'X',\n'DMV', 'X',\n'DMY', 'X',\n'DNC', \
-'X',\n'DND', 'X',\n'DNH', 'X',\n'DNJ', 'X',\n'DNN'\
-, 'X',\n'DNP', 'X',\n'DNQ', 'X',\n'DNR', 'X',\n'DO\
-2', 'X',\n'DO3', 'X',\n'DOA', 'X',\n'DOB', 'X',\n'\
-DOC', 'X',\n'DOH', 'D',\n'DOM', 'X',\n'DOS', 'X',\\
-n'DOX', 'X',\n'DP5', 'X',\n'DP7', 'X',\n'DPA', 'X'\
-,\n'DPC', 'X',\n'DPD', 'X',\n'DPE', 'X',\n'DPG', '\
-X',\n'DPH', 'F',\n'DPM', 'X',\n'DPN', 'F',\n'DPO',\
- 'X',\n'DPP', 'X',\n'DPR', 'P',\n'DPS', 'X',\n'DPT\
-', 'X',\n'DPX', 'X',\n'DPY', 'X',\n'DPZ', 'X',\n'D\
-QH', 'X',\n'DQN', 'X',\n'DR1', 'X',\n'DRB', 'X',\n\
-'DRC', 'X',\n'DRI', 'X',\n'DRP', 'X',\n'DRT', 'X',\
-\n'DRU', 'X',\n'DSA', 'X',\n'DSB', 'X',\n'DSC', 'X\
-',\n'DSD', 'X',\n'DSE', 'S',\n'DSI', 'X',\n'DSN', \
-'S',\n'DSP', 'D',\n'DSR', 'X',\n'DSS', 'X',\n'DSX'\
-, 'X',\n'DSY', 'X',\n'DTB', 'X',\n'DTD', 'X',\n'DT\
-H', 'T',\n'DTN', 'X',\n'DTO', 'X',\n'DTP', 'X',\n'\
-DTQ', 'X',\n'DTR', 'W',\n'DTT', 'X',\n'DTY', 'Y',\\
-n'DUD', 'X',\n'DUO', 'X',\n'DUR', 'X',\n'DUT', 'X'\
-,\n'DVA', 'V',\n'DVR', 'X',\n'DX9', 'X',\n'DXA', '\
-X',\n'DXB', 'X',\n'DXC', 'X',\n'DXG', 'X',\n'DXX',\
- 'X',\n'DZF', 'X',\n'E09', 'X',\n'E20', 'X',\n'E2P\
-', 'X',\n'E3G', 'X',\n'E4N', 'X',\n'E4P', 'X',\n'E\
-64', 'X',\n'E6C', 'X',\n'E96', 'X',\n'E97', 'X',\n\
-'EA2', 'X',\n'EAA', 'X',\n'EAP', 'X',\n'EBP', 'X',\
-\n'EBW', 'X',\n'ECO', 'X',\n'EDA', 'X',\n'EDC', 'X\
-',\n'EDE', 'X',\n'EDO', 'X',\n'EDR', 'X',\n'EEB', \
-'X',\n'EEE', 'X',\n'EFC', 'X',\n'EFZ', 'X',\n'EG1'\
-, 'X',\n'EG2', 'X',\n'EG3', 'X',\n'EGC', 'X',\n'EG\
-L', 'X',\n'EHP', 'A',\n'EIC', 'X',\n'EJT', 'X',\n'\
-ELA', 'X',\n'EMB', 'X',\n'EMC', 'X',\n'EMD', 'X',\\
-n'EMM', 'X',\n'EMO', 'X',\n'EMP', 'X',\n'EMR', 'X'\
-,\n'ENA', 'X',\n'ENC', 'X',\n'ENH', 'X',\n'ENO', '\
-X',\n'ENP', 'X',\n'EOA', 'X',\n'EOH', 'X',\n'EOT',\
- 'X',\n'EOX', 'X',\n'EPA', 'X',\n'EPE', 'X',\n'EPH\
-', 'X',\n'EPI', 'X',\n'EPN', 'X',\n'EPO', 'X',\n'E\
-PT', 'X',\n'EPU', 'X',\n'EPX', 'X',\n'EPY', 'X',\n\
-'EQI', 'X',\n'EQP', 'X',\n'EQU', 'X',\n'ERG', 'X',\
-\n'ERI', 'X',\n'ERY', 'X',\n'ESC', 'X',\n'ESD', 'X\
-',\n'ESI', 'X',\n'ESO', 'X',\n'ESP', 'X',\n'EST', \
-'X',\n'ESX', 'X',\n'ETA', 'X',\n'ETC', 'X',\n'ETD'\
-, 'X',\n'ETF', 'X',\n'ETH', 'X',\n'ETI', 'X',\n'ET\
-N', 'X',\n'ETO', 'X',\n'ETP', 'X',\n'ETR', 'X',\n'\
-ETS', 'X',\n'ETY', 'X',\n'EU3', 'X',\n'EUG', 'X',\\
-n'EYS', 'C',\n'F09', 'X',\n'F2B', 'X',\n'F3S', 'X'\
-,\n'F42', 'X',\n'F43', 'X',\n'F4S', 'X',\n'F6B', '\
-X',\n'F6P', 'X',\n'F89', 'X',\n'FA1', 'X',\n'FA5',\
- 'F',\n'FAA', 'X',\n'FAB', 'X',\n'FAC', 'X',\n'FAD\
-', 'X',\n'FAF', 'X',\n'FAG', 'X',\n'FAM', 'X',\n'F\
-AR', 'X',\n'FAS', 'X',\n'FAT', 'X',\n'FBA', 'X',\n\
-'FBE', 'X',\n'FBI', 'X',\n'FBP', 'X',\n'FBQ', 'X',\
-\n'FBS', 'X',\n'FBT', 'X',\n'FBU', 'X',\n'FCA', 'X\
-',\n'FCB', 'X',\n'FCI', 'X',\n'FCN', 'X',\n'FCO', \
-'X',\n'FCR', 'X',\n'FCT', 'X',\n'FCX', 'X',\n'FCY'\
-, 'C',\n'FD1', 'F',\n'FD2', 'F',\n'FD3', 'F',\n'FD\
-4', 'F',\n'FDA', 'X',\n'FDC', 'X',\n'FDI', 'X',\n'\
-FDP', 'X',\n'FDS', 'X',\n'FE2', 'X',\n'FEA', 'X',\\
-n'FEL', 'X',\n'FEM', 'X',\n'FEN', 'X',\n'FEO', 'X'\
-,\n'FEP', 'X',\n'FER', 'X',\n'FES', 'X',\n'FFB', '\
-X',\n'FFC', 'X',\n'FFF', 'X',\n'FFO', 'X',\n'FGL',\
- 'G',\n'FHB', 'X',\n'FHC', 'X',\n'FHP', 'X',\n'FHU\
-', 'X',\n'FID', 'X',\n'FII', 'X',\n'FIP', 'X',\n'F\
-K5', 'X',\n'FKA', 'X',\n'FKI', 'X',\n'FKP', 'X',\n\
-'FL2', 'X',\n'FL9', 'X',\n'FLA', 'A',\n'FLC', 'X',\
-\n'FLD', 'X',\n'FLE', 'L',\n'FLF', 'X',\n'FLO', 'X\
-',\n'FLP', 'X',\n'FLT', 'Y',\n'FLU', 'X',\n'FLX', \
-'X',\n'FM1', 'X',\n'FM2', 'X',\n'FMA', 'X',\n'FMB'\
-, 'X',\n'FMC', 'X',\n'FME', 'M',\n'FMN', 'X',\n'FM\
-P', 'X',\n'FMR', 'X',\n'FMS', 'X',\n'FMT', 'X',\n'\
-FNE', 'X',\n'FNP', 'X',\n'FNS', 'X',\n'FOC', 'X',\\
-n'FOE', 'X',\n'FOG', 'F',\n'FOH', 'X',\n'FOK', 'X'\
-,\n'FOL', 'X',\n'FON', 'X',\n'FOP', 'X',\n'FOR', '\
-X',\n'FOS', 'X',\n'FPA', 'X',\n'FPC', 'X',\n'FPI',\
- 'X',\n'FPO', 'X',\n'FPP', 'X',\n'FPT', 'X',\n'FQP\
-', 'X',\n'FRA', 'X',\n'FRD', 'F',\n'FRU', 'X',\n'F\
-S3', 'X',\n'FS4', 'X',\n'FSB', 'X',\n'FSO', 'X',\n\
-'FSX', 'X',\n'FTC', 'X',\n'FTP', 'X',\n'FTR', 'W',\
-\n'FTT', 'X',\n'FTY', 'Y',\n'FUA', 'X',\n'FUC', 'X\
-',\n'FUM', 'X',\n'FUP', 'X',\n'FVF', 'X',\n'FXP', \
-'X',\n'FXV', 'X',\n'FYA', 'F',\n'G16', 'X',\n'G1P'\
-, 'X',\n'G20', 'X',\n'G21', 'X',\n'G23', 'X',\n'G2\
-6', 'X',\n'G28', 'X',\n'G2F', 'X',\n'G37', 'X',\n'\
-G39', 'X',\n'G3H', 'X',\n'G3P', 'X',\n'G4D', 'X',\\
-n'G6D', 'X',\n'G6P', 'X',\n'G6Q', 'X',\n'G7M', 'X'\
-,\n'GA2', 'X',\n'GAA', 'X',\n'GAB', 'X',\n'GAC', '\
-X',\n'GAI', 'X',\n'GAL', 'X',\n'GAM', 'X',\n'GAN',\
- 'X',\n'GAO', 'X',\n'GAP', 'X',\n'GAR', 'G',\n'GAS\
-', 'X',\n'GAT', 'X',\n'GBC', 'X',\n'GBI', 'X',\n'G\
-BP', 'X',\n'GBS', 'X',\n'GBX', 'X',\n'GC4', 'X',\n\
-'GCA', 'X',\n'GCD', 'X',\n'GCG', 'G',\n'GCH', 'G',\
-\n'GCK', 'X',\n'GCL', 'X',\n'GCM', 'X',\n'GCN', 'X\
-',\n'GCO', 'X',\n'GCP', 'X',\n'GCR', 'X',\n'GCS', \
-'X',\n'GCU', 'X',\n'GD3', 'X',\n'GDB', 'X',\n'GDM'\
-, 'X',\n'GDN', 'X',\n'GDP', 'X',\n'GDS', 'X',\n'GD\
-U', 'X',\n'GE1', 'X',\n'GE2', 'X',\n'GE3', 'X',\n'\
-GEA', 'X',\n'GEL', 'X',\n'GEM', 'X',\n'GEN', 'X',\\
-n'GEP', 'X',\n'GER', 'X',\n'GFP', 'X',\n'GGB', 'X'\
-,\n'GGL', 'E',\n'GGP', 'X',\n'GHP', 'G',\n'GIP', '\
-X',\n'GIS', 'X',\n'GKR', 'X',\n'GL2', 'X',\n'GL3',\
- 'G',\n'GL4', 'X',\n'GL5', 'X',\n'GL7', 'X',\n'GL9\
-', 'X',\n'GLA', 'X',\n'GLB', 'X',\n'GLC', 'X',\n'G\
-LD', 'X',\n'GLE', 'X',\n'GLF', 'X',\n'GLG', 'X',\n\
-'GLH', 'Q',\n'GLI', 'X',\n'GLL', 'X',\n'GLM', 'G',\
-\n'GLN', 'Q',\n'GLO', 'X',\n'GLP', 'X',\n'GLR', 'X\
-',\n'GLS', 'X',\n'GLT', 'X',\n'GLU', 'E',\n'GLV', \
-'X',\n'GLW', 'X',\n'GLY', 'G',\n'GLZ', 'X',\n'GM1'\
-, 'X',\n'GMA', 'X',\n'GMC', 'X',\n'GMH', 'X',\n'GM\
-P', 'X',\n'GMY', 'X',\n'GN7', 'X',\n'GNA', 'X',\n'\
-GNB', 'X',\n'GNH', 'X',\n'GNP', 'X',\n'GNT', 'X',\\
-n'GOA', 'X',\n'GOL', 'X',\n'GOX', 'X',\n'GP1', 'X'\
-,\n'GP3', 'X',\n'GP4', 'X',\n'GP6', 'X',\n'GP8', '\
-X',\n'GPB', 'E',\n'GPC', 'X',\n'GPE', 'X',\n'GPG',\
- 'X',\n'GPI', 'X',\n'GPJ', 'X',\n'GPL', 'K',\n'GPM\
-', 'X',\n'GPN', 'G',\n'GPP', 'X',\n'GPR', 'X',\n'G\
-PS', 'X',\n'GPX', 'X',\n'GR1', 'X',\n'GR3', 'X',\n\
-'GR4', 'X',\n'GSA', 'X',\n'GSB', 'X',\n'GSC', 'G',\
-\n'GSE', 'S',\n'GSH', 'X',\n'GSP', 'X',\n'GSR', 'X\
-',\n'GSS', 'X',\n'GT9', 'C',\n'GTA', 'X',\n'GTB', \
-'X',\n'GTD', 'X',\n'GTE', 'X',\n'GTH', 'T',\n'GTN'\
-, 'X',\n'GTO', 'X',\n'GTP', 'X',\n'GTR', 'X',\n'GT\
-S', 'X',\n'GTT', 'X',\n'GTX', 'X',\n'GTZ', 'X',\n'\
-GU7', 'X',\n'GUA', 'X',\n'GUD', 'X',\n'GUM', 'X',\\
-n'GUN', 'X',\n'GUP', 'X',\n'GUR', 'X',\n'GW3', 'X'\
-,\n'GZZ', 'X',\n'H2B', 'X',\n'H2P', 'H',\n'H2S', '\
-X',\n'H2U', 'X',\n'H4B', 'X',\n'H5M', 'P',\n'H5P',\
- 'X',\n'HAA', 'X',\n'HAB', 'X',\n'HAC', 'A',\n'HAD\
-', 'X',\n'HAE', 'X',\n'HAG', 'X',\n'HAI', 'X',\n'H\
-AM', 'X',\n'HAP', 'X',\n'HAQ', 'X',\n'HAR', 'R',\n\
-'HAS', 'X',\n'HAV', 'V',\n'HAX', 'X',\n'HAZ', 'X',\
-\n'HBA', 'X',\n'HBC', 'X',\n'HBD', 'X',\n'HBI', 'X\
-',\n'HBO', 'X',\n'HBU', 'X',\n'HBY', 'X',\n'HC0', \
-'X',\n'HC1', 'X',\n'HC4', 'X',\n'HCA', 'X',\n'HCC'\
-, 'X',\n'HCI', 'X',\n'HCS', 'X',\n'HDA', 'X',\n'HD\
-D', 'X',\n'HDF', 'X',\n'HDN', 'X',\n'HDS', 'X',\n'\
-HDZ', 'X',\n'HE1', 'X',\n'HE6', 'X',\n'HEA', 'X',\\
-n'HEB', 'X',\n'HEC', 'X',\n'HED', 'X',\n'HEE', 'X'\
-,\n'HEF', 'X',\n'HEG', 'X',\n'HEM', 'X',\n'HEN', '\
-X',\n'HEO', 'X',\n'HEP', 'X',\n'HEU', 'X',\n'HEV',\
- 'X',\n'HEX', 'X',\n'HEZ', 'X',\n'HF1', 'X',\n'HFA\
-', 'X',\n'HFP', 'X',\n'HGA', 'Q',\n'HGB', 'X',\n'H\
-GC', 'X',\n'HGI', 'X',\n'HGU', 'X',\n'HHO', 'X',\n\
-'HHP', 'X',\n'HIB', 'X',\n'HIC', 'H',\n'HII', 'X',\
-\n'HIN', 'X',\n'HIO', 'X',\n'HIP', 'H',\n'HIS', 'H\
-',\n'HLE', 'X',\n'HLT', 'X',\n'HMA', 'A',\n'HMB', \
-'X',\n'HMC', 'X',\n'HMD', 'X',\n'HMF', 'A',\n'HMG'\
-, 'X',\n'HMH', 'X',\n'HMI', 'L',\n'HMM', 'X',\n'HM\
-N', 'X',\n'HMO', 'X',\n'HMP', 'X',\n'HMR', 'R',\n'\
-HNI', 'X',\n'HNP', 'X',\n'HOA', 'X',\n'HOE', 'X',\\
-n'HOH', 'X',\n'HOM', 'X',\n'HOP', 'X',\n'HOQ', 'X'\
-,\n'HP1', 'A',\n'HP2', 'A',\n'HP3', 'X',\n'HPA', '\
-X',\n'HPB', 'X',\n'HPC', 'X',\n'HPD', 'X',\n'HPE',\
- 'A',\n'HPG', 'X',\n'HPH', 'F',\n'HPP', 'X',\n'HPQ\
-', 'F',\n'HPR', 'X',\n'HPT', 'X',\n'HPY', 'X',\n'H\
-QO', 'X',\n'HQQ', 'X',\n'HQU', 'X',\n'HRG', 'R',\n\
-'HRI', 'X',\n'HSA', 'X',\n'HSE', 'S',\n'HSF', 'X',\
-\n'HSM', 'X',\n'HSO', 'H',\n'HSP', 'X',\n'HT1', 'X\
-',\n'HT2', 'X',\n'HTA', 'X',\n'HTL', 'X',\n'HTO', \
-'X',\n'HTP', 'X',\n'HTR', 'W',\n'HUP', 'X',\n'HUX'\
-, 'X',\n'HV5', 'A',\n'HV7', 'X',\n'HV8', 'X',\n'HX\
-A', 'X',\n'HXC', 'X',\n'HXP', 'X',\n'HY1', 'X',\n'\
-HYA', 'X',\n'HYB', 'X',\n'HYD', 'X',\n'HYG', 'X',\\
-n'HYP', 'P',\n'I06', 'X',\n'I10', 'X',\n'I11', 'X'\
-,\n'I17', 'X',\n'I2P', 'X',\n'I3N', 'X',\n'I3P', '\
-X',\n'I40', 'X',\n'I48', 'X',\n'I4B', 'X',\n'I52',\
- 'X',\n'I5P', 'X',\n'I84', 'G',\n'IAG', 'G',\n'IAS\
-', 'X',\n'IB2', 'X',\n'IBB', 'X',\n'IBP', 'X',\n'I\
-BR', 'X',\n'IBS', 'X',\n'IBZ', 'X',\n'IC1', 'X',\n\
-'ICA', 'X',\n'ICI', 'X',\n'ICL', 'X',\n'ICP', 'X',\
-\n'ICT', 'X',\n'ICU', 'X',\n'ID2', 'X',\n'IDC', 'X\
-',\n'IDG', 'X',\n'IDH', 'X',\n'IDM', 'X',\n'IDO', \
-'X',\n'IDP', 'X',\n'IDR', 'X',\n'IDS', 'X',\n'IDT'\
-, 'X',\n'IDU', 'X',\n'IFG', 'X',\n'IFP', 'X',\n'IG\
-L', 'X',\n'IGN', 'X',\n'IGP', 'X',\n'IGU', 'X',\n'\
-IH1', 'X',\n'IH2', 'X',\n'IH3', 'X',\n'IHB', 'X',\\
-n'IHN', 'X',\n'IHP', 'X',\n'IIC', 'X',\n'IIL', 'I'\
-,\n'IIP', 'X',\n'IK2', 'X',\n'IKT', 'X',\n'ILA', '\
-I',\n'ILE', 'I',\n'ILG', 'X',\n'ILO', 'X',\n'ILX',\
- 'I',\n'IM1', 'X',\n'IM2', 'X',\n'IMC', 'X',\n'IMD\
-', 'X',\n'IME', 'X',\n'IMF', 'X',\n'IMG', 'X',\n'I\
-MH', 'X',\n'IMI', 'X',\n'IML', 'I',\n'IMM', 'X',\n\
-'IMN', 'X',\n'IMO', 'X',\n'IMP', 'X',\n'IMR', 'X',\
-\n'IMU', 'X',\n'IN0', 'D',\n'IN1', 'R',\n'IN2', 'K\
-',\n'IN3', 'L',\n'IN4', 'X',\n'IN5', 'A',\n'IN6', \
-'L',\n'IN7', 'X',\n'IN8', 'X',\n'IN9', 'X',\n'INA'\
-, 'L',\n'INB', 'X',\n'INC', 'X',\n'IND', 'X',\n'IN\
-E', 'X',\n'INF', 'F',\n'ING', 'F',\n'INH', 'R',\n'\
-INI', 'X',\n'INJ', 'X',\n'INK', 'X',\n'INL', 'X',\\
-n'INM', 'X',\n'INN', 'A',\n'INO', 'X',\n'INP', 'X'\
-,\n'INQ', 'X',\n'INR', 'X',\n'INS', 'X',\n'INT', '\
-V',\n'INU', 'X',\n'INV', 'X',\n'INW', 'X',\n'INX',\
- 'X',\n'INY', 'X',\n'INZ', 'X',\n'IOA', 'X',\n'IOB\
-', 'X',\n'IOC', 'X',\n'IOD', 'X',\n'IOE', 'X',\n'I\
-OF', 'X',\n'IOH', 'X',\n'IOL', 'X',\n'IOP', 'X',\n\
-'IP1', 'X',\n'IP2', 'X',\n'IP3', 'X',\n'IP4', 'X',\
-\n'IPA', 'X',\n'IPB', 'X',\n'IPD', 'X',\n'IPG', 'G\
-',\n'IPH', 'X',\n'IPL', 'X',\n'IPM', 'X',\n'IPN', \
-'X',\n'IPO', 'F',\n'IPP', 'X',\n'IPS', 'X',\n'IPT'\
-, 'X',\n'IPU', 'X',\n'IPY', 'A',\n'IQB', 'X',\n'IQ\
-P', 'X',\n'IQS', 'X',\n'IR3', 'X',\n'IRI', 'X',\n'\
-IRP', 'X',\n'ISA', 'X',\n'ISF', 'X',\n'ISO', 'X',\\
-n'ISP', 'X',\n'ISQ', 'X',\n'ISU', 'X',\n'ITM', 'X'\
-,\n'ITP', 'X',\n'ITR', 'W',\n'ITS', 'X',\n'ITU', '\
-X',\n'IU5', 'X',\n'IUM', 'X',\n'IUR', 'X',\n'IVA',\
- 'X',\n'IYG', 'G',\n'IYR', 'Y',\n'J77', 'X',\n'J78\
-', 'X',\n'J80', 'X',\n'JE2', 'X',\n'JEN', 'X',\n'J\
-ST', 'X',\n'K21', 'X',\n'KAH', 'X',\n'KAI', 'X',\n\
-'KAM', 'X',\n'KAN', 'X',\n'KAP', 'X',\n'KCP', 'X',\
-\n'KCX', 'K',\n'KDO', 'X',\n'KEF', 'X',\n'KET', 'X\
-',\n'KGR', 'X',\n'KH1', 'X',\n'KIF', 'X',\n'KIV', \
-'V',\n'KNI', 'X',\n'KPH', 'K',\n'KTH', 'X',\n'KTN'\
-, 'X',\n'KTP', 'X',\n'KWT', 'X',\n'L04', 'X',\n'L1\
-P', 'X',\n'L24', 'E',\n'L2P', 'X',\n'L34', 'E',\n'\
-L37', 'E',\n'L3P', 'X',\n'L4P', 'X',\n'L75', 'X',\\
-n'LAC', 'X',\n'LAD', 'X',\n'LAK', 'X',\n'LAM', 'X'\
-,\n'LAR', 'X',\n'LAT', 'X',\n'LAX', 'X',\n'LCO', '\
-X',\n'LCP', 'X',\n'LCS', 'X',\n'LDA', 'X',\n'LDO',\
- 'L',\n'LDP', 'X',\n'LEA', 'X',\n'LEO', 'X',\n'LEU\
-', 'L',\n'LG2', 'X',\n'LG6', 'X',\n'LGC', 'X',\n'L\
-GP', 'X',\n'LHG', 'X',\n'LHY', 'F',\n'LI1', 'X',\n\
-'LIG', 'X',\n'LIL', 'X',\n'LIM', 'X',\n'LIN', 'X',\
-\n'LIO', 'X',\n'LIP', 'X',\n'LLA', 'X',\n'LLP', 'K\
-',\n'LLY', 'K',\n'LMG', 'X',\n'LML', 'X',\n'LMT', \
-'X',\n'LMU', 'X',\n'LMZ', 'X',\n'LNK', 'X',\n'LNL'\
-, 'X',\n'LNO', 'X',\n'LOF', 'X',\n'LOL', 'L',\n'LO\
-M', 'X',\n'LOR', 'X',\n'LOS', 'X',\n'LOV', 'L',\n'\
-LOX', 'X',\n'LP1', 'X',\n'LP2', 'R',\n'LPA', 'X',\\
-n'LPC', 'X',\n'LPF', 'X',\n'LPL', 'X',\n'LPM', 'X'\
-,\n'LPP', 'X',\n'LRB', 'X',\n'LRU', 'X',\n'LS1', '\
-X',\n'LS2', 'X',\n'LS3', 'X',\n'LS4', 'X',\n'LS5',\
- 'X',\n'LTA', 'X',\n'LTL', 'X',\n'LTR', 'W',\n'LUM\
-', 'X',\n'LVS', 'L',\n'LXC', 'X',\n'LY2', 'X',\n'L\
-Y3', 'X',\n'LYA', 'X',\n'LYB', 'X',\n'LYC', 'X',\n\
-'LYD', 'X',\n'LYM', 'K',\n'LYN', 'X',\n'LYS', 'K',\
-\n'LYT', 'X',\n'LYW', 'X',\n'LYZ', 'K',\n'M1A', 'X\
-',\n'M1G', 'X',\n'M2G', 'X',\n'M3L', 'K',\n'M6P', \
-'X',\n'M6T', 'X',\n'M7G', 'X',\n'MA1', 'X',\n'MA2'\
-, 'X',\n'MA3', 'X',\n'MA4', 'X',\n'MA6', 'X',\n'MA\
-A', 'A',\n'MAB', 'X',\n'MAC', 'X',\n'MAE', 'X',\n'\
-MAG', 'X',\n'MAH', 'X',\n'MAI', 'R',\n'MAK', 'X',\\
-n'MAL', 'X',\n'MAM', 'X',\n'MAN', 'X',\n'MAO', 'X'\
-,\n'MAP', 'X',\n'MAR', 'X',\n'MAS', 'X',\n'MAT', '\
-X',\n'MAU', 'X',\n'MAZ', 'X',\n'MBA', 'X',\n'MBD',\
- 'X',\n'MBG', 'X',\n'MBH', 'X',\n'MBN', 'X',\n'MBO\
-', 'X',\n'MBR', 'X',\n'MBS', 'X',\n'MBV', 'X',\n'M\
-BZ', 'X',\n'MCA', 'X',\n'MCD', 'X',\n'MCE', 'X',\n\
-'MCG', 'G',\n'MCI', 'X',\n'MCN', 'X',\n'MCP', 'X',\
-\n'MCT', 'X',\n'MCY', 'X',\n'MD2', 'X',\n'MDA', 'X\
-',\n'MDC', 'X',\n'MDG', 'X',\n'MDH', 'X',\n'MDL', \
-'X',\n'MDM', 'X',\n'MDN', 'X',\n'MDP', 'X',\n'ME6'\
-, 'X',\n'MEB', 'X',\n'MEC', 'X',\n'MEL', 'X',\n'ME\
-N', 'N',\n'MEP', 'X',\n'MER', 'X',\n'MES', 'X',\n'\
-MET', 'M',\n'MEV', 'X',\n'MF2', 'X',\n'MF3', 'M',\\
-n'MFB', 'X',\n'MFD', 'X',\n'MFU', 'X',\n'MG7', 'X'\
-,\n'MGA', 'X',\n'MGB', 'X',\n'MGD', 'X',\n'MGG', '\
-R',\n'MGL', 'X',\n'MGN', 'Q',\n'MGO', 'X',\n'MGP',\
- 'X',\n'MGR', 'X',\n'MGS', 'X',\n'MGT', 'X',\n'MGU\
-', 'X',\n'MGY', 'G',\n'MHB', 'X',\n'MHF', 'X',\n'M\
-HL', 'L',\n'MHM', 'X',\n'MHO', 'M',\n'MHS', 'H',\n\
-'MHZ', 'X',\n'MIA', 'X',\n'MIC', 'X',\n'MID', 'X',\
-\n'MIL', 'X',\n'MIM', 'X',\n'MIN', 'G',\n'MIP', 'X\
-',\n'MIS', 'S',\n'MIT', 'X',\n'MJI', 'X',\n'MK1', \
-'X',\n'MKC', 'X',\n'MLA', 'X',\n'MLC', 'X',\n'MLE'\
-, 'L',\n'MLN', 'X',\n'MLT', 'X',\n'MLY', 'K',\n'ML\
-Z', 'K',\n'MM3', 'X',\n'MM4', 'X',\n'MMA', 'X',\n'\
-MMC', 'X',\n'MME', 'M',\n'MMO', 'R',\n'MMP', 'X',\\
-n'MMQ', 'X',\n'MMT', 'X',\n'MN1', 'X',\n'MN2', 'X'\
-,\n'MN3', 'X',\n'MN5', 'X',\n'MN7', 'X',\n'MN8', '\
-X',\n'MNA', 'X',\n'MNB', 'X',\n'MNC', 'X',\n'MNG',\
- 'X',\n'MNL', 'L',\n'MNO', 'X',\n'MNP', 'X',\n'MNQ\
-', 'X',\n'MNS', 'X',\n'MNT', 'X',\n'MNV', 'V',\n'M\
-O1', 'X',\n'MO2', 'X',\n'MO3', 'X',\n'MO4', 'X',\n\
-'MO5', 'X',\n'MO6', 'X',\n'MOA', 'X',\n'MOB', 'X',\
-\n'MOC', 'X',\n'MOE', 'X',\n'MOG', 'X',\n'MOH', 'X\
-',\n'MOL', 'X',\n'MOO', 'X',\n'MOP', 'X',\n'MOR', \
-'X',\n'MOS', 'X',\n'MOT', 'X',\n'MOX', 'X',\n'MP1'\
-, 'X',\n'MP3', 'X',\n'MPA', 'X',\n'MPB', 'X',\n'MP\
-C', 'X',\n'MPD', 'X',\n'MPG', 'X',\n'MPH', 'M',\n'\
-MPI', 'X',\n'MPJ', 'M',\n'MPL', 'X',\n'MPN', 'X',\\
-n'MPO', 'X',\n'MPP', 'X',\n'MPQ', 'G',\n'MPR', 'X'\
-,\n'MPS', 'X',\n'MQ0', 'X',\n'MQ7', 'X',\n'MQ8', '\
-X',\n'MQ9', 'X',\n'MQI', 'X',\n'MR2', 'X',\n'MRC',\
- 'X',\n'MRM', 'X',\n'MRP', 'X',\n'MS2', 'X',\n'MSA\
-', 'X',\n'MSB', 'X',\n'MSD', 'X',\n'MSE', 'M',\n'M\
-SF', 'X',\n'MSI', 'X',\n'MSO', 'M',\n'MSQ', 'X',\n\
-'MST', 'X',\n'MSU', 'X',\n'MTA', 'X',\n'MTB', 'X',\
-\n'MTC', 'X',\n'MTD', 'X',\n'MTE', 'X',\n'MTF', 'X\
-',\n'MTG', 'X',\n'MTO', 'X',\n'MTS', 'X',\n'MTT', \
-'X',\n'MTX', 'X',\n'MTY', 'Y',\n'MUG', 'X',\n'MUP'\
-, 'X',\n'MUR', 'X',\n'MVA', 'V',\n'MW1', 'X',\n'MW\
-2', 'X',\n'MXA', 'X',\n'MXY', 'X',\n'MYA', 'X',\n'\
-MYC', 'X',\n'MYG', 'X',\n'MYR', 'X',\n'MYS', 'X',\\
-n'MYT', 'X',\n'MZM', 'X',\n'N1T', 'X',\n'N25', 'X'\
-,\n'N2B', 'X',\n'N3T', 'X',\n'N4B', 'X',\n'NA2', '\
-X',\n'NA5', 'X',\n'NA6', 'X',\n'NAA', 'X',\n'NAB',\
- 'X',\n'NAC', 'X',\n'NAD', 'X',\n'NAE', 'X',\n'NAF\
-', 'X',\n'NAG', 'X',\n'NAH', 'X',\n'NAI', 'X',\n'N\
-AL', 'A',\n'NAM', 'A',\n'NAN', 'X',\n'NAO', 'X',\n\
-'NAP', 'X',\n'NAQ', 'X',\n'NAR', 'X',\n'NAS', 'X',\
-\n'NAU', 'X',\n'NAV', 'X',\n'NAW', 'X',\n'NAX', 'X\
-',\n'NAY', 'X',\n'NBA', 'X',\n'NBD', 'X',\n'NBE', \
-'X',\n'NBG', 'X',\n'NBN', 'X',\n'NBP', 'X',\n'NBS'\
-, 'X',\n'NBU', 'X',\n'NCA', 'X',\n'NCB', 'A',\n'NC\
-D', 'X',\n'NCH', 'X',\n'NCM', 'X',\n'NCN', 'X',\n'\
-NCO', 'X',\n'NCR', 'X',\n'NCS', 'X',\n'ND4', 'X',\\
-n'NDA', 'X',\n'NDC', 'X',\n'NDD', 'X',\n'NDO', 'X'\
-,\n'NDP', 'X',\n'NDT', 'X',\n'NEA', 'X',\n'NEB', '\
-X',\n'NED', 'X',\n'NEM', 'H',\n'NEN', 'X',\n'NEO',\
- 'X',\n'NEP', 'H',\n'NEQ', 'X',\n'NES', 'X',\n'NET\
-', 'X',\n'NEV', 'X',\n'NFA', 'F',\n'NFE', 'X',\n'N\
-FG', 'X',\n'NFP', 'X',\n'NFS', 'X',\n'NG6', 'X',\n\
-'NGA', 'X',\n'NGL', 'X',\n'NGM', 'X',\n'NGO', 'X',\
-\n'NGP', 'X',\n'NGT', 'X',\n'NGU', 'X',\n'NH2', 'X\
-',\n'NH3', 'X',\n'NH4', 'X',\n'NHD', 'X',\n'NHE', \
-'X',\n'NHM', 'X',\n'NHP', 'X',\n'NHR', 'X',\n'NHS'\
-, 'X',\n'NI1', 'X',\n'NI2', 'X',\n'NIC', 'X',\n'NI\
-D', 'X',\n'NIK', 'X',\n'NIO', 'X',\n'NIP', 'X',\n'\
-NIT', 'X',\n'NIU', 'X',\n'NIY', 'Y',\n'NLA', 'X',\\
-n'NLE', 'L',\n'NLG', 'X',\n'NLN', 'L',\n'NLP', 'L'\
-,\n'NM1', 'X',\n'NMA', 'A',\n'NMB', 'X',\n'NMC', '\
-G',\n'NMD', 'X',\n'NME', 'X',\n'NMN', 'X',\n'NMO',\
- 'X',\n'NMQ', 'X',\n'NMX', 'X',\n'NMY', 'X',\n'NNH\
-', 'R',\n'NNO', 'X',\n'NO2', 'X',\n'NO3', 'X',\n'N\
-OA', 'X',\n'NOD', 'X',\n'NOJ', 'X',\n'NON', 'X',\n\
-'NOP', 'X',\n'NOR', 'X',\n'NOS', 'X',\n'NOV', 'X',\
-\n'NOX', 'X',\n'NP3', 'X',\n'NPA', 'X',\n'NPC', 'X\
-',\n'NPD', 'X',\n'NPE', 'X',\n'NPF', 'X',\n'NPH', \
-'C',\n'NPI', 'X',\n'NPL', 'X',\n'NPN', 'X',\n'NPO'\
-, 'X',\n'NPP', 'X',\n'NPT', 'X',\n'NPY', 'X',\n'NR\
-G', 'R',\n'NRI', 'X',\n'NS1', 'X',\n'NS5', 'X',\n'\
-NSP', 'X',\n'NTA', 'X',\n'NTB', 'X',\n'NTC', 'X',\\
-n'NTH', 'X',\n'NTM', 'X',\n'NTP', 'X',\n'NTS', 'X'\
-,\n'NTU', 'X',\n'NTZ', 'X',\n'NU1', 'X',\n'NVA', '\
-V',\n'NVI', 'X',\n'NVP', 'X',\n'NW1', 'X',\n'NYP',\
- 'X',\n'O4M', 'X',\n'OAA', 'X',\n'OAI', 'X',\n'OAP\
-', 'X',\n'OAR', 'X',\n'OAS', 'S',\n'OBA', 'X',\n'O\
-BN', 'X',\n'OC1', 'X',\n'OC2', 'X',\n'OC3', 'X',\n\
-'OC4', 'X',\n'OC5', 'X',\n'OC6', 'X',\n'OC7', 'X',\
-\n'OCL', 'X',\n'OCM', 'X',\n'OCN', 'X',\n'OCO', 'X\
-',\n'OCP', 'X',\n'OCS', 'C',\n'OCT', 'X',\n'OCV', \
-'K',\n'OCY', 'C',\n'ODA', 'X',\n'ODS', 'X',\n'OES'\
-, 'X',\n'OET', 'X',\n'OF1', 'X',\n'OF2', 'X',\n'OF\
-3', 'X',\n'OFL', 'X',\n'OFO', 'X',\n'OHE', 'X',\n'\
-OHO', 'X',\n'OHT', 'X',\n'OIC', 'X',\n'OIP', 'X',\\
-n'OKA', 'X',\n'OLA', 'X',\n'OLE', 'X',\n'OLI', 'X'\
-,\n'OLO', 'X',\n'OMB', 'X',\n'OMC', 'X',\n'OMD', '\
-X',\n'OME', 'X',\n'OMG', 'X',\n'OMP', 'X',\n'OMT',\
- 'M',\n'OMU', 'X',\n'ONE', 'X',\n'ONL', 'L',\n'ONP\
-', 'X',\n'OPA', 'X',\n'OPD', 'X',\n'OPE', 'X',\n'O\
-PG', 'X',\n'OPH', 'X',\n'OPN', 'X',\n'OPP', 'X',\n\
-'OPR', 'R',\n'ORN', 'X',\n'ORO', 'X',\n'ORP', 'X',\
-\n'OSB', 'X',\n'OSS', 'X',\n'OTA', 'X',\n'OTB', 'X\
-',\n'OTE', 'X',\n'OTG', 'X',\n'OUT', 'X',\n'OVA', \
-'X',\n'OWQ', 'X',\n'OXA', 'X',\n'OXE', 'X',\n'OXI'\
-, 'X',\n'OXL', 'X',\n'OXM', 'X',\n'OXN', 'X',\n'OX\
-O', 'X',\n'OXP', 'X',\n'OXS', 'X',\n'OXY', 'X',\n'\
-P11', 'A',\n'P24', 'X',\n'P28', 'X',\n'P2P', 'X',\\
-n'P2U', 'X',\n'P3M', 'X',\n'P4C', 'X',\n'P4P', 'X'\
-,\n'P5P', 'X',\n'P6G', 'X',\n'PA1', 'X',\n'PA2', '\
-X',\n'PA3', 'X',\n'PA4', 'X',\n'PA5', 'X',\n'PAA',\
- 'X',\n'PAB', 'X',\n'PAC', 'X',\n'PAD', 'X',\n'PAE\
-', 'X',\n'PAG', 'X',\n'PAH', 'X',\n'PAI', 'X',\n'P\
-AL', 'D',\n'PAM', 'X',\n'PAN', 'X',\n'PAO', 'X',\n\
-'PAP', 'A',\n'PAQ', 'F',\n'PAR', 'X',\n'PAS', 'X',\
-\n'PAT', 'W',\n'PBA', 'X',\n'PBB', 'X',\n'PBC', 'X\
-',\n'PBF', 'F',\n'PBG', 'X',\n'PBI', 'X',\n'PBM', \
-'X',\n'PBN', 'X',\n'PBP', 'X',\n'PBR', 'X',\n'PBZ'\
-, 'X',\n'PC2', 'X',\n'PCA', 'E',\n'PCB', 'X',\n'PC\
-D', 'X',\n'PCE', 'X',\n'PCG', 'X',\n'PCH', 'X',\n'\
-PCL', 'X',\n'PCM', 'X',\n'PCP', 'X',\n'PCR', 'X',\\
-n'PCS', 'X',\n'PCU', 'X',\n'PCV', 'X',\n'PCY', 'X'\
-,\n'PD1', 'X',\n'PDA', 'X',\n'PDC', 'X',\n'PDD', '\
-A',\n'PDE', 'A',\n'PDI', 'X',\n'PDL', 'A',\n'PDN',\
- 'X',\n'PDO', 'X',\n'PDP', 'X',\n'PDT', 'X',\n'PDU\
-', 'X',\n'PE2', 'X',\n'PE6', 'X',\n'PEA', 'X',\n'P\
-EB', 'X',\n'PEC', 'X',\n'PED', 'X',\n'PEE', 'X',\n\
-'PEF', 'X',\n'PEG', 'X',\n'PEL', 'X',\n'PEO', 'X',\
-\n'PEP', 'X',\n'PEQ', 'X',\n'PER', 'X',\n'PET', 'X\
-',\n'PFB', 'X',\n'PFC', 'X',\n'PFG', 'X',\n'PFL', \
-'X',\n'PFM', 'X',\n'PFZ', 'X',\n'PG4', 'X',\n'PG5'\
-, 'X',\n'PG6', 'X',\n'PGA', 'X',\n'PGC', 'X',\n'PG\
-D', 'X',\n'PGE', 'X',\n'PGG', 'G',\n'PGH', 'X',\n'\
-PGL', 'X',\n'PGO', 'X',\n'PGP', 'X',\n'PGQ', 'X',\\
-n'PGR', 'X',\n'PGS', 'X',\n'PGU', 'X',\n'PGX', 'X'\
-,\n'PGY', 'G',\n'PH1', 'X',\n'PH2', 'X',\n'PH3', '\
-X',\n'PHA', 'F',\n'PHB', 'X',\n'PHC', 'X',\n'PHD',\
- 'X',\n'PHE', 'F',\n'PHG', 'X',\n'PHH', 'X',\n'PHI\
-', 'F',\n'PHL', 'F',\n'PHM', 'X',\n'PHN', 'X',\n'P\
-HO', 'X',\n'PHP', 'X',\n'PHQ', 'X',\n'PHS', 'H',\n\
-'PHT', 'X',\n'PHW', 'P',\n'PHY', 'X',\n'PI1', 'X',\
-\n'PI2', 'X',\n'PI3', 'X',\n'PI4', 'X',\n'PI5', 'X\
-',\n'PI6', 'X',\n'PI7', 'X',\n'PI8', 'X',\n'PI9', \
-'X',\n'PIA', 'X',\n'PIB', 'X',\n'PIC', 'X',\n'PID'\
-, 'X',\n'PIG', 'X',\n'PIH', 'X',\n'PIM', 'X',\n'PI\
-N', 'X',\n'PIO', 'X',\n'PIP', 'X',\n'PIQ', 'X',\n'\
-PIR', 'X',\n'PIV', 'X',\n'PKF', 'X',\n'PL1', 'X',\\
-n'PL9', 'X',\n'PLA', 'D',\n'PLC', 'X',\n'PLE', 'L'\
-,\n'PLG', 'G',\n'PLH', 'X',\n'PLM', 'X',\n'PLP', '\
-X',\n'PLS', 'S',\n'PLT', 'W',\n'PLU', 'L',\n'PLY',\
- 'X',\n'PMA', 'X',\n'PMB', 'X',\n'PMC', 'X',\n'PME\
-', 'F',\n'PML', 'X',\n'PMM', 'X',\n'PMO', 'X',\n'P\
-MP', 'X',\n'PMS', 'X',\n'PMY', 'X',\n'PN2', 'X',\n\
-'PNA', 'X',\n'PNB', 'X',\n'PNC', 'G',\n'PND', 'X',\
-\n'PNE', 'A',\n'PNF', 'X',\n'PNG', 'X',\n'PNI', 'X\
-',\n'PNL', 'X',\n'PNM', 'X',\n'PNN', 'X',\n'PNO', \
-'X',\n'PNP', 'X',\n'PNQ', 'X',\n'PNS', 'X',\n'PNT'\
-, 'X',\n'PNU', 'X',\n'PO2', 'X',\n'PO4', 'X',\n'PO\
-B', 'X',\n'POC', 'X',\n'POL', 'X',\n'POM', 'P',\n'\
-PON', 'X',\n'POP', 'X',\n'POR', 'X',\n'POS', 'X',\\
-n'PP1', 'X',\n'PP2', 'X',\n'PP3', 'A',\n'PP4', 'X'\
-,\n'PP5', 'X',\n'PP6', 'X',\n'PP7', 'X',\n'PP8', '\
-N',\n'PP9', 'X',\n'PPB', 'X',\n'PPC', 'X',\n'PPD',\
- 'X',\n'PPE', 'E',\n'PPG', 'X',\n'PPH', 'F',\n'PPI\
-', 'X',\n'PPJ', 'V',\n'PPL', 'X',\n'PPM', 'X',\n'P\
-PN', 'A',\n'PPO', 'X',\n'PPP', 'X',\n'PPQ', 'X',\n\
-'PPR', 'X',\n'PPS', 'X',\n'PPT', 'X',\n'PPU', 'X',\
-\n'PPX', 'F',\n'PPY', 'X',\n'PPZ', 'X',\n'PQ0', 'X\
-',\n'PQN', 'X',\n'PQQ', 'X',\n'PR1', 'X',\n'PR2', \
-'X',\n'PR3', 'X',\n'PRA', 'X',\n'PRB', 'X',\n'PRC'\
-, 'X',\n'PRD', 'X',\n'PRE', 'X',\n'PRF', 'X',\n'PR\
-H', 'X',\n'PRI', 'P',\n'PRL', 'X',\n'PRN', 'X',\n'\
-PRO', 'P',\n'PRP', 'X',\n'PRR', 'A',\n'PRS', 'P',\\
-n'PRZ', 'X',\n'PS0', 'X',\n'PSA', 'X',\n'PSD', 'X'\
-,\n'PSE', 'X',\n'PSF', 'S',\n'PSG', 'X',\n'PSI', '\
-X',\n'PSO', 'X',\n'PSQ', 'X',\n'PSS', 'X',\n'PST',\
- 'X',\n'PSU', 'X',\n'PT1', 'X',\n'PT3', 'X',\n'PTA\
-', 'X',\n'PTC', 'X',\n'PTD', 'X',\n'PTE', 'X',\n'P\
-TH', 'Y',\n'PTL', 'X',\n'PTM', 'Y',\n'PTN', 'X',\n\
-'PTO', 'X',\n'PTP', 'X',\n'PTR', 'Y',\n'PTS', 'X',\
-\n'PTT', 'X',\n'PTU', 'X',\n'PTY', 'X',\n'PUA', 'X\
-',\n'PUB', 'X',\n'PUR', 'X',\n'PUT', 'X',\n'PVA', \
-'X',\n'PVB', 'X',\n'PVH', 'H',\n'PVL', 'X',\n'PXA'\
-, 'X',\n'PXF', 'X',\n'PXG', 'X',\n'PXP', 'X',\n'PX\
-Y', 'X',\n'PXZ', 'X',\n'PY2', 'X',\n'PY4', 'X',\n'\
-PY5', 'X',\n'PY6', 'X',\n'PYA', 'A',\n'PYC', 'X',\\
-n'PYD', 'X',\n'PYE', 'X',\n'PYL', 'X',\n'PYM', 'X'\
-,\n'PYO', 'X',\n'PYP', 'X',\n'PYQ', 'X',\n'PYR', '\
-X',\n'PYS', 'X',\n'PYT', 'X',\n'PYX', 'X',\n'PYY',\
- 'X',\n'PYZ', 'X',\n'PZQ', 'X',\n'Q82', 'X',\n'QNC\
-', 'X',\n'QND', 'X',\n'QSI', 'Q',\n'QTR', 'X',\n'Q\
-UA', 'X',\n'QUE', 'X',\n'QUI', 'X',\n'QUO', 'X',\n\
-'R11', 'X',\n'R12', 'X',\n'R13', 'X',\n'R18', 'X',\
-\n'R1P', 'X',\n'R56', 'X',\n'R5P', 'X',\n'RA2', 'X\
-',\n'RAD', 'X',\n'RAI', 'X',\n'RAL', 'X',\n'RAM', \
-'X',\n'RAN', 'X',\n'RAP', 'X',\n'RBF', 'X',\n'RBU'\
-, 'X',\n'RCA', 'X',\n'RCL', 'X',\n'RCO', 'X',\n'RD\
-C', 'X',\n'RDF', 'W',\n'RE9', 'X',\n'REA', 'X',\n'\
-RED', 'K',\n'REO', 'X',\n'REP', 'X',\n'RET', 'X',\\
-n'RFA', 'X',\n'RFB', 'X',\n'RFL', 'X',\n'RFP', 'X'\
-,\n'RG1', 'X',\n'RGS', 'X',\n'RH1', 'X',\n'RHA', '\
-X',\n'RHC', 'X',\n'RHD', 'X',\n'RHM', 'X',\n'RHO',\
- 'X',\n'RHQ', 'X',\n'RHS', 'X',\n'RIA', 'X',\n'RIB\
-', 'X',\n'RIC', 'X',\n'RIF', 'X',\n'RIN', 'X',\n'R\
-IP', 'X',\n'RIT', 'X',\n'RMB', 'X',\n'RMN', 'X',\n\
-'RMP', 'X',\n'RNG', 'X',\n'RNS', 'X',\n'RNT', 'X',\
-\n'RO2', 'X',\n'RO4', 'X',\n'ROC', 'N',\n'ROI', 'X\
-',\n'ROM', 'X',\n'RON', 'V',\n'ROP', 'X',\n'ROS', \
-'X',\n'ROX', 'X',\n'RPA', 'X',\n'RPD', 'X',\n'RPH'\
-, 'X',\n'RPL', 'X',\n'RPP', 'X',\n'RPR', 'X',\n'RP\
-X', 'X',\n'RQ3', 'X',\n'RR1', 'X',\n'RR6', 'X',\n'\
-RRS', 'X',\n'RS1', 'X',\n'RS2', 'X',\n'RS7', 'X',\\
-n'RSS', 'X',\n'RTA', 'X',\n'RTB', 'X',\n'RTC', 'X'\
-,\n'RTL', 'X',\n'RUB', 'X',\n'RUN', 'X',\n'RWJ', '\
-X',\n'RXP', 'X',\n'S02', 'X',\n'S11', 'X',\n'S1H',\
- 'S',\n'S27', 'X',\n'S2C', 'C',\n'S3P', 'X',\n'S4U\
-', 'X',\n'S57', 'X',\n'S58', 'X',\n'S5H', 'X',\n'S\
-6G', 'X',\n'S80', 'X',\n'SAA', 'X',\n'SAB', 'X',\n\
-'SAC', 'S',\n'SAD', 'X',\n'SAE', 'X',\n'SAF', 'X',\
-\n'SAH', 'C',\n'SAI', 'C',\n'SAL', 'X',\n'SAM', 'M\
-',\n'SAN', 'X',\n'SAP', 'X',\n'SAR', 'X',\n'SAS', \
-'X',\n'SB1', 'X',\n'SB2', 'X',\n'SB3', 'X',\n'SB4'\
-, 'X',\n'SB5', 'X',\n'SB6', 'X',\n'SBA', 'L',\n'SB\
-B', 'X',\n'SBD', 'A',\n'SBI', 'X',\n'SBL', 'A',\n'\
-SBN', 'X',\n'SBO', 'X',\n'SBR', 'X',\n'SBS', 'X',\\
-n'SBT', 'X',\n'SBU', 'X',\n'SBX', 'X',\n'SC4', 'X'\
-,\n'SCA', 'X',\n'SCC', 'X',\n'SCD', 'X',\n'SCH', '\
-C',\n'SCI', 'X',\n'SCL', 'X',\n'SCM', 'X',\n'SCN',\
- 'X',\n'SCO', 'X',\n'SCP', 'S',\n'SCR', 'X',\n'SCS\
-', 'X',\n'SCV', 'C',\n'SCY', 'C',\n'SD8', 'X',\n'S\
-DK', 'X',\n'SDZ', 'X',\n'SE4', 'X',\n'SEA', 'X',\n\
-'SEB', 'S',\n'SEC', 'X',\n'SEG', 'A',\n'SEI', 'X',\
-\n'SEL', 'S',\n'SEM', 'X',\n'SEO', 'X',\n'SEP', 'S\
-',\n'SER', 'S',\n'SES', 'X',\n'SET', 'S',\n'SEU', \
-'X',\n'SF4', 'X',\n'SFG', 'X',\n'SFN', 'X',\n'SFO'\
-, 'X',\n'SGA', 'X',\n'SGC', 'X',\n'SGL', 'X',\n'SG\
-M', 'X',\n'SGN', 'X',\n'SGP', 'X',\n'SHA', 'X',\n'\
-SHC', 'X',\n'SHF', 'X',\n'SHH', 'X',\n'SHP', 'G',\\
-n'SHR', 'E',\n'SHT', 'T',\n'SHU', 'X',\n'SI2', 'X'\
-,\n'SIA', 'X',\n'SIF', 'X',\n'SIG', 'X',\n'SIH', '\
-X',\n'SIM', 'X',\n'SIN', 'X',\n'SKD', 'X',\n'SKF',\
- 'X',\n'SLB', 'X',\n'SLE', 'X',\n'SLZ', 'K',\n'SMA\
-', 'X',\n'SMC', 'C',\n'SME', 'M',\n'SML', 'X',\n'S\
-MM', 'M',\n'SMN', 'X',\n'SMP', 'X',\n'SMS', 'X',\n\
-'SN1', 'X',\n'SN6', 'X',\n'SN7', 'X',\n'SNC', 'C',\
-\n'SNN', 'X',\n'SNP', 'X',\n'SO1', 'X',\n'SO2', 'X\
-',\n'SO3', 'X',\n'SO4', 'X',\n'SOA', 'X',\n'SOC', \
-'C',\n'SOM', 'X',\n'SOR', 'X',\n'SOT', 'X',\n'SOX'\
-, 'X',\n'SPA', 'X',\n'SPB', 'X',\n'SPC', 'X',\n'SP\
-D', 'X',\n'SPE', 'X',\n'SPG', 'X',\n'SPH', 'X',\n'\
-SPI', 'X',\n'SPK', 'X',\n'SPM', 'X',\n'SPN', 'X',\\
-n'SPO', 'X',\n'SPP', 'X',\n'SPS', 'X',\n'SPY', 'X'\
-,\n'SQU', 'X',\n'SRA', 'X',\n'SRB', 'X',\n'SRD', '\
-X',\n'SRL', 'X',\n'SRM', 'X',\n'SRS', 'X',\n'SRY',\
- 'X',\n'SSA', 'X',\n'SSB', 'X',\n'SSG', 'X',\n'SSP\
-', 'X',\n'ST1', 'X',\n'ST2', 'X',\n'ST3', 'X',\n'S\
-T4', 'X',\n'ST5', 'X',\n'ST6', 'X',\n'STA', 'X',\n\
-'STB', 'X',\n'STE', 'X',\n'STG', 'X',\n'STI', 'X',\
-\n'STL', 'X',\n'STN', 'X',\n'STO', 'X',\n'STP', 'X\
-',\n'STR', 'X',\n'STU', 'X',\n'STY', 'Y',\n'SU1', \
-'X',\n'SU2', 'X',\n'SUC', 'X',\n'SUI', 'X',\n'SUL'\
-, 'X',\n'SUR', 'X',\n'SVA', 'S',\n'SWA', 'X',\n'T1\
-6', 'X',\n'T19', 'X',\n'T23', 'X',\n'T29', 'X',\n'\
-T33', 'X',\n'T3P', 'X',\n'T42', 'A',\n'T44', 'X',\\
-n'T5A', 'X',\n'T6A', 'T',\n'T6P', 'X',\n'T80', 'X'\
-,\n'T87', 'X',\n'TA1', 'X',\n'TAA', 'X',\n'TAB', '\
-X',\n'TAC', 'X',\n'TAD', 'X',\n'TAF', 'X',\n'TAM',\
- 'X',\n'TAP', 'X',\n'TAR', 'X',\n'TAS', 'X',\n'TAU\
-', 'X',\n'TAX', 'X',\n'TAZ', 'X',\n'TB9', 'X',\n'T\
-BA', 'X',\n'TBD', 'X',\n'TBG', 'G',\n'TBH', 'X',\n\
-'TBM', 'T',\n'TBO', 'X',\n'TBP', 'X',\n'TBR', 'X',\
-\n'TBS', 'X',\n'TBT', 'X',\n'TBU', 'X',\n'TBZ', 'X\
-',\n'TC4', 'X',\n'TCA', 'X',\n'TCB', 'X',\n'TCH', \
-'X',\n'TCK', 'X',\n'TCL', 'X',\n'TCM', 'X',\n'TCN'\
-, 'X',\n'TCP', 'X',\n'TCR', 'W',\n'TCS', 'X',\n'TC\
-Z', 'X',\n'TDA', 'X',\n'TDB', 'X',\n'TDG', 'X',\n'\
-TDP', 'X',\n'TDR', 'X',\n'TDX', 'X',\n'TEA', 'X',\\
-n'TEM', 'X',\n'TEN', 'X',\n'TEO', 'X',\n'TEP', 'X'\
-,\n'TER', 'X',\n'TES', 'X',\n'TET', 'X',\n'TFA', '\
-X',\n'TFB', 'X',\n'TFH', 'X',\n'TFI', 'X',\n'TFK',\
- 'X',\n'TFP', 'X',\n'THA', 'X',\n'THB', 'X',\n'THC\
-', 'T',\n'THD', 'X',\n'THE', 'X',\n'THF', 'X',\n'T\
-HJ', 'X',\n'THK', 'X',\n'THM', 'X',\n'THN', 'X',\n\
-'THO', 'T',\n'THP', 'X',\n'THQ', 'X',\n'THR', 'T',\
-\n'THS', 'X',\n'THT', 'X',\n'THU', 'X',\n'THX', 'X\
-',\n'THZ', 'X',\n'TI1', 'X',\n'TI2', 'X',\n'TI3', \
-'P',\n'TIA', 'X',\n'TIH', 'A',\n'TK4', 'X',\n'TLA'\
-, 'X',\n'TLC', 'X',\n'TLM', 'X',\n'TLN', 'X',\n'TL\
-X', 'X',\n'TM5', 'X',\n'TM6', 'X',\n'TMA', 'X',\n'\
-TMB', 'T',\n'TMC', 'X',\n'TMD', 'T',\n'TME', 'X',\\
-n'TMF', 'X',\n'TML', 'K',\n'TMM', 'X',\n'TMN', 'X'\
-,\n'TMP', 'X',\n'TMQ', 'X',\n'TMR', 'X',\n'TMT', '\
-X',\n'TMZ', 'X',\n'TNB', 'C',\n'TND', 'X',\n'TNK',\
- 'X',\n'TNP', 'X',\n'TNT', 'X',\n'TOA', 'X',\n'TOB\
-', 'X',\n'TOC', 'X',\n'TOL', 'X',\n'TOP', 'X',\n'T\
-OS', 'X',\n'TOT', 'X',\n'TP1', 'G',\n'TP2', 'P',\n\
-'TP3', 'E',\n'TP4', 'E',\n'TP7', 'T',\n'TPA', 'X',\
-\n'TPE', 'X',\n'TPF', 'X',\n'TPI', 'X',\n'TPL', 'W\
-',\n'TPM', 'X',\n'TPN', 'G',\n'TPO', 'T',\n'TPP', \
-'X',\n'TPQ', 'A',\n'TPR', 'P',\n'TPS', 'X',\n'TPT'\
-, 'X',\n'TPV', 'X',\n'TPX', 'X',\n'TPY', 'X',\n'TQ\
-3', 'X',\n'TQ4', 'X',\n'TQ5', 'X',\n'TQ6', 'X',\n'\
-TR1', 'X',\n'TRA', 'X',\n'TRB', 'X',\n'TRC', 'X',\\
-n'TRD', 'X',\n'TRE', 'X',\n'TRF', 'W',\n'TRG', 'K'\
-,\n'TRH', 'X',\n'TRI', 'X',\n'TRJ', 'X',\n'TRM', '\
-X',\n'TRN', 'W',\n'TRO', 'W',\n'TRP', 'W',\n'TRQ',\
- 'X',\n'TRS', 'X',\n'TRX', 'W',\n'TRZ', 'X',\n'TS2\
-', 'X',\n'TS3', 'X',\n'TS4', 'X',\n'TS5', 'X',\n'T\
-SA', 'X',\n'TSB', 'X',\n'TSI', 'X',\n'TSM', 'X',\n\
-'TSN', 'X',\n'TSP', 'X',\n'TSU', 'X',\n'TTA', 'X',\
-\n'TTE', 'X',\n'TTN', 'X',\n'TTO', 'X',\n'TTP', 'X\
-',\n'TTX', 'X',\n'TXL', 'X',\n'TYA', 'Y',\n'TYB', \
-'Y',\n'TYD', 'X',\n'TYI', 'Y',\n'TYL', 'X',\n'TYM'\
-, 'W',\n'TYN', 'Y',\n'TYQ', 'Y',\n'TYR', 'Y',\n'TY\
-S', 'Y',\n'TYV', 'X',\n'TYY', 'A',\n'TZB', 'X',\n'\
-TZC', 'X',\n'TZE', 'X',\n'TZL', 'X',\n'TZO', 'X',\\
-n'TZP', 'X',\n'U01', 'X',\n'U02', 'X',\n'U03', 'X'\
-,\n'U04', 'X',\n'U05', 'X',\n'U0E', 'X',\n'U10', '\
-X',\n'U18', 'X',\n'U2G', 'X',\n'U3P', 'X',\n'U49',\
- 'X',\n'U55', 'X',\n'U5P', 'X',\n'U66', 'X',\n'U89\
-', 'X',\n'U8U', 'X',\n'UAA', 'X',\n'UAG', 'A',\n'U\
-AP', 'X',\n'UAR', 'X',\n'UC1', 'X',\n'UC2', 'X',\n\
-'UC3', 'X',\n'UC4', 'X',\n'UD1', 'X',\n'UD2', 'X',\
-\n'UDP', 'X',\n'UDX', 'X',\n'UFG', 'X',\n'UFM', 'X\
-',\n'UFP', 'X',\n'UGA', 'X',\n'UIN', 'X',\n'UKP', \
-'A',\n'UM3', 'X',\n'UMA', 'A',\n'UMG', 'X',\n'UMP'\
-, 'X',\n'UNA', 'X',\n'UND', 'X',\n'UNI', 'X',\n'UN\
-K', 'X',\n'UNN', 'X',\n'UNX', 'X',\n'UP5', 'X',\n'\
-UP6', 'X',\n'UPA', 'X',\n'UPF', 'X',\n'UPG', 'X',\\
-n'UPP', 'X',\n'UQ1', 'X',\n'UQ2', 'X',\n'UQ6', 'X'\
-,\n'UR2', 'X',\n'URA', 'X',\n'URE', 'X',\n'URF', '\
-X',\n'URI', 'X',\n'URS', 'X',\n'UTP', 'X',\n'UVC',\
- 'X',\n'UVW', 'X',\n'V35', 'X',\n'V36', 'X',\n'V4O\
-', 'X',\n'V7O', 'X',\n'VAA', 'V',\n'VAC', 'X',\n'V\
-AD', 'V',\n'VAF', 'V',\n'VAG', 'X',\n'VAL', 'V',\n\
-'VAN', 'X',\n'VAS', 'X',\n'VAX', 'X',\n'VDX', 'X',\
-\n'VDY', 'X',\n'VG1', 'X',\n'VIB', 'X',\n'VIR', 'X\
-',\n'VIT', 'X',\n'VK3', 'X',\n'VO3', 'X',\n'VO4', \
-'X',\n'VS1', 'F',\n'VS2', 'F',\n'VS3', 'F',\n'VS4'\
-, 'F',\n'VXA', 'X',\n'W01', 'X',\n'W02', 'X',\n'W0\
-3', 'X',\n'W11', 'X',\n'W33', 'X',\n'W35', 'X',\n'\
-W42', 'X',\n'W43', 'X',\n'W54', 'X',\n'W56', 'X',\\
-n'W59', 'X',\n'W71', 'X',\n'W84', 'X',\n'W8R', 'X'\
-,\n'W91', 'X',\n'WAY', 'X',\n'WCC', 'X',\n'WO2', '\
-X',\n'WO4', 'X',\n'WRB', 'X',\n'WRR', 'X',\n'WRS',\
- 'X',\n'WW7', 'X',\n'X2F', 'X',\n'X7O', 'X',\n'XAA\
-', 'X',\n'XAN', 'X',\n'XAO', 'X',\n'XBB', 'X',\n'X\
-BP', 'X',\n'XDN', 'X',\n'XDP', 'X',\n'XIF', 'X',\n\
-'XIM', 'X',\n'XK2', 'X',\n'XL1', 'X',\n'XLS', 'X',\
-\n'XMP', 'X',\n'XN1', 'X',\n'XN2', 'X',\n'XN3', 'X\
-',\n'XUL', 'X',\n'XV6', 'X',\n'XYD', 'X',\n'XYH', \
-'X',\n'XYL', 'X',\n'XYP', 'X',\n'XYS', 'X',\n'YOF'\
-, 'Y',\n'YRR', 'X',\n'YT3', 'X',\n'YZ9', 'X',\n'Z3\
-4', 'G',\n'Z5A', 'X',\n'ZAF', 'X',\n'ZAP', 'X',\n'\
-ZEB', 'X',\n'ZEN', 'X',\n'ZES', 'X',\n'ZID', 'X',\\
-n'ZMR', 'X',\n'ZN3', 'X',\n'ZNH', 'X',\n'ZNO', 'X'\
-,\n'ZO3', 'X',\n'ZPR', 'P',\n'ZRA', 'A',\n'ZST', '\
-X',\n'ZYA', 'A',\n\n\n'ASN','N');\n} \n\n\nsub fil\
-e2head\n {\n my $file = shift;\n my $size = s\
-hift;\n my $f= new FileHandle;\n my $line;\n open \
-($f,$file);\n read ($f,$line, $size);\n close ($f)\
-;\n return $line;\n }\nsub file2tail\n {\
-\n my $file = shift;\n my $size = shift;\n my $f= \
-new FileHandle;\n my $line;\n \n open ($f,$file);\\
-n seek ($f,$size*-1, 2);\n read ($f,$line, $size);\
-\n close ($f);\n return $line;\n }\n\n\nsub v\
-tmpnam\n {\n my $r=rand(100000);\n my $f=\"fi\
-le.$r.$$\";\n while (-e $f)\n {\n $f=vtmpnam\
-();\n }\n push (@TMPFILE_LIST, $f);\n return $f;\
-\n }\n\nsub myexit\n {\n my $code=@_[0];\\
-n if ($CLEAN_EXIT_STARTED==1){return;}\n els\
-e {$CLEAN_EXIT_STARTED=1;}\n ### ONLY BARE EXIT\
-\n exit ($code);\n }\nsub set_error_lock\n \
-{\n my $name = shift;\n my $pid=$$;\n\n \
- \n &lock4tc ($$,\"LERROR\", \"LSET\", \"\
-$$ -- ERROR: $name $PROGRAM\\n\");\n return;\\
-n }\nsub set_lock\n {\n my $pid=shift;\n \
- my $msg= shift;\n my $p=getppid();\n &lock4\
-tc ($pid,\"LLOCK\",\"LRESET\",\"$p$msg\\n\");\n }\
-\nsub unset_lock\n {\n \n my $pid=shift;\\
-n &lock4tc ($pid,\"LLOCK\",\"LRELEASE\",\"\");\\
-n }\nsub shift_lock\n {\n my $from=shift;\n \
- my $to=shift;\n my $from_type=shift;\n my \
-$to_type=shift;\n my $action=shift;\n my $ms\
-g;\n \n if (!&lock4tc($from, $from_type, \"L\
-CHECK\", \"\")){return 0;}\n $msg=&lock4tc ($fr\
-om, $from_type, \"LREAD\", \"\");\n &lock4tc ($\
-from, $from_type,\"LRELEASE\", $msg);\n &lock4t\
-c ($to, $to_type, $action, $msg);\n return;\n \
-}\nsub isshellpid\n {\n my $p=shift;\n if (\
-!lock4tc ($p, \"LLOCK\", \"LCHECK\")){return 0;}\n\
- else\n {\n my $c=lock4tc($p, \"LLOCK\", \\
-"LREAD\");\n if ( $c=~/-SHELL-/){return 1;}\n \
- }\n return 0;\n }\nsub isrootpid\n {\n if\
-(lock4tc (getppid(), \"LLOCK\", \"LCHECK\")){retur\
-n 0;}\n else {return 1;}\n }\nsub lock4tc\n {\\
-n my ($pid,$type,$action,$value)=@_;\n my $fna\
-me;\n my $host=hostname;\n \n if ($type eq \\
-"LLOCK\"){$fname=\"$LOCKDIR/.$pid.$host.lock4tcoff\
-ee\";}\n elsif ( $type eq \"LERROR\"){ $fname=\"\
-$LOCKDIR/.$pid.$host.error4tcoffee\";}\n elsif (\
- $type eq \"LWARNING\"){ $fname=\"$LOCKDIR/.$pid.$\
-host.warning4tcoffee\";}\n \n if ($debug_lock)\
-\n {\n print STDERR \"\\n\\t---lock4tc(t\
-cg): $action => $fname =>$value (RD: $LOCKDIR)\\n\\
-";\n }\n\n if ($action eq \"LCHECK\") {re\
-turn -e $fname;}\n elsif ($action eq \"LREAD\"){\
-return file2string($fname);}\n elsif ($action eq\
- \"LSET\") {return string2file ($value, $fname, \"\
->>\");}\n elsif ($action eq \"LRESET\") {return \
-string2file ($value, $fname, \">\");}\n elsif ($\
-action eq \"LRELEASE\") \n {\n if ( $deb\
-ug_lock)\n {\n my $g=new FileHandle;\n open\
- ($g, \">>$fname\");\n print $g \"\\nDestroyed \
-by $$\\n\";\n close ($g);\n safe_system (\"m\
-v $fname $fname.old\");\n }\n else\n {\n \
- unlink ($fname);\n }\n }\n return \"\";\n\
- }\n \nsub file2string\n {\n my $file=@_[0];\n \
- my $f=new FileHandle;\n my $r;\n open ($f, \"\
-$file\");\n while (<$f>){$r.=$_;}\n close ($f)\
-;\n return $r;\n }\nsub string2file \n {\n \
- my ($s,$file,$mode)=@_;\n my $f=new FileHandle\
-;\n \n open ($f, \"$mode$file\");\n print\
- $f \"$s\";\n close ($f);\n }\n\nBEGIN\n {\
-\n srand;\n \n $SIG{'SIGUP'}='signal_\
-cleanup';\n $SIG{'SIGINT'}='signal_cleanup';\\
-n $SIG{'SIGQUIT'}='signal_cleanup';\n $S\
-IG{'SIGILL'}='signal_cleanup';\n $SIG{'SIGTRA\
-P'}='signal_cleanup';\n $SIG{'SIGABRT'}='sign\
-al_cleanup';\n $SIG{'SIGEMT'}='signal_cleanup\
-';\n $SIG{'SIGFPE'}='signal_cleanup';\n \
-\n $SIG{'SIGKILL'}='signal_cleanup';\n $\
-SIG{'SIGPIPE'}='signal_cleanup';\n $SIG{'SIGS\
-TOP'}='signal_cleanup';\n $SIG{'SIGTTIN'}='si\
-gnal_cleanup';\n $SIG{'SIGXFSZ'}='signal_clea\
-nup';\n $SIG{'SIGINFO'}='signal_cleanup';\n \
- \n $SIG{'SIGBUS'}='signal_cleanup';\n \
- $SIG{'SIGALRM'}='signal_cleanup';\n $SIG{'S\
-IGTSTP'}='signal_cleanup';\n $SIG{'SIGTTOU'}=\
-'signal_cleanup';\n $SIG{'SIGVTALRM'}='signal\
-_cleanup';\n $SIG{'SIGUSR1'}='signal_cleanup'\
-;\n\n\n $SIG{'SIGSEGV'}='signal_cleanup';\n \
- $SIG{'SIGTERM'}='signal_cleanup';\n $SIG{\
-'SIGCONT'}='signal_cleanup';\n $SIG{'SIGIO'}=\
-'signal_cleanup';\n $SIG{'SIGPROF'}='signal_c\
-leanup';\n $SIG{'SIGUSR2'}='signal_cleanup';\\
-n\n $SIG{'SIGSYS'}='signal_cleanup';\n $\
-SIG{'SIGURG'}='signal_cleanup';\n $SIG{'SIGCH\
-LD'}='signal_cleanup';\n $SIG{'SIGXCPU'}='sig\
-nal_cleanup';\n $SIG{'SIGWINCH'}='signal_clea\
-nup';\n \n $SIG{'INT'}='signal_cleanup';\
-\n $SIG{'TERM'}='signal_cleanup';\n $SIG\
-{'KILL'}='signal_cleanup';\n $SIG{'QUIT'}='si\
-gnal_cleanup';\n \n our $debug_lock=$ENV\
-{\"DEBUG_LOCK\"};\n \n \n \n \\
-n foreach my $a (@ARGV){$CL.=\" $a\";}\n \
- if ( $debug_lock ){print STDERR \"\\n\\n\\n******\
-**** START PG: $PROGRAM *************\\n\";}\n \
- if ( $debug_lock ){print STDERR \"\\n\\n\\n*****\
-*****(tcg) LOCKDIR: $LOCKDIR $$ *************\\n\"\
-;}\n if ( $debug_lock ){print STDERR \"\\n --\
-- $$ -- $CL\\n\";}\n \n \n \n \
-\n }\nsub flush_error\n {\n my $msg=shift;\\
-n return add_error ($EXIT_FAILURE,$$, $$,getppi\
-d(), $msg, $CL);\n }\nsub add_error \n {\n my\
- $code=shift;\n my $rpid=shift;\n my $pid=sh\
-ift;\n my $ppid=shift;\n my $type=shift;\n \
- my $com=shift;\n \n $ERROR_DONE=1;\n lo\
-ck4tc ($rpid, \"LERROR\",\"LSET\",\"$pid -- ERROR:\
- $type\\n\");\n lock4tc ($$, \"LERROR\",\"LSET\\
-", \"$pid -- COM: $com\\n\");\n lock4tc ($$, \"\
-LERROR\",\"LSET\", \"$pid -- STACK: $ppid -> $pid\\
-\n\");\n \n return $code;\n }\nsub add_warni\
-ng \n {\n my $rpid=shift;\n my $pid =shift;\
-\n my $command=shift;\n my $msg=\"$$ -- WARN\
-ING: $command\\n\";\n print STDERR \"$msg\";\n \
- lock4tc ($$, \"LWARNING\", \"LSET\", $msg);\n \
-}\n\nsub signal_cleanup\n {\n print dtderr \"\\
-\n**** $$ (tcg) was killed\\n\";\n &cleanup;\n \
- exit ($EXIT_FAILURE);\n }\nsub clean_dir\n {\\
-n my $dir=@_[0];\n if ( !-d $dir){return ;}\\
-n elsif (!($dir=~/tmp/)){return ;}#safety check\
- 1\n elsif (($dir=~/\\*/)){return ;}#safety che\
-ck 2\n else\n {\n `rm -rf $dir`;\n }\\
-n return;\n }\nsub cleanup\n {\n #print st\
-derr \"\\n----tc: $$ Kills $PIDCHILD\\n\";\n #k\
-ill (SIGTERM,$PIDCHILD);\n my $p=getppid();\n \
- $CLEAN_EXIT_STARTED=1;\n \n \n \n if\
- (&lock4tc($$,\"LERROR\", \"LCHECK\", \"\"))\n \
- {\n my $ppid=getppid();\n if (!$ERROR_DONE) \n \
- {\n &lock4tc($$,\"LERROR\", \"LSET\", \"$$ --\
- STACK: $p -> $$\\n\");\n &lock4tc($$,\"LERROR\
-\", \"LSET\", \"$$ -- COM: $CL\\n\");\n }\n \
- }\n my $warning=&lock4tc($$, \"LWARNING\", \"L\
-READ\", \"\");\n my $error=&lock4tc($$, \"LERR\
-OR\", \"LREAD\", \"\");\n #release error and wa\
-rning lock if root\n \n if (isrootpid() && (\
-$warning || $error) )\n {\n \n print STDERR \\
-"**************** Summary *************\\n$error\\\
-n$warning\\n\";\n\n &lock4tc($$,\"LERROR\",\"RELEA\
-SE\",\"\");\n &lock4tc($$,\"LWARNING\",\"RELEASE\"\
-,\"\");\n } \n \n \n foreach my $f (\
-@TMPFILE_LIST)\n {\n if (-e $f){unlink ($f);}\
- \n }\n foreach my $d (@TMPDIR_LIST)\n \
- {\n clean_dir ($d);\n }\n #No More Lock \
-Release\n #&lock4tc($$,\"LLOCK\",\"LRELEASE\",\\
-"\"); #release lock \n\n if ( $debug_lock ){pri\
-nt STDERR \"\\n\\n\\n********** END PG: $PROGRAM (\
-$$) *************\\n\";}\n if ( $debug_lock ){p\
-rint STDERR \"\\n\\n\\n**********(tcg) LOCKDIR: $L\
-OCKDIR $$ *************\\n\";}\n }\nEND \n {\n \
- \n &cleanup();\n }\n \n\nsub safe_system \\
-n{\n my $com=shift;\n my $ntry=shift;\n my $ctr\
-y=shift;\n my $pid;\n my $status;\n my $ppid=ge\
-tppid();\n if ($com eq \"\"){return 1;}\n \n \n\
-\n if (($pid = fork ()) < 0){return (-1);}\n if \
-($pid == 0)\n {\n set_lock($$, \" -SHELL- \
-$com (tcg)\");\n exec ($com);\n }\n else\\
-n {\n lock4tc ($$, \"LLOCK\", \"LSET\", \"\
-$pid\\n\");#update parent\n $PIDCHILD=$pid;\n\
- }\n if ($debug_lock){printf STDERR \"\\n\\t .\
-... safe_system (fasta_seq2hmm) p: $$ c: $pid COM\
-: $com\\n\";}\n\n waitpid ($pid,WTERMSIG);\n\n s\
-hift_lock ($pid,$$, \"LWARNING\",\"LWARNING\", \"L\
-SET\");\n\n if ($? == $EXIT_FAILURE || lock4tc($p\
-id, \"LERROR\", \"LCHECK\", \"\"))\n {\n i\
-f ($ntry && $ctry <$ntry)\n {\n add_warning ($$,\
-$$,\"$com failed [retry: $ctry]\");\n lock4tc ($\
-pid, \"LRELEASE\", \"LERROR\", \"\");\n return s\
-afe_system ($com, $ntry, ++$ctry);\n }\n elsi\
-f ($ntry == -1)\n {\n if (!shift_lock ($pid, $$,\
- \"LERROR\", \"LWARNING\", \"LSET\"))\n {\n \
- add_warning ($$,$$,\"$com failed\");\n }\n\
- else\n {\n lock4tc ($pid, \"LRELEASE\\
-", \"LERROR\", \"\");\n }\n return $?;}\n \
- else\n {\n if (!shift_lock ($pid,$$, \"LERROR\
-\",\"LERROR\", \"LSET\"))\n {\n myexit(a\
-dd_error ($EXIT_FAILURE,$$,$pid,getppid(), \"UNSPE\
-CIFIED system\", $com));\n }\n }\n }\n ret\
-urn $?;\n}\n\nsub check_configuration \n {\n \
- my @l=@_;\n my $v;\n foreach my $p (@\
-l)\n {\n \n if ( $p eq \"EMAIL\")\n { \n\
- if ( !($EMAIL=~/@/))\n {\n add_warning($$\
-,$$,\"Could Not Use EMAIL\");\n myexit(add_error \
-($EXIT_FAILURE,$$,$$,getppid(),\"EMAIL\",\"$CL\"))\
-;\n }\n }\n elsif( $p eq \"INTERNET\")\
-\n {\n if ( !&check_internet_connection(\
-))\n {\n myexit(add_error ($EXIT_FAILURE,$$,$$\
-,getppid(),\"INTERNET\",\"$CL\"));\n }\n }\n \
- elsif( $p eq \"wget\")\n {\n if (!&pg_\
-is_installed (\"wget\") && !&pg_is_installed (\"cu\
-rl\"))\n {\n myexit(add_error ($EXIT_FAILURE,$\
-$,$$,getppid(),\"PG_NOT_INSTALLED:wget\",\"$CL\"))\
-;\n }\n }\n elsif( !(&pg_is_installed ($p))\
-)\n {\n myexit(add_error ($EXIT_FAILURE,\
-$$,$$,getppid(),\"PG_NOT_INSTALLED:$p\",\"$CL\"));\
-\n }\n }\n return 1;\n }\nsub pg_is_in\
-stalled\n {\n my @ml=@_;\n my $r, $p, $m;\n\
- my $supported=0;\n \n my $p=shift (@ml);\
-\n if ($p=~/::/)\n {\n if (safe_system (\"\
-perl -M$p -e 1\")==$EXIT_SUCCESS){return 1;}\n els\
-e {return 0;}\n }\n else\n {\n $r=`wh\
-ich $p 2>/dev/null`;\n if ($r eq \"\"){return 0;}\\
-n else {return 1;}\n }\n }\n\n\n\nsub check_\
-internet_connection\n {\n my $internet;\n m\
-y $tmp;\n &check_configuration ( \"wget\"); \n \
- \n $tmp=&vtmpnam ();\n \n if (&pg_\
-is_installed (\"wget\")){`wget www.google.com -\
-O$tmp >/dev/null 2>/dev/null`;}\n elsif (&pg_i\
-s_installed (\"curl\")){`curl www.google.com -o\
-$tmp >/dev/null 2>/dev/null`;}\n \n if ( !-e\
- $tmp || -s $tmp < 10){$internet=0;}\n else {$i\
-nternet=1;}\n if (-e $tmp){unlink $tmp;}\n\n \
- return $internet;\n }\nsub check_pg_is_installed\
-\n {\n my @ml=@_;\n my $r=&pg_is_installed \
-(@ml);\n if (!$r && $p=~/::/)\n {\n print \
-STDERR \"\\nYou Must Install the perl package $p o\
-n your system.\\nRUN:\\n\\tsudo perl -MCPAN -e 'in\
-stall $pg'\\n\";\n }\n elsif (!$r)\n \
-{\n myexit(flush_error(\"\\nProgram $p Supported b\
-ut Not Installed on your system\"));\n }\n \
- else\n {\n return 1;\n }\n }\n\n\n","u\
-se Cwd;\nuse Env;\nuse File::Path;\nuse FileHandle\
-;\nuse strict;\n\n\nour (%MODE, %PG, %ENV_SET, %SU\
-PPORTED_OS);\n\n\nour $EXIT_SUCCESS=0;\nour $EXIT_\
-FAILURE=1;\nour $INTERNET=0;\n\nour $CP=\"cp \"; #\
-was causing a crash on MacOSX\nour $SILENT=\">/dev\
-/null 2>/dev/null\";\nour $WEB_BASE=\"http://www.t\
-coffee.org\";\nour $TCLINKDB_ADDRESS=\"$WEB_BASE/R\
-esources/tclinkdb.txt\";\nour $OS=get_os();\nour $\
-ROOT=&get_root();\nour $CD=cwd();\nour $CDIR=$CD;\\
-nour $HOME=$ENV{'HOME'};\n\nour $OSNAME=$ENV{'OSNA\
-ME'};\nour $OSARCH=$ENV{'OSARCH'};\nour $REPO_ROOT\
-=\"\";\n\nour $TCDIR;\nour $TCCACHE;\nour $TCTMP;\\
-nour $TCM;\nour $TCMETHODS;\nour $TCPLUGINS;\nour \
-$PLUGINS_DIR=\"\";\nour $INSTALL_DIR=\"\";\n\nour \
-$CXX=\"g++\";\nour $CXXFLAGS=\"\";\n\nour $CPP=\"g\
-++\";\nour $CPPFLAGS=\"\";\n\nour $CC=\"gcc\";\nou\
-r $CFLAGS=\"\";\n\nour $FC=\"f77\";\nour $FFLAGS=\\
-"\";\n\nmy $install=\"all\";\nmy $default_update_a\
-ction=\"no_update\";\nmy @required_applications=(\\
-"wget_OR_curl\");\nmy @smode=(\"all\", \"clean\", \
-\"install\");\n\n&initialize_PG();\n\nmy $cl=join(\
- \" \", @ARGV);\nif ($#ARGV==-1 || ($cl=~/-h/) ||(\
-$cl=~/-H/) )\n {\n print \"\\n!!!!!!! ./insta\
-ll t_coffee --> installs t_coffee onl\
-y\";\n print \"\\n!!!!!!! ./install all \
- --> installs all the modes [mcoffee, e\
-xpresso, psicoffee,rcoffee..]\";\n print \"\\n\
-!!!!!!! ./install [mcoffee|rcoffee|..] --> instal\
-ls the specified mode\";\n print \"\\n!!!!!!! \
-./install -h --> print usage\\n\
-\\n\";\n if ( $#ARGV==-1){exit ($EXIT_FAILURE)\
-;}\n }\n \nif (($cl=~/-h/) ||($cl=~/-H/) )\n\
- {\n my $m;\n print \"\\n\\n!!!!!!! advance\
-d mode\\n\";\n foreach $m ((keys (%MODE)),@smod\
-e)\n {\n print \"!!!!!!! ./install $m\\\
-n\";\n }\n \n print \"!!!!!!! ./install\
- [target:package|mode|] [-update|-force|-exec=dir|\
--dis=dir|-root|-tclinkdb=file|-] [CC=|FCC=|CXX=|CF\
-LAGS=|CXXFLAGS=]\\n\";\n print \"!!!!!!! ./inst\
-all clean [removes all executables]\\n\";\n \
-print \"!!!!!!! ./install [optional:target] -updat\
-e [updates package already installed\
-]\\n\";\n print \"!!!!!!! ./install [optional:t\
-arget] -force [Forces recompilation\
- over everything]\\n\";\n \n print \"!!!!!!!\
- ./install [optional:target] -root \
- [You are running as root]\\n\";\n print \"!!!!\
-!!! ./install [optional:target] -exec=/foo/bar/ \
- [address for the T-Coffee executable]\\n\";\n \
- print \"!!!!!!! ./install [optional:target] -di\
-s=/foo/bar/ [Address where distributions sh\
-ould be stored]\\n\";\n print \"!!!!!!! ./insta\
-ll [optional:target] -tclinkdb=foo|update [file c\
-ontaining all the packages to be installed]\\n\";\\
-n print \"!!!!!!! ./install [optional:target] -\
-clean [clean everything]\\n\";\n \
- print \"!!!!!!! ./install [optional:target] -plug\
-ins [plugins directory]\\n\";\n pr\
-int \"!!!!!!! ./install [optional:target] -tcdir=/\
-foor/bar [base path where T-Coffee will be in\
-stalled]\\n\";\n print \"!!!!!!! ./install [opt\
-ional:target] -repo=/path/to/repo [binaries repo\
-sitory root directory]\\n\";\n print \"!!!!!!! \
-mode:\";\n foreach $m (keys(%MODE)){print \"$m \
-\";}\n print \"\\n\";\n print \"!!!!!!! Pack\
-ages:\";\n foreach $m (keys (%PG)){print \"$m \\
-";}\n print \"\\n\";\n \n print \"\\n\\n\\
-";\n exit ($EXIT_FAILURE);\n }\n\n\n\nmy (@arg\
-l)=($cl=~/(\\S+=[^=]+)\\s\\w+=/g);\npush (@argl, (\
-$cl=~/(\\S+=[^=]+\\S)\\s*$/g));\n\nforeach $a (@ar\
-gl)\n {\n if ( ($cl=~/CXX=(.*)/)){$CXX=$1;}\n \
- if ( ($cl=~/-CC=(.*)/ )){$CC=$1;}\n if ( \
-($cl=~/-FC=(.*)/ )){$FC=$1;}\n if ( ($cl=~/-\
-CFLAGS=(.*)/)){$CFLAGS=$1;}\n if ( ($cl=~/-CXXF\
-LAGS=(.*)/)){$CXXFLAGS=$1;}\n }\nour ($ROOT_INSTA\
-LL, $NO_QUESTION, $default_update_action,$BINARIES\
-_ONLY,$force, $default_update_action, $INSTALL_DIR\
-, $PLUGINS_DIR, $DISTRIBUTIONS,$tclinkdb, $proxy, \
-$clean);\nif ( ($cl=~/-root/)){$ROOT_INSTALL=1;}\n\
-if ( ($cl=~/-no_question/)){$NO_QUESTION=1;}\nif (\
- ($cl=~/-update/)){$default_update_action=\"update\
-\";}\nif ( ($cl=~/-binaries/)){$BINARIES_ONLY=1;}\\
-nif ( ($cl=~/-force/)){$force=1;$default_update_ac\
-tion=\"update\"}\nif ( ($cl=~/-exec=\\s*(\\S+)/)){\
-$INSTALL_DIR=$1;}\nif ( ($cl=~/-plugins=\\s*(\\S+)\
-/)){$PLUGINS_DIR=$1;}\nif ( ($cl=~/-dis=\\s*(\\S+)\
-/)){$DISTRIBUTIONS=$1;}\n\nif ( ($cl=~/-tclinkdb=\\
-\s*(\\S+)/)){$tclinkdb=$1;}\nif ( ($cl=~/-proxy=\\\
-s*(\\S+)/)){$proxy=$1;}\nif ( ($cl=~/-clean/)){$cl\
-ean=1;}\nif ( ($cl=~/-repo=\\s*(\\S+)/)){ $REPO_RO\
-OT=$1; }\nif ( ($cl=~/-tcdir=\\s*(\\S+)/)){ $TCDIR\
-=$1; }\nif ($tclinkdb){&update_tclinkdb ($tclinkdb\
-);}\n\n\nif( $REPO_ROOT ne \"\" ) {\n if( $OSNAME \
-eq \"\" ) { print \"You have specified the reposit\
-ory folder but the required \\\"OSNAME\\\" envirom\
-ent variable is missing. \\n\"; exit 1; } \n if( $\
-OSARCH eq \"\" ) { print \"You have specified the \
-repository folder but the required \\\"OSARCH\\\" \
-enviroment variable is missing. \\n\"; exit 1; } \\
-n}\n\n\nif(!$TCDIR) { $TCDIR=\"$HOME/.t_coffee\"; \
-}\n&add_dir ($TCDIR);\n&add_dir ($TCCACHE=\"$TCDIR\
-/cache\");\n&add_dir ($TCTMP=\"$CDIR/tmp\");\n&add\
-_dir ($TCM=\"$TCDIR/mcoffee\");\n&add_dir ($TCMETH\
-ODS=\"$TCDIR/methods\");\n&add_dir ($TCPLUGINS=\"$\
-TCDIR/plugins/$OS\");\n\n\nour $BASE=\"$CD/bin\";\\
-nour $BIN=\"$BASE/binaries/$OS\";\nour $DOWNLOAD_D\
-IR=\"$BASE/download\";\nour $DOWNLOAD_FILE=\"$DOWN\
-LOAD_DIR/files\";\nour $TMP=\"$BASE/tmp\";\n\n&add\
-_dir($BASE);\n&add_dir($BIN);\n&add_dir($DOWNLOAD_\
-DIR);\n&add_dir($DOWNLOAD_FILE);\nif (!$DISTRIBUTI\
-ONS){$DISTRIBUTIONS=\"$DOWNLOAD_DIR/distributions\\
-";}\n&add_dir ($DISTRIBUTIONS);\n&add_dir ($TMP);\\
-n\n\nif (!$PLUGINS_DIR && !$ROOT_INSTALL){$PLUG\
-INS_DIR=$TCPLUGINS;}\nelsif (!$PLUGINS_DIR && $RO\
-OT_INSTALL){$PLUGINS_DIR=\"/usr/local/bin/\";}\n\n\
-if (!$INSTALL_DIR && !$ROOT_INSTALL){$INSTALL_D\
-IR=\"$HOME/bin/\";mkpath ($INSTALL_DIR);}\nelsif (\
-!$INSTALL_DIR && $ROOT_INSTALL){$INSTALL_DIR=\"/u\
-sr/local/bin/\";}\n\nif (-d \"mcoffee\"){`cp mcoff\
-ee/* $TCM`;}\n\n\nour $ENV_FILE=\"$TCDIR/t_coffee_\
-env\";\n&env_file2putenv ($ENV_FILE);\n&set_proxy(\
-$proxy);\nmy ($target, $p, $r);\n$target=$p;\n\nfo\
-reach $p ( ((keys (%PG)),(keys(%MODE)),(@smode)) \
-)\n {\n if ($ARGV[0] eq $p && $target eq \"\")\
-{$target=$p;}\n }\nif ($target eq \"\"){exit ($EX\
-IT_FAILURE);}\n\n\nforeach $r (@required_applicati\
-ons)\n {\n my @app_list;\n my $i;\n $i=0\
-;\n \n @app_list=split (/_OR_/, $r);\n fo\
-reach my $pg (@app_list)\n {\n $i+=&pg_is_ins\
-talled ($pg);\n }\n if ($i==0)\n {\n \
- print \"One of the following packages must be\
- installed to proceed: \";\n foreach my $pg (\
-@app_list)\n {\n print (\"$pg \");\n }\n di\
-e;\n }\n }\n\n\n\n\n\n\n&sign_license_ni();\n\\
-n\n$PG{C}{compiler}=get_C_compiler($CC);\n$PG{Fort\
-ran}{compiler}=get_F_compiler($FC);\n$PG{CXX}{comp\
-iler}=$PG{CPP}{compiler}=$PG{GPP}{compiler}=get_CX\
-X_compiler($CXX);\nif ($CXXFLAGS){$PG{CPP}{options\
-}=$PG{GPP}{options}=$PG{CXX}{options}=$CXXFLAGS;}\\
-nif ($CFLAGS){$PG{C}{options}=$CFLAGS;}\nforeach m\
-y $c (keys(%PG))\n {\n my $arguments;\n if \
-($PG{$c}{compiler})\n {\n $arguments=\"$PG{$c\
-}{compiler_flag}=$PG{$c}{compiler} \";\n if ($PG{$\
-c}{options})\n {\n $arguments.=\"$PG{$c}{opt\
-ions_flag}=$PG{$c}{options} \";\n }\n $PG{$c}{ar\
-guments}=$arguments;\n }\n }\n\nif ($PG{$tar\
-get}){$PG{$target}{install}=1;}\nelse\n {\n fo\
-reach my $pg (keys(%PG))\n {\n if ( $target e\
-q \"all\" || ($PG{$pg}{mode}=~/$target/))\n {\n \
- $PG{$pg} {install}=1;\n }\n }\n }\n\nf\
-oreach my $pg (keys(%PG))\n {\n if (!$PG{$pg}{\
-update_action}){$PG{$pg}{update_action}=$default_u\
-pdate_action;}\n elsif ($PG{$pg}{update_action}\
- eq \"never\"){$PG{$pg}{install}=0;}\n if ( $fo\
-rce && $PG{$pg}{install})\n {\n `rm $BIN/$pg \
-$BIN/$pg.exe $SILENT`;\n }\n if ($PG{$pg}{\
-update_action} eq \"update\" && $PG{$pg}{install})\
-{$PG{$pg}{update}=1;}\n }\n\nif (($target=~/clean\
-/))\n {\n print \"------- cleaning executables\
- -----\\n\";\n `rm bin/* $SILENT`;\n exit ($\
-EXIT_SUCCESS);\n }\n\nif ( !$PG{$target}){print \\
-"------- Installing T-Coffee Modes\\n\";}\n\nforea\
-ch my $m (keys(%MODE))\n {\n if ( $target eq \\
-"all\" || $target eq $m)\n {\n print \"\\n---\
----- The installer will now install the $m compone\
-nts $MODE{$m}{description}\\n\";\n foreach my $pg \
-(keys(%PG))\n {\n if ( $PG{$pg}{mode} =~/$m/\
- && $PG{$pg}{install})\n {\n if ($PG{$pg}{t\
-ouched}){print \"------- $PG{$pg}{dname}: already \
-processed\\n\";}\n else {$PG{$pg}{success}=&insta\
-ll_pg($pg);$PG{$pg}{touched}=1;}\n }\n }\n\
- }\n }\n\nif ( $PG{$target}){print \"-------\
- Installing Individual Package\\n\";}\nforeach my \
-$pg (keys (%PG))\n {\n \n if ( $PG{$pg}{ins\
-tall} && !$PG{$pg}{touched})\n {\n print \"\\\
-n------- Install $pg\\n\";\n $PG{$pg}{success}=&in\
-stall_pg($pg);$PG{$pg}{touched}=1;\n }\n }\n\
-print \"------- Finishing The installation\\n\";\n\
-my $final_report=&install ($INSTALL_DIR);\n\nprint\
- \"\\n\";\nprint \"*******************************\
-**************************************\\n\";\nprin\
-t \"******** INSTALLATION SUMMARY \
- *****************\\n\";\nprint \"***********\
+pdb_file0 (\"$pdb_file.gz\"))){$return_value=$resu\
+lt;}\n elsif ( ($result=get_pdb_file0 (\"$pdb_f\
+ile.GZ\"))){$return_value=$result;}\n return $r\
+eturn_value;\n}\nsub get_pdb_file0 \n{ \n my ($\
+pdb_file, $attempt)=(@_);\n my $pdb_file=@_[0];\
+\n my $tmp_pdb_file; \n my $return_value;\
+\n\n if ( !$attempt){$attempt=1;}\n \n $l\
+ocal_pdb_file=\"$pdb_file\";\n if ( $local_pdb_\
+file eq \"\")\n{\n $tmp_pdb_file=vtmpnam();\n open\
+ F, \">$tmp_pdb_file\";\n \n while (<STDIN>){print\
+ F \"$_\";}\n close (F);\n \n if (-e $tmp_pdb_file\
+ && &is_pdb_file ( $local_pdb_file))\n{return $tmp\
+_pdb_file;}\n}\n\n $local_pdb_file=\"$pdb_file\\
+";\n &debug_print (\"\\nTry access local file: \
+$local_pdb_file\");\n \n $local_pdb_file=&ch\
+eck_pdb_file4compression ($local_pdb_file);\n i\
+f ( -e $local_pdb_file && (&is_pdb_file ($local_pd\
+b_file) || $force_pdb))\n{\n &debug_print ( \"\\n\\
+\tIs in Current Dir\");\n $tmp_pdb_file=vtmpnam();\
+\n `cp $local_pdb_file $tmp_pdb_file`;\n return $t\
+mp_pdb_file;\n}\n else\n{\n &debug_print (\"\\n\
+\\tFile Not in Current Dir\");\n}\n\n if ($pdb_\
+file=~/^pdb/||$pdb_file=~/^PDB/){$pdb_div=substr (\
+$pdb_file, 4, 2);}\n else\n{\n $pdb_div=subst\
+r ($pdb_file, 1, 2);\n}\n $local_pdb_file=\"$pd\
+b_dir/$pdb_div/$pdb_file\";\n $local_pdb_file=&\
+check_pdb_file4compression ( $local_pdb_file);\n \
+ &debug_print (\"\\nTry access file From PDB_DIR:\
+ $local_pdb_file\");\n if ($pdb_dir && -e $loca\
+l_pdb_file && &is_pdb_file ($local_pdb_file))\n{\n\
+ &debug_print ( \"\\n\\tIs in Local PDB DIR\");\n \
+$tmp_pdb_file=vtmpnam();\n `cp $local_pdb_file $tm\
+p_pdb_file`;\n return $tmp_pdb_file;\n}\n\n $lo\
+cal_pdb_file=\"$pdb_dir/$pdb_file\";\n $local_p\
+db_file=&check_pdb_file4compression ( $local_pdb_f\
+ile);\n &debug_print (\"\\nTry access file From\
+ PDB_DIR: local_pdb_file\");\n if ($pdb_dir && \
+-e $local_pdb_file && &is_pdb_file ($local_pdb_fil\
+e))\n{\n &debug_print ( \"\\n\\tIs in Local PDB DI\
+R\");\n $tmp_pdb_file=vtmpnam();\n `cp $local_pdb_\
+file $tmp_pdb_file`;\n return $tmp_pdb_file;\n}\n\\
+n $local_pdb_file=\"$pdb_dir$pdb_file\";\n $\
+local_pdb_file=&check_pdb_file4compression ( $loca\
+l_pdb_file);\n &debug_print (\"\\nTry access fi\
+le From PDB_DIR: $local_pdb_file\");\n if ($pdb\
+_dir && -e $local_pdb_file && &is_pdb_file ($local\
+_pdb_file))\n{\n &debug_print ( \"\\n\\tIs in Loca\
+l PDB DIR\");\n $tmp_pdb_file=vtmpnam();\n `cp $lo\
+cal_pdb_file $tmp_pdb_file`;\n return $tmp_pdb_fil\
+e;\n}\n else\n{&debug_print ( \"\\n\\tNot In Lo\
+cal Pdb Dir\");}\n\n if ($cache ne \"NO\" && $c\
+ache ne \"no\")\n{\n\n $local_pdb_file=\"$cache/$p\
+db_file\";\n $local_pdb_file=&check_pdb_file4compr\
+ession ( $local_pdb_file);\n &debug_print(\"\\nTry\
+ access file From Cache: $local_pdb_file\");\n if \
+(-e $local_pdb_file && &is_pdb_file ($local_pdb_fi\
+le))\n{\n &debug_print ( \"\\n\\tIs in T-Coffe\
+e Cache\");\n $tmp_pdb_file=vtmpnam();\n `\
+cp $local_pdb_file $tmp_pdb_file`;\n return $t\
+mp_pdb_file;\n}\n else{&debug_print ( \"\\n\\tNot \
+in Cache Dir\");}\n}\n\nif (!$no_remote_pdb_dir) \\
+n {\n my $value=&is_released ($pdb_file);\n \
+ my $return_value=\"\";\n if ($value==1)\n \
+ {\n \n &debug_print (\"\\n***********************\
+******************************\\nTry Remote Access\
+ for $pdb_file\");\n $tmp_pdb_file=vtmpnam();\n $n\
+etcommand=$netaddress;\n $netcommand=~s/%%/$pdb_fi\
+le/g;\n &url2file(\"$netcommand\", \"$tmp_pdb_file\
+.$netcompression\");\n &debug_print(\"\\nREMOTE: $\
+netcommand\\n\");\n \n $compressed_tmp_file_name=\\
+"$tmp_pdb_file.$netcompression\";\n \n if ($netcom\
+pression && -B $compressed_tmp_file_name)\n {\n \
+ my $r;\n &debug_print (\"\\n\\tFile Found \
+Remotely\");\n if (($r=safe_system ( \"$netcom\
+pression_pg $compressed_tmp_file_name\")!=$EXIT_SU\
+CCESS) && $attempts<5)\n {\n &debug_print (\
+\"\\n\\tProper Download Failed Try again\");\n un\
+link $compressed_tmp_file_name;\n print \"\\nFail\
+ed to Download $compressed_tmp_file_name. New Atte\
+mpt $attempt/5\\n\";\n return &get_pdb_file0($pdb\
+_file, $attempt+1);\n }\n elsif ($r== $E\
+XIT_SUCCESS)\n {\n &debug_print (\"\\n\\tPr\
+oper Download Succeeded \");\n $return_value=$tmp\
+_pdb_file;\n }\n else\n {\n &debu\
+g_print (\"\\n\\tProper Download Failed \");\n &d\
+ebug_print (\"\\nFile Not Found Remotely\");\n un\
+link $compressed_tmp_file_name;\n }\n }\n \
+else\n {\n\n &debug_print (\"\\nFile Not Fou\
+nd Remotely\");\n unlink $compressed_tmp_file_\
+name;\n }\n #Update cache if required\n if ($cac\
+he ne \"no\" && $cache ne \"update\" && -e $return\
+_value)\n {\n `cp $return_value $cache/$pdb_\
+file.pdb`;\n #`t_coffee -other_pg clean_cache.\
+pl -file $pdb_file.pdb -dir $cache`;\n }\n \
+}\n &debug_print (\"\\nRemote Download Finished\
+\");\n return $return_value;\n }\nreturn \"\";\
+\n}\n\nsub check_pdb_file4compression \n{\n my \
+$file=@_[0];\n my $tmp;\n my $r;\n \n \
+$tmp=&vtmpnam();\n if (-e $tmp){unlink $tmp;}\n\
+ \n $file=~s/\\/\\//\\//g;\n if (-B $f\
+ile && ($file=~/\\.Z/)) {`cp $file $tmp.Z`;`rm $tm\
+p`;`gunzip $tmp.Z $SILENT`;$r=$tmp;}\n elsif (-\
+B $file && ($file=~/\\.gz/)){`cp $file $tmp.gz`;`g\
+unzip $tmp.gz $SILENT`;return $r=$tmp;}\n elsif\
+ (-B $file ){`cp $file $tmp.gz`;`gunzip $tmp.gz $S\
+ILENT`;$r=$tmp;}\n elsif ( -e $file ) {$r= $fil\
+e;}\n elsif ( -e \"$file.gz\" ){ `cp $file.gz $\
+tmp.gz`;`gunzip $tmp.gz $SILENT`;$r=$tmp;} \
+\n elsif ( -e \"$file.Z\") {`cp $file.Z $tmp.Z\
+`; `gunzip $tmp.Z $SILENT`;$r=$tmp;}\n else {$\
+r= $file;}\n\n if ( -e \"$tmp.Z\"){unlink \"$tm\
+p.Z\";}\n if ( -e \"$tmp.gz\"){unlink \"$tmp.gz\
+\";}\n \n return $r;\n \n}\n\n\n\n\n\n \
+ \n\n\n\n\n\n\n\nsub vfopen \n{\n my $file=@_[0\
+];\n my $mode=@_[1];\n my $tmp;\n my $F =\
+ new FileHandle;\n \n \n $tmp=$file;\n \n\
+ \n if ( $mode eq \"r\" && !-e $file){ myexi\
+t(flush_error (\"Cannot open file $file\"));}\n \
+ elsif ($mode eq \"w\"){$tmp=\">$file\";}\n els\
+if ($mode eq \"a\"){$tmp=\">>$file\";}\n \n \
+\n open ($F,$tmp);\n return $F;\n}\nsub debu\
+g_print\n{\n my $message =@_[0];\n if ($debu\
+g){print STDERR \"NO_REMOTE_PDB_DIR: $no_remote_pd\
+b_dir - $message [DEBUG:extract_from_pdb]\";}\n \
+ return;\n}\nsub is_aa \n{\n my ($aa, $chain) =\
+@_;\n\n my $one;\n my $trhee;\n \n if \
+( $onelett{$molecule_type{$chain}}->{$aa} eq 'X' |\
+| !$onelett{$molecule_type{$chain}}->{$aa} ){retur\
+n '';}\n else\n {\n $one=$onelett{$molecul\
+e_type{$chain}}->{$aa};\n\n $three=$threelett{$mol\
+ecule_type{$chain}}->{$one};\n \n\n return $three;\
+\n }\n }\n\n\n\n\n\nsub url2file\n{\n my \
+($address, $out, $wget_arg, $curl_arg)=(@_);\n \
+my ($pg, $flag, $r, $arg, $count);\n \n if (\
+!$CONFIGURATION){&check_configuration (\"wget\", \\
+"INTERNET\", \"gzip\");$CONFIGURATION=1;}\n \n \
+ if (&pg_is_installed (\"wget\")) {$pg=\"wget\\
+"; $flag=\"-O\";$arg=$wget_arg;}\n elsif (&pg_i\
+s_installed (\"curl\")){$pg=\"curl\"; $flag=\"-o\"\
+;$arg=$curl_arg;}\n return safe_system (\"$pg $\
+flag$out $address >/dev/null 2>/dev/null\");\n\n}\\
+n\n\n\n\nsub pdbfile2chaintype\n {\n my $file=\
+@_[0];\n my %ct;\n my $F;\n \n $F=vfop\
+en ($file, \"r\");\n while (<$F>)\n {\n my\
+ $line=$_;\n if ($line =~/^ATOM/)\n {\n my $\
+C=substr($line,21,1);\n if (!$ct{$C})\n \
+{ \n my $r=substr($line,17,3);\n $r=~s/\\s+//;\n\
+ if (length ($r)==1){$ct{$C}=\"R\";}\n elsif (le\
+ngth ($r)==2){$ct{$C}=\"D\";}\n elsif (length ($r\
+)==3){$ct{$C}=\"P\";}\n else \n {\n myexi\
+t(flush_error(\"ERROR: Could not read RES_ID field\
+ in file $file\"));\n }\n }\n }\n \
+}\n close ($F);\n return %ct;\n }\n \n \
+ \n\n\n\nsub fill_threelett_RNA\n{\n\n my %threele\
+tt=(\n 'A', ' A',\n 'T', ' T',\n 'U', ' U',\n '\
+C', ' C',\n 'G', ' G',\n 'I', ' I', #Inosine\n \
+);\n \n return %threelett;\n\n}\n\n\nsub fill_onel\
+ett_RNA\n{\n my %onelett=(\n ' A' => 'A',\n ' \
+T' => 'T',\n ' U' => 'U',\n ' C' => 'C',\n ' G'\
+ => 'G',\n 'CSL' => 'X',\n 'UMS' => 'X',\n ' I' =\
+> 'I',\n 'A' => 'A',\n 'T' => 'T',\n 'U' => 'U',\n\
+ 'C' => 'C',\n 'G' => 'G',\n 'I' => 'I',\n );\n\n \
+return %onelett;\n\n}\n\n\nsub fill_onelett_DNA\n{\
+\n my %onelett=(\n ' DA', 'A',\n ' DT', 'T',\n '\
+ DC', 'C',\n ' DG', 'G',\n 'DA', 'A',\n 'DT', 'T',\
+\n 'DC', 'C',\n 'DG', 'G',\n );\n\n return %onelet\
+t;\n\n}\n\nsub fill_threelett_DNA\n{\n\n my %three\
+lett=(\n 'A', ' DA',\n 'T', ' DT',\n 'C', ' DC',\n\
+ 'G', ' DG',\n );\n\n return %threelett;\n\n}\n\n\\
+n\n\nsub fill_threelett_prot\n{ \n my %threelett\
+;\n\n %threelett=(\n'A', 'ALA',\n'C', 'CYS',\n'D'\
+, 'ASP',\n'E', 'GLU',\n'F', 'PHE',\n'G', 'GLY',\n'\
+H', 'HIS',\n'I', 'ILE',\n'K', 'LYS',\n'L', 'LEU',\\
+n'N', 'ASN',\n'M', 'MET',\n'P', 'PRO',\n'Q', 'GLN'\
+,\n'R', 'ARG',\n'S', 'SER',\n'T', 'THR',\n'V', 'VA\
+L',\n'W', 'TRP',\n'Y', 'TYR',\n);\n\nreturn %three\
+lett;\n\n\n}\n\nsub fill_onelett_prot\n{\n my %\
+onelett;\n \n %onelett=(\n\n'10A', 'X',\n'11\
+O', 'X',\n'12A', 'X',\n'13P', 'X',\n'13R', 'X',\n'\
+13S', 'X',\n'14W', 'X',\n'15P', 'X',\n'16A', 'X',\\
+n'16G', 'X',\n'1AN', 'X',\n'1AP', 'X',\n'1AR', 'X'\
+,\n'1BH', 'X',\n'1BO', 'X',\n'1C5', 'X',\n'1CU', '\
+X',\n'1DA', 'X',\n'1GL', 'X',\n'1GN', 'X',\n'1IN',\
+ 'X',\n'1LU', 'L',\n'1MA', 'X',\n'1MC', 'X',\n'1MG\
+', 'X',\n'1MZ', 'X',\n'1NA', 'X',\n'1NB', 'X',\n'1\
+NI', 'X',\n'1PA', 'A',\n'1PC', 'X',\n'1PE', 'X',\n\
+'1PG', 'X',\n'1PI', 'A',\n'1PM', 'X',\n'1PN', 'X',\
+\n'1PU', 'X',\n'1PY', 'X',\n'1UN', 'X',\n'24T', 'X\
+',\n'25T', 'X',\n'26P', 'X',\n'2AB', 'X',\n'2AM', \
+'X',\n'2AN', 'X',\n'2AP', 'X',\n'2AR', 'X',\n'2AS'\
+, 'D',\n'2BL', 'X',\n'2BM', 'X',\n'2CP', 'X',\n'2D\
+A', 'X',\n'2DG', 'X',\n'2DP', 'X',\n'2DT', 'X',\n'\
+2EP', 'X',\n'2EZ', 'X',\n'2FG', 'X',\n'2FL', 'X',\\
+n'2FP', 'X',\n'2FU', 'X',\n'2GL', 'X',\n'2GP', 'X'\
+,\n'2HP', 'X',\n'2IB', 'X',\n'2IP', 'X',\n'2LU', '\
+L',\n'2MA', 'X',\n'2MD', 'X',\n'2ME', 'X',\n'2MG',\
+ 'X',\n'2ML', 'L',\n'2MO', 'X',\n'2MR', 'R',\n'2MU\
+', 'X',\n'2MZ', 'X',\n'2NO', 'X',\n'2NP', 'X',\n'2\
+OG', 'X',\n'2PA', 'X',\n'2PC', 'X',\n'2PE', 'X',\n\
+'2PG', 'X',\n'2PH', 'X',\n'2PI', 'X',\n'2PL', 'X',\
+\n'2PP', 'X',\n'2PU', 'X',\n'2SI', 'X',\n'2TB', 'X\
+',\n'34C', 'X',\n'35G', 'X',\n'3AA', 'X',\n'3AD', \
+'X',\n'3AH', 'H',\n'3AN', 'X',\n'3AP', 'X',\n'3AT'\
+, 'X',\n'3BT', 'X',\n'3CH', 'X',\n'3CN', 'X',\n'3C\
+O', 'X',\n'3CP', 'X',\n'3DR', 'X',\n'3EP', 'X',\n'\
+3FM', 'X',\n'3GA', 'X',\n'3GP', 'X',\n'3HB', 'X',\\
+n'3HC', 'X',\n'3HP', 'X',\n'3IB', 'X',\n'3ID', 'X'\
+,\n'3IN', 'X',\n'3MA', 'X',\n'3MB', 'X',\n'3MC', '\
+X',\n'3MD', 'D',\n'3MF', 'X',\n'3MP', 'X',\n'3MT',\
+ 'X',\n'3OL', 'X',\n'3PA', 'X',\n'3PG', 'X',\n'3PO\
+', 'X',\n'3PP', 'X',\n'3PY', 'X',\n'49A', 'X',\n'4\
+AB', 'X',\n'4AM', 'X',\n'4AN', 'X',\n'4AP', 'X',\n\
+'4BA', 'X',\n'4BT', 'X',\n'4CA', 'X',\n'4CO', 'X',\
+\n'4HP', 'X',\n'4IP', 'X',\n'4MO', 'X',\n'4MV', 'X\
+',\n'4MZ', 'X',\n'4NC', 'X',\n'4NP', 'X',\n'4OX', \
+'X',\n'4PB', 'X',\n'4PN', 'X',\n'4PP', 'X',\n'4SC'\
+, 'X',\n'4SU', 'X',\n'4TB', 'X',\n'55C', 'X',\n'5A\
+D', 'X',\n'5AN', 'X',\n'5AT', 'X',\n'5CM', 'X',\n'\
+5GP', 'X',\n'5HP', 'E',\n'5HT', 'X',\n'5IT', 'X',\\
+n'5IU', 'X',\n'5MB', 'X',\n'5MC', 'X',\n'5MD', 'X'\
+,\n'5MP', 'X',\n'5MU', 'X',\n'5NC', 'X',\n'5OB', '\
+X',\n'5PA', 'X',\n'5PV', 'X',\n'6AB', 'X',\n'6CT',\
+ 'X',\n'6HA', 'X',\n'6HC', 'X',\n'6HG', 'X',\n'6HT\
+', 'X',\n'6IN', 'X',\n'6MO', 'X',\n'6MP', 'X',\n'6\
+PG', 'X',\n'6WO', 'X',\n'70U', 'X',\n'7DG', 'X',\n\
+'7HP', 'X',\n'7I2', 'X',\n'7MG', 'X',\n'7MQ', 'X',\
+\n'7NI', 'X',\n'87Y', 'X',\n'8AD', 'X',\n'8BR', 'X\
+',\n'8IG', 'X',\n'8IN', 'X',\n'8OG', 'X',\n'95A', \
+'X',\n'9AD', 'X',\n'9AM', 'X',\n'9AP', 'X',\n'9DG'\
+, 'X',\n'9DI', 'X',\n'9HX', 'X',\n'9OH', 'X',\n'9T\
+A', 'X',\n'A12', 'X',\n'A15', 'X',\n'A23', 'X',\n'\
+A24', 'X',\n'A26', 'X',\n'A2G', 'X',\n'A2P', 'X',\\
+n'A32', 'X',\n'A3P', 'X',\n'A4P', 'X',\n'A5P', 'X'\
+,\n'A70', 'X',\n'A76', 'X',\n'A77', 'X',\n'A78', '\
+X',\n'A79', 'X',\n'A80', 'X',\n'A85', 'X',\n'A88',\
+ 'X',\n'A9A', 'X',\n'AA3', 'X',\n'AA4', 'X',\n'AA6\
+', 'X',\n'AAA', 'X',\n'AAB', 'X',\n'AAC', 'X',\n'A\
+AE', 'X',\n'AAG', 'R',\n'AAH', 'X',\n'AAM', 'X',\n\
+'AAN', 'X',\n'AAP', 'X',\n'AAR', 'R',\n'AAS', 'X',\
+\n'AAT', 'X',\n'ABA', 'X',\n'ABC', 'X',\n'ABD', 'X\
+',\n'ABE', 'X',\n'ABH', 'X',\n'ABI', 'X',\n'ABK', \
+'X',\n'ABM', 'X',\n'ABN', 'X',\n'ABP', 'X',\n'ABR'\
+, 'X',\n'ABS', 'X',\n'ABU', 'X',\n'AC1', 'X',\n'AC\
+2', 'X',\n'ACA', 'X',\n'ACB', 'D',\n'ACC', 'C',\n'\
+ACD', 'X',\n'ACE', 'X',\n'ACH', 'X',\n'ACI', 'X',\\
+n'ACL', 'R',\n'ACM', 'X',\n'ACN', 'X',\n'ACO', 'X'\
+,\n'ACP', 'X',\n'ACQ', 'X',\n'ACR', 'X',\n'ACS', '\
+X',\n'ACT', 'X',\n'ACV', 'V',\n'ACX', 'X',\n'ACY',\
+ 'X',\n'AD2', 'X',\n'AD3', 'X',\n'ADC', 'X',\n'ADD\
+', 'X',\n'ADE', 'X',\n'ADH', 'X',\n'ADI', 'X',\n'A\
+DM', 'X',\n'ADN', 'X',\n'ADP', 'X',\n'ADQ', 'X',\n\
+'ADR', 'X',\n'ADS', 'X',\n'ADT', 'X',\n'ADU', 'X',\
+\n'ADW', 'X',\n'ADX', 'X',\n'AE2', 'X',\n'AEA', 'X\
+',\n'AEB', 'X',\n'AEI', 'D',\n'AEN', 'X',\n'AET', \
+'T',\n'AF1', 'X',\n'AF3', 'X',\n'AFA', 'D',\n'AFP'\
+, 'X',\n'AG7', 'X',\n'AGB', 'X',\n'AGF', 'X',\n'AG\
+L', 'X',\n'AGM', 'R',\n'AGN', 'X',\n'AGP', 'X',\n'\
+AGS', 'X',\n'AGU', 'X',\n'AH0', 'X',\n'AH1', 'X',\\
+n'AHA', 'X',\n'AHB', 'D',\n'AHC', 'X',\n'AHF', 'X'\
+,\n'AHG', 'X',\n'AHH', 'X',\n'AHM', 'X',\n'AHO', '\
+X',\n'AHP', 'X',\n'AHS', 'X',\n'AHT', 'Y',\n'AHU',\
+ 'X',\n'AHX', 'X',\n'AI1', 'X',\n'AI2', 'X',\n'AIB\
+', 'X',\n'AIC', 'X',\n'AIM', 'X',\n'AIP', 'X',\n'A\
+IQ', 'X',\n'AIR', 'X',\n'AJ3', 'X',\n'AKB', 'X',\n\
+'AKG', 'X',\n'AKR', 'X',\n'AL1', 'X',\n'AL2', 'X',\
+\n'AL3', 'X',\n'AL4', 'X',\n'AL5', 'X',\n'AL6', 'X\
+',\n'AL7', 'X',\n'AL8', 'X',\n'AL9', 'X',\n'ALA', \
+'A',\n'ALB', 'X',\n'ALC', 'X',\n'ALD', 'L',\n'ALE'\
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+ 'X',\n'STA', 'X',\n'STB', 'X',\n'STE', 'X',\n'STG\
+', 'X',\n'STI', 'X',\n'STL', 'X',\n'STN', 'X',\n'S\
+TO', 'X',\n'STP', 'X',\n'STR', 'X',\n'STU', 'X',\n\
+'STY', 'Y',\n'SU1', 'X',\n'SU2', 'X',\n'SUC', 'X',\
+\n'SUI', 'X',\n'SUL', 'X',\n'SUR', 'X',\n'SVA', 'S\
+',\n'SWA', 'X',\n'T16', 'X',\n'T19', 'X',\n'T23', \
+'X',\n'T29', 'X',\n'T33', 'X',\n'T3P', 'X',\n'T42'\
+, 'A',\n'T44', 'X',\n'T5A', 'X',\n'T6A', 'T',\n'T6\
+P', 'X',\n'T80', 'X',\n'T87', 'X',\n'TA1', 'X',\n'\
+TAA', 'X',\n'TAB', 'X',\n'TAC', 'X',\n'TAD', 'X',\\
+n'TAF', 'X',\n'TAM', 'X',\n'TAP', 'X',\n'TAR', 'X'\
+,\n'TAS', 'X',\n'TAU', 'X',\n'TAX', 'X',\n'TAZ', '\
+X',\n'TB9', 'X',\n'TBA', 'X',\n'TBD', 'X',\n'TBG',\
+ 'G',\n'TBH', 'X',\n'TBM', 'T',\n'TBO', 'X',\n'TBP\
+', 'X',\n'TBR', 'X',\n'TBS', 'X',\n'TBT', 'X',\n'T\
+BU', 'X',\n'TBZ', 'X',\n'TC4', 'X',\n'TCA', 'X',\n\
+'TCB', 'X',\n'TCH', 'X',\n'TCK', 'X',\n'TCL', 'X',\
+\n'TCM', 'X',\n'TCN', 'X',\n'TCP', 'X',\n'TCR', 'W\
+',\n'TCS', 'X',\n'TCZ', 'X',\n'TDA', 'X',\n'TDB', \
+'X',\n'TDG', 'X',\n'TDP', 'X',\n'TDR', 'X',\n'TDX'\
+, 'X',\n'TEA', 'X',\n'TEM', 'X',\n'TEN', 'X',\n'TE\
+O', 'X',\n'TEP', 'X',\n'TER', 'X',\n'TES', 'X',\n'\
+TET', 'X',\n'TFA', 'X',\n'TFB', 'X',\n'TFH', 'X',\\
+n'TFI', 'X',\n'TFK', 'X',\n'TFP', 'X',\n'THA', 'X'\
+,\n'THB', 'X',\n'THC', 'T',\n'THD', 'X',\n'THE', '\
+X',\n'THF', 'X',\n'THJ', 'X',\n'THK', 'X',\n'THM',\
+ 'X',\n'THN', 'X',\n'THO', 'T',\n'THP', 'X',\n'THQ\
+', 'X',\n'THR', 'T',\n'THS', 'X',\n'THT', 'X',\n'T\
+HU', 'X',\n'THX', 'X',\n'THZ', 'X',\n'TI1', 'X',\n\
+'TI2', 'X',\n'TI3', 'P',\n'TIA', 'X',\n'TIH', 'A',\
+\n'TK4', 'X',\n'TLA', 'X',\n'TLC', 'X',\n'TLM', 'X\
+',\n'TLN', 'X',\n'TLX', 'X',\n'TM5', 'X',\n'TM6', \
+'X',\n'TMA', 'X',\n'TMB', 'T',\n'TMC', 'X',\n'TMD'\
+, 'T',\n'TME', 'X',\n'TMF', 'X',\n'TML', 'K',\n'TM\
+M', 'X',\n'TMN', 'X',\n'TMP', 'X',\n'TMQ', 'X',\n'\
+TMR', 'X',\n'TMT', 'X',\n'TMZ', 'X',\n'TNB', 'C',\\
+n'TND', 'X',\n'TNK', 'X',\n'TNP', 'X',\n'TNT', 'X'\
+,\n'TOA', 'X',\n'TOB', 'X',\n'TOC', 'X',\n'TOL', '\
+X',\n'TOP', 'X',\n'TOS', 'X',\n'TOT', 'X',\n'TP1',\
+ 'G',\n'TP2', 'P',\n'TP3', 'E',\n'TP4', 'E',\n'TP7\
+', 'T',\n'TPA', 'X',\n'TPE', 'X',\n'TPF', 'X',\n'T\
+PI', 'X',\n'TPL', 'W',\n'TPM', 'X',\n'TPN', 'G',\n\
+'TPO', 'T',\n'TPP', 'X',\n'TPQ', 'A',\n'TPR', 'P',\
+\n'TPS', 'X',\n'TPT', 'X',\n'TPV', 'X',\n'TPX', 'X\
+',\n'TPY', 'X',\n'TQ3', 'X',\n'TQ4', 'X',\n'TQ5', \
+'X',\n'TQ6', 'X',\n'TR1', 'X',\n'TRA', 'X',\n'TRB'\
+, 'X',\n'TRC', 'X',\n'TRD', 'X',\n'TRE', 'X',\n'TR\
+F', 'W',\n'TRG', 'K',\n'TRH', 'X',\n'TRI', 'X',\n'\
+TRJ', 'X',\n'TRM', 'X',\n'TRN', 'W',\n'TRO', 'W',\\
+n'TRP', 'W',\n'TRQ', 'X',\n'TRS', 'X',\n'TRX', 'W'\
+,\n'TRZ', 'X',\n'TS2', 'X',\n'TS3', 'X',\n'TS4', '\
+X',\n'TS5', 'X',\n'TSA', 'X',\n'TSB', 'X',\n'TSI',\
+ 'X',\n'TSM', 'X',\n'TSN', 'X',\n'TSP', 'X',\n'TSU\
+', 'X',\n'TTA', 'X',\n'TTE', 'X',\n'TTN', 'X',\n'T\
+TO', 'X',\n'TTP', 'X',\n'TTX', 'X',\n'TXL', 'X',\n\
+'TYA', 'Y',\n'TYB', 'Y',\n'TYD', 'X',\n'TYI', 'Y',\
+\n'TYL', 'X',\n'TYM', 'W',\n'TYN', 'Y',\n'TYQ', 'Y\
+',\n'TYR', 'Y',\n'TYS', 'Y',\n'TYV', 'X',\n'TYY', \
+'A',\n'TZB', 'X',\n'TZC', 'X',\n'TZE', 'X',\n'TZL'\
+, 'X',\n'TZO', 'X',\n'TZP', 'X',\n'U01', 'X',\n'U0\
+2', 'X',\n'U03', 'X',\n'U04', 'X',\n'U05', 'X',\n'\
+U0E', 'X',\n'U10', 'X',\n'U18', 'X',\n'U2G', 'X',\\
+n'U3P', 'X',\n'U49', 'X',\n'U55', 'X',\n'U5P', 'X'\
+,\n'U66', 'X',\n'U89', 'X',\n'U8U', 'X',\n'UAA', '\
+X',\n'UAG', 'A',\n'UAP', 'X',\n'UAR', 'X',\n'UC1',\
+ 'X',\n'UC2', 'X',\n'UC3', 'X',\n'UC4', 'X',\n'UD1\
+', 'X',\n'UD2', 'X',\n'UDP', 'X',\n'UDX', 'X',\n'U\
+FG', 'X',\n'UFM', 'X',\n'UFP', 'X',\n'UGA', 'X',\n\
+'UIN', 'X',\n'UKP', 'A',\n'UM3', 'X',\n'UMA', 'A',\
+\n'UMG', 'X',\n'UMP', 'X',\n'UNA', 'X',\n'UND', 'X\
+',\n'UNI', 'X',\n'UNK', 'X',\n'UNN', 'X',\n'UNX', \
+'X',\n'UP5', 'X',\n'UP6', 'X',\n'UPA', 'X',\n'UPF'\
+, 'X',\n'UPG', 'X',\n'UPP', 'X',\n'UQ1', 'X',\n'UQ\
+2', 'X',\n'UQ6', 'X',\n'UR2', 'X',\n'URA', 'X',\n'\
+URE', 'X',\n'URF', 'X',\n'URI', 'X',\n'URS', 'X',\\
+n'UTP', 'X',\n'UVC', 'X',\n'UVW', 'X',\n'V35', 'X'\
+,\n'V36', 'X',\n'V4O', 'X',\n'V7O', 'X',\n'VAA', '\
+V',\n'VAC', 'X',\n'VAD', 'V',\n'VAF', 'V',\n'VAG',\
+ 'X',\n'VAL', 'V',\n'VAN', 'X',\n'VAS', 'X',\n'VAX\
+', 'X',\n'VDX', 'X',\n'VDY', 'X',\n'VG1', 'X',\n'V\
+IB', 'X',\n'VIR', 'X',\n'VIT', 'X',\n'VK3', 'X',\n\
+'VO3', 'X',\n'VO4', 'X',\n'VS1', 'F',\n'VS2', 'F',\
+\n'VS3', 'F',\n'VS4', 'F',\n'VXA', 'X',\n'W01', 'X\
+',\n'W02', 'X',\n'W03', 'X',\n'W11', 'X',\n'W33', \
+'X',\n'W35', 'X',\n'W42', 'X',\n'W43', 'X',\n'W54'\
+, 'X',\n'W56', 'X',\n'W59', 'X',\n'W71', 'X',\n'W8\
+4', 'X',\n'W8R', 'X',\n'W91', 'X',\n'WAY', 'X',\n'\
+WCC', 'X',\n'WO2', 'X',\n'WO4', 'X',\n'WRB', 'X',\\
+n'WRR', 'X',\n'WRS', 'X',\n'WW7', 'X',\n'X2F', 'X'\
+,\n'X7O', 'X',\n'XAA', 'X',\n'XAN', 'X',\n'XAO', '\
+X',\n'XBB', 'X',\n'XBP', 'X',\n'XDN', 'X',\n'XDP',\
+ 'X',\n'XIF', 'X',\n'XIM', 'X',\n'XK2', 'X',\n'XL1\
+', 'X',\n'XLS', 'X',\n'XMP', 'X',\n'XN1', 'X',\n'X\
+N2', 'X',\n'XN3', 'X',\n'XUL', 'X',\n'XV6', 'X',\n\
+'XYD', 'X',\n'XYH', 'X',\n'XYL', 'X',\n'XYP', 'X',\
+\n'XYS', 'X',\n'YOF', 'Y',\n'YRR', 'X',\n'YT3', 'X\
+',\n'YZ9', 'X',\n'Z34', 'G',\n'Z5A', 'X',\n'ZAF', \
+'X',\n'ZAP', 'X',\n'ZEB', 'X',\n'ZEN', 'X',\n'ZES'\
+, 'X',\n'ZID', 'X',\n'ZMR', 'X',\n'ZN3', 'X',\n'ZN\
+H', 'X',\n'ZNO', 'X',\n'ZO3', 'X',\n'ZPR', 'P',\n'\
+ZRA', 'A',\n'ZST', 'X',\n'ZYA', 'A',\n\n\n'ASN','N\
+');\n} \n\n\nsub file2head\n {\n my $file = s\
+hift;\n my $size = shift;\n my $f= new FileHandle;\
+\n my $line;\n open ($f,$file);\n read ($f,$line, \
+$size);\n close ($f);\n return $line;\n }\nsu\
+b file2tail\n {\n my $file = shift;\n my $siz\
+e = shift;\n my $f= new FileHandle;\n my $line;\n \
+\n open ($f,$file);\n seek ($f,$size*-1, 2);\n rea\
+d ($f,$line, $size);\n close ($f);\n return $line;\
+\n }\n\n\nsub vtmpnam\n {\n my $r=rand(1\
+00000);\n my $f=\"file.$r.$$\";\n while (-e $f)\n \
+ {\n $f=vtmpnam();\n }\n push (@TMPFILE_LIS\
+T, $f);\n return $f;\n }\n\nsub myexit\n {\n\
+ my $code=@_[0];\n if ($CLEAN_EXIT_STARTED==\
+1){return;}\n else {$CLEAN_EXIT_STARTED=1;}\n \
+ ### ONLY BARE EXIT\n exit ($code);\n }\nsub \
+set_error_lock\n {\n my $name = shift;\n \
+ my $pid=$$;\n\n \n &lock4tc ($$,\"LE\
+RROR\", \"LSET\", \"$$ -- ERROR: $name $PROGRAM\\n\
+\");\n return;\n }\nsub set_lock\n {\n \
+ my $pid=shift;\n my $msg= shift;\n my $p=ge\
+tppid();\n &lock4tc ($pid,\"LLOCK\",\"LRESET\",\
+\"$p$msg\\n\");\n }\nsub unset_lock\n {\n \\
+n my $pid=shift;\n &lock4tc ($pid,\"LLOCK\",\
+\"LRELEASE\",\"\");\n }\nsub shift_lock\n {\n \
+ my $from=shift;\n my $to=shift;\n my $from_\
+type=shift;\n my $to_type=shift;\n my $actio\
+n=shift;\n my $msg;\n \n if (!&lock4tc($f\
+rom, $from_type, \"LCHECK\", \"\")){return 0;}\n \
+ $msg=&lock4tc ($from, $from_type, \"LREAD\", \"\\
+");\n &lock4tc ($from, $from_type,\"LRELEASE\",\
+ $msg);\n &lock4tc ($to, $to_type, $action, $ms\
+g);\n return;\n }\nsub isshellpid\n {\n my\
+ $p=shift;\n if (!lock4tc ($p, \"LLOCK\", \"LCH\
+ECK\")){return 0;}\n else\n {\n my $c=lock\
+4tc($p, \"LLOCK\", \"LREAD\");\n if ( $c=~/-SHELL-\
+/){return 1;}\n }\n return 0;\n }\nsub is\
+rootpid\n {\n if(lock4tc (getppid(), \"LLOCK\"\
+, \"LCHECK\")){return 0;}\n else {return 1;}\n \
+ }\nsub lock4tc\n {\n my ($pid,$type,$action,$va\
+lue)=@_;\n my $fname;\n my $host=hostname;\n \
+ \n if ($type eq \"LLOCK\"){$fname=\"$LOCKDIR/.$\
+pid.$host.lock4tcoffee\";}\n elsif ( $type eq \"\
+LERROR\"){ $fname=\"$LOCKDIR/.$pid.$host.error4tco\
+ffee\";}\n elsif ( $type eq \"LWARNING\"){ $fnam\
+e=\"$LOCKDIR/.$pid.$host.warning4tcoffee\";}\n \\
+n if ($debug_lock)\n {\n print STDERR \
+\"\\n\\t---lock4tc(tcg): $action => $fname =>$valu\
+e (RD: $LOCKDIR)\\n\";\n }\n\n if ($actio\
+n eq \"LCHECK\") {return -e $fname;}\n elsif ($a\
+ction eq \"LREAD\"){return file2string($fname);}\n\
+ elsif ($action eq \"LSET\") {return string2file\
+ ($value, $fname, \">>\");}\n elsif ($action eq \
+\"LRESET\") {return string2file ($value, $fname, \\
+">\");}\n elsif ($action eq \"LRELEASE\") \n \
+ {\n if ( $debug_lock)\n {\n my $g=new F\
+ileHandle;\n open ($g, \">>$fname\");\n prin\
+t $g \"\\nDestroyed by $$\\n\";\n close ($g);\n\
+ safe_system (\"mv $fname $fname.old\");\n }\n\
+ else\n {\n unlink ($fname);\n }\n \
+}\n return \"\";\n }\n \nsub file2string\n {\n \
+ my $file=@_[0];\n my $f=new FileHandle;\n my \
+$r;\n open ($f, \"$file\");\n while (<$f>){$r.\
+=$_;}\n close ($f);\n return $r;\n }\nsub stri\
+ng2file \n {\n my ($s,$file,$mode)=@_;\n \
+my $f=new FileHandle;\n \n open ($f, \"$mode\
+$file\");\n print $f \"$s\";\n close ($f);\\
+n }\n\nBEGIN\n {\n srand;\n \n $S\
+IG{'SIGUP'}='signal_cleanup';\n $SIG{'SIGINT'\
+}='signal_cleanup';\n $SIG{'SIGQUIT'}='signal\
+_cleanup';\n $SIG{'SIGILL'}='signal_cleanup';\
+\n $SIG{'SIGTRAP'}='signal_cleanup';\n $\
+SIG{'SIGABRT'}='signal_cleanup';\n $SIG{'SIGE\
+MT'}='signal_cleanup';\n $SIG{'SIGFPE'}='sign\
+al_cleanup';\n \n $SIG{'SIGKILL'}='signa\
+l_cleanup';\n $SIG{'SIGPIPE'}='signal_cleanup\
+';\n $SIG{'SIGSTOP'}='signal_cleanup';\n \
+ $SIG{'SIGTTIN'}='signal_cleanup';\n $SIG{'SI\
+GXFSZ'}='signal_cleanup';\n $SIG{'SIGINFO'}='\
+signal_cleanup';\n \n $SIG{'SIGBUS'}='si\
+gnal_cleanup';\n $SIG{'SIGALRM'}='signal_clea\
+nup';\n $SIG{'SIGTSTP'}='signal_cleanup';\n \
+ $SIG{'SIGTTOU'}='signal_cleanup';\n $SIG{\
+'SIGVTALRM'}='signal_cleanup';\n $SIG{'SIGUSR\
+1'}='signal_cleanup';\n\n\n $SIG{'SIGSEGV'}='\
+signal_cleanup';\n $SIG{'SIGTERM'}='signal_cl\
+eanup';\n $SIG{'SIGCONT'}='signal_cleanup';\n\
+ $SIG{'SIGIO'}='signal_cleanup';\n $SIG{\
+'SIGPROF'}='signal_cleanup';\n $SIG{'SIGUSR2'\
+}='signal_cleanup';\n\n $SIG{'SIGSYS'}='signa\
+l_cleanup';\n $SIG{'SIGURG'}='signal_cleanup'\
+;\n $SIG{'SIGCHLD'}='signal_cleanup';\n \
+$SIG{'SIGXCPU'}='signal_cleanup';\n $SIG{'SIG\
+WINCH'}='signal_cleanup';\n \n $SIG{'INT\
+'}='signal_cleanup';\n $SIG{'TERM'}='signal_c\
+leanup';\n $SIG{'KILL'}='signal_cleanup';\n \
+ $SIG{'QUIT'}='signal_cleanup';\n \n \
+our $debug_lock=$ENV{\"DEBUG_LOCK\"};\n \n \
+ \n \n \n foreach my $a (@ARGV){$\
+CL.=\" $a\";}\n if ( $debug_lock ){print STDE\
+RR \"\\n\\n\\n********** START PG: $PROGRAM ******\
+*******\\n\";}\n if ( $debug_lock ){print STD\
+ERR \"\\n\\n\\n**********(tcg) LOCKDIR: $LOCKDIR $\
+$ *************\\n\";}\n if ( $debug_lock ){p\
+rint STDERR \"\\n --- $$ -- $CL\\n\";}\n \n \
+ \n \n \n }\nsub flush_error\n {\\
+n my $msg=shift;\n return add_error ($EXIT_F\
+AILURE,$$, $$,getppid(), $msg, $CL);\n }\nsub add\
+_error \n {\n my $code=shift;\n my $rpid=sh\
+ift;\n my $pid=shift;\n my $ppid=shift;\n \
+ my $type=shift;\n my $com=shift;\n \n $E\
+RROR_DONE=1;\n lock4tc ($rpid, \"LERROR\",\"LSE\
+T\",\"$pid -- ERROR: $type\\n\");\n lock4tc ($$\
+, \"LERROR\",\"LSET\", \"$pid -- COM: $com\\n\");\\
+n lock4tc ($$, \"LERROR\",\"LSET\", \"$pid -- S\
+TACK: $ppid -> $pid\\n\");\n \n return $code;\
+\n }\nsub add_warning \n {\n my $rpid=shift;\\
+n my $pid =shift;\n my $command=shift;\n \
+my $msg=\"$$ -- WARNING: $command\\n\";\n print\
+ STDERR \"$msg\";\n lock4tc ($$, \"LWARNING\", \
+\"LSET\", $msg);\n }\n\nsub signal_cleanup\n {\n\
+ print dtderr \"\\n**** $$ (tcg) was killed\\n\\
+";\n &cleanup;\n exit ($EXIT_FAILURE);\n }\\
+nsub clean_dir\n {\n my $dir=@_[0];\n if ( \
+!-d $dir){return ;}\n elsif (!($dir=~/tmp/)){re\
+turn ;}#safety check 1\n elsif (($dir=~/\\*/)){\
+return ;}#safety check 2\n else\n {\n `rm \
+-rf $dir`;\n }\n return;\n }\nsub cleanup\
+\n {\n #print stderr \"\\n----tc: $$ Kills $PI\
+DCHILD\\n\";\n #kill (SIGTERM,$PIDCHILD);\n \
+my $p=getppid();\n $CLEAN_EXIT_STARTED=1;\n \
+\n \n \n if (&lock4tc($$,\"LERROR\", \"LC\
+HECK\", \"\"))\n {\n my $ppid=getppid();\n if\
+ (!$ERROR_DONE) \n {\n &lock4tc($$,\"LERROR\\
+", \"LSET\", \"$$ -- STACK: $p -> $$\\n\");\n \
+&lock4tc($$,\"LERROR\", \"LSET\", \"$$ -- COM: $CL\
+\\n\");\n }\n }\n my $warning=&lock4tc($\
+$, \"LWARNING\", \"LREAD\", \"\");\n my $error=\
+&lock4tc($$, \"LERROR\", \"LREAD\", \"\");\n #\
+release error and warning lock if root\n \n \
+if (isrootpid() && ($warning || $error) )\n {\
+\n \n print STDERR \"**************** Summary ****\
+*********\\n$error\\n$warning\\n\";\n\n &lock4tc($\
+$,\"LERROR\",\"RELEASE\",\"\");\n &lock4tc($$,\"LW\
+ARNING\",\"RELEASE\",\"\");\n } \n \n \\
+n foreach my $f (@TMPFILE_LIST)\n {\n if (\
+-e $f){unlink ($f);} \n }\n foreach my $d \
+(@TMPDIR_LIST)\n {\n clean_dir ($d);\n }\
+\n #No More Lock Release\n #&lock4tc($$,\"LL\
+OCK\",\"LRELEASE\",\"\"); #release lock \n\n if\
+ ( $debug_lock ){print STDERR \"\\n\\n\\n*********\
+* END PG: $PROGRAM ($$) *************\\n\";}\n \
+if ( $debug_lock ){print STDERR \"\\n\\n\\n*******\
+***(tcg) LOCKDIR: $LOCKDIR $$ *************\\n\";}\
+\n }\nEND \n {\n \n &cleanup();\n }\n \\
+n\nsub safe_system \n{\n my $com=shift;\n my $nt\
+ry=shift;\n my $ctry=shift;\n my $pid;\n my $st\
+atus;\n my $ppid=getppid();\n if ($com eq \"\"){\
+return 1;}\n \n \n\n if (($pid = fork ()) < 0){\
+return (-1);}\n if ($pid == 0)\n {\n set_\
+lock($$, \" -SHELL- $com (tcg)\");\n exec ($c\
+om);\n }\n else\n {\n lock4tc ($$, \"L\
+LOCK\", \"LSET\", \"$pid\\n\");#update parent\n \
+ $PIDCHILD=$pid;\n }\n if ($debug_lock){prin\
+tf STDERR \"\\n\\t .... safe_system (fasta_seq2hmm\
+) p: $$ c: $pid COM: $com\\n\";}\n\n waitpid ($p\
+id,WTERMSIG);\n\n shift_lock ($pid,$$, \"LWARNING\
+\",\"LWARNING\", \"LSET\");\n\n if ($? == $EXIT_F\
+AILURE || lock4tc($pid, \"LERROR\", \"LCHECK\", \"\
+\"))\n {\n if ($ntry && $ctry <$ntry)\n {\\
+n add_warning ($$,$$,\"$com failed [retry: $ctry\
+]\");\n lock4tc ($pid, \"LRELEASE\", \"LERROR\",\
+ \"\");\n return safe_system ($com, $ntry, ++$ct\
+ry);\n }\n elsif ($ntry == -1)\n {\n if (!s\
+hift_lock ($pid, $$, \"LERROR\", \"LWARNING\", \"L\
+SET\"))\n {\n add_warning ($$,$$,\"$com \
+failed\");\n }\n else\n {\n lock4t\
+c ($pid, \"LRELEASE\", \"LERROR\", \"\");\n }\\
+n return $?;}\n else\n {\n if (!shift_loc\
+k ($pid,$$, \"LERROR\",\"LERROR\", \"LSET\"))\n \
+ {\n myexit(add_error ($EXIT_FAILURE,$$,$pi\
+d,getppid(), \"UNSPECIFIED system\", $com));\n \
+ }\n }\n }\n return $?;\n}\n\nsub check_config\
+uration \n {\n my @l=@_;\n my $v;\n \
+ foreach my $p (@l)\n {\n \n if ( $p eq \\
+"EMAIL\")\n { \n if ( !($EMAIL=~/@/))\n \
+ {\n add_warning($$,$$,\"Could Not Use EMAIL\");\\
+n myexit(add_error ($EXIT_FAILURE,$$,$$,getppid()\
+,\"EMAIL\",\"$CL\"));\n }\n }\n elsif(\
+ $p eq \"INTERNET\")\n {\n if ( !&check_\
+internet_connection())\n {\n myexit(add_error \
+($EXIT_FAILURE,$$,$$,getppid(),\"INTERNET\",\"$CL\\
+"));\n }\n }\n elsif( $p eq \"wget\")\n \
+ {\n if (!&pg_is_installed (\"wget\") && !&p\
+g_is_installed (\"curl\"))\n {\n myexit(add_er\
+ror ($EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTAL\
+LED:wget\",\"$CL\"));\n }\n }\n elsif( !(&p\
+g_is_installed ($p)))\n {\n myexit(add_e\
+rror ($EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTA\
+LLED:$p\",\"$CL\"));\n }\n }\n return 1;\\
+n }\nsub pg_is_installed\n {\n my @ml=@_;\n\
+ my $r, $p, $m;\n my $supported=0;\n \n \
+ my $p=shift (@ml);\n if ($p=~/::/)\n {\n\
+ if (safe_system (\"perl -M$p -e 1\")==$EXIT_SUCCE\
+SS){return 1;}\n else {return 0;}\n }\n el\
+se\n {\n $r=`which $p 2>/dev/null`;\n if ($r \
+eq \"\"){return 0;}\n else {return 1;}\n }\n \
+ }\n\n\n\nsub check_internet_connection\n {\n \
+my $internet;\n my $tmp;\n &check_configurat\
+ion ( \"wget\"); \n \n $tmp=&vtmpnam ();\n \
+ \n if (&pg_is_installed (\"wget\")){`w\
+get www.google.com -O$tmp >/dev/null 2>/dev/null`;\
+}\n elsif (&pg_is_installed (\"curl\")){`cu\
+rl www.google.com -o$tmp >/dev/null 2>/dev/null`;}\
+\n \n if ( !-e $tmp || -s $tmp < 10){$intern\
+et=0;}\n else {$internet=1;}\n if (-e $tmp){\
+unlink $tmp;}\n\n return $internet;\n }\nsub c\
+heck_pg_is_installed\n {\n my @ml=@_;\n my \
+$r=&pg_is_installed (@ml);\n if (!$r && $p=~/::\
+/)\n {\n print STDERR \"\\nYou Must Install t\
+he perl package $p on your system.\\nRUN:\\n\\tsud\
+o perl -MCPAN -e 'install $pg'\\n\";\n }\n \
+ elsif (!$r)\n {\n myexit(flush_error(\"\\nPr\
+ogram $p Supported but Not Installed on your syste\
+m\"));\n }\n else\n {\n return 1;\n \
+ }\n }\n\n\n","use Cwd;\nuse Env;\nuse File::P\
+ath;\nuse FileHandle;\nuse strict;\n\n\nour (%MODE\
+, %PG, %ENV_SET, %SUPPORTED_OS);\n\n\nour $EXIT_SU\
+CCESS=0;\nour $EXIT_FAILURE=1;\nour $INTERNET=0;\n\
+\nour $CP=\"cp \"; #was causing a crash on MacOSX\\
+nour $SILENT=\">/dev/null 2>/dev/null\";\nour $WEB\
+_BASE=\"http://www.tcoffee.org\";\nour $TCLINKDB_A\
+DDRESS=\"$WEB_BASE/Resources/tclinkdb.txt\";\nour \
+$OS=get_os();\nour $ROOT=&get_root();\nour $CD=cwd\
+();\nour $CDIR=$CD;\nour $HOME=$ENV{'HOME'};\n\nou\
+r $OSNAME=$ENV{'OSNAME'};\nour $OSARCH=$ENV{'OSARC\
+H'};\nour $REPO_ROOT=\"\";\n\nour $TCDIR;\nour $TC\
+CACHE;\nour $TCTMP;\nour $TCM;\nour $TCMETHODS;\no\
+ur $TCPLUGINS;\nour $PLUGINS_DIR=\"\";\nour $INSTA\
+LL_DIR=\"\";\n\nour $CXX=\"g++\";\nour $CXXFLAGS=\\
+"\";\n\nour $CPP=\"g++\";\nour $CPPFLAGS=\"\";\n\n\
+our $CC=\"gcc\";\nour $CFLAGS=$ENV{'CFLAGS'};\n\no\
+ur $FC=\"f77\";\nour $FFLAGS=\"\";\n\nmy $install=\
+\"all\";\nmy $default_update_action=\"no_update\";\
+\nmy @required_applications=(\"wget_OR_curl\");\nm\
+y @smode=(\"all\", \"clean\", \"install\");\n\n&in\
+itialize_PG();\n\nmy $cl=join( \" \", @ARGV);\nif \
+($#ARGV==-1 || ($cl=~/-h/) ||($cl=~/-H/) )\n {\n \
+ print \"\\n!!!!!!! ./install t_coffee \
+ --> installs t_coffee only\";\n print \"\\
+\n!!!!!!! ./install all --> inst\
+alls all the modes [mcoffee, expresso, psicoffee,r\
+coffee..]\";\n print \"\\n!!!!!!! ./install [\
+mcoffee|rcoffee|..] --> installs the specified mod\
+e\";\n print \"\\n!!!!!!! ./install -h \
+ --> print usage\\n\\n\";\n if ( $#\
+ARGV==-1){exit ($EXIT_FAILURE);}\n }\n \nif \
+(($cl=~/-h/) ||($cl=~/-H/) )\n {\n my $m;\n \
+ print \"\\n\\n!!!!!!! advanced mode\\n\";\n fo\
+reach $m ((keys (%MODE)),@smode)\n {\n print \
+\"!!!!!!! ./install $m\\n\";\n }\n \\
+n print \"!!!!!!! ./install [target:package|mod\
+e|] [-update|-force|-exec=dir|-dis=dir|-root|-tcli\
+nkdb=file|-] [CC=|FCC=|CXX=|CFLAGS=|CXXFLAGS=]\\n\\
+";\n print \"!!!!!!! ./install clean [remove\
+s all executables]\\n\";\n print \"!!!!!!! ./in\
+stall [optional:target] -update [upd\
+ates package already installed]\\n\";\n print \\
+"!!!!!!! ./install [optional:target] -force \
+ [Forces recompilation over everything]\\n\
+\";\n \n print \"!!!!!!! ./install [optional\
+:target] -root [You are running as\
+ root]\\n\";\n print \"!!!!!!! ./install [optio\
+nal:target] -exec=/foo/bar/ [address for the\
+ T-Coffee executable]\\n\";\n print \"!!!!!!! .\
+/install [optional:target] -dis=/foo/bar/ [\
+Address where distributions should be stored]\\n\"\
+;\n print \"!!!!!!! ./install [optional:target]\
+ -tclinkdb=foo|update [file containing all the pa\
+ckages to be installed]\\n\";\n print \"!!!!!!!\
+ ./install [optional:target] -clean \
+ [clean everything]\\n\";\n print \"!!!!!!! ./i\
+nstall [optional:target] -plugins [pl\
+ugins directory]\\n\";\n print \"!!!!!!! ./inst\
+all [optional:target] -tcdir=/foor/bar [base \
+path where T-Coffee will be installed]\\n\";\n \
+print \"!!!!!!! ./install [optional:target] -repo=\
+/path/to/repo [binaries repository root director\
+y]\\n\";\n print \"!!!!!!! mode:\";\n foreac\
+h $m (keys(%MODE)){print \"$m \";}\n print \"\\\
+n\";\n print \"!!!!!!! Packages:\";\n foreac\
+h $m (keys (%PG)){print \"$m \";}\n print \"\\n\
+\";\n \n print \"\\n\\n\";\n exit ($EXIT_\
+FAILURE);\n }\n\n\n\nmy (@argl)=($cl=~/(\\S+=[^=]\
++)\\s\\w+=/g);\npush (@argl, ($cl=~/(\\S+=[^=]+\\S\
+)\\s*$/g));\n\nforeach $a (@argl)\n {\n if ( (\
+$cl=~/CXX=(.*)/)){$CXX=$1;}\n if ( ($cl=~/-CC=(\
+.*)/ )){$CC=$1;}\n if ( ($cl=~/-FC=(.*)/ \
+)){$FC=$1;}\n if ( ($cl=~/-CFLAGS=(.*)/)){$CFLA\
+GS=$1;}\n if ( ($cl=~/-CXXFLAGS=(.*)/)){$CXXFLA\
+GS=$1;}\n }\nour ($ROOT_INSTALL, $NO_QUESTION, $d\
+efault_update_action,$BINARIES_ONLY,$force, $defau\
+lt_update_action, $INSTALL_DIR, $PLUGINS_DIR, $DIS\
+TRIBUTIONS,$tclinkdb, $proxy, $clean);\nif ( ($cl=\
+~/-root/)){$ROOT_INSTALL=1;}\nif ( ($cl=~/-no_ques\
+tion/)){$NO_QUESTION=1;}\nif ( ($cl=~/-update/)){$\
+default_update_action=\"update\";}\nif ( ($cl=~/-b\
+inaries/)){$BINARIES_ONLY=1;}\nif ( ($cl=~/-force/\
+)){$force=1;$default_update_action=\"update\"}\nif\
+ ( ($cl=~/-exec=\\s*(\\S+)/)){$INSTALL_DIR=$1;}\ni\
+f ( ($cl=~/-plugins=\\s*(\\S+)/)){$PLUGINS_DIR=$1;\
+}\nif ( ($cl=~/-dis=\\s*(\\S+)/)){$DISTRIBUTIONS=$\
+1;}\n\nif ( ($cl=~/-tclinkdb=\\s*(\\S+)/)){$tclink\
+db=$1;}\nif ( ($cl=~/-proxy=\\s*(\\S+)/)){$proxy=$\
+1;}\nif ( ($cl=~/-clean/)){$clean=1;}\nif ( ($cl=~\
+/-repo=\\s*(\\S+)/)){ $REPO_ROOT=$1; }\nif ( ($cl=\
+~/-tcdir=\\s*(\\S+)/)){ $TCDIR=$1; }\nif ($tclinkd\
+b){&update_tclinkdb ($tclinkdb);}\n\n\nif( $REPO_R\
+OOT ne \"\" ) {\n if( $OSNAME eq \"\" ) { print \"\
+You have specified the repository folder but the r\
+equired \\\"OSNAME\\\" enviroment variable is miss\
+ing. \\n\"; exit 1; } \n if( $OSARCH eq \"\" ) { p\
+rint \"You have specified the repository folder bu\
+t the required \\\"OSARCH\\\" enviroment variable \
+is missing. \\n\"; exit 1; } \n}\n\n\nif(!$TCDIR) \
+{ $TCDIR=\"$HOME/.t_coffee\"; }\n&add_dir ($TCDIR)\
+;\n&add_dir ($TCCACHE=\"$TCDIR/cache\");\n&add_dir\
+ ($TCTMP=\"$CDIR/tmp\");\n&add_dir ($TCM=\"$TCDIR/\
+mcoffee\");\n&add_dir ($TCMETHODS=\"$TCDIR/methods\
+\");\n&add_dir ($TCPLUGINS=\"$TCDIR/plugins/$OS\")\
+;\n\n\nour $BASE=\"$CD/bin\";\nour $BIN=\"$BASE/bi\
+naries/$OS\";\nour $DOWNLOAD_DIR=\"$BASE/download\\
+";\nour $DOWNLOAD_FILE=\"$DOWNLOAD_DIR/files\";\no\
+ur $TMP=\"$BASE/tmp\";\n\n&add_dir($BASE);\n&add_d\
+ir($BIN);\n&add_dir($DOWNLOAD_DIR);\n&add_dir($DOW\
+NLOAD_FILE);\nif (!$DISTRIBUTIONS){$DISTRIBUTIONS=\
+\"$DOWNLOAD_DIR/distributions\";}\n&add_dir ($DIST\
+RIBUTIONS);\n&add_dir ($TMP);\n\n\nif (!$PLUGIN\
+S_DIR && !$ROOT_INSTALL){$PLUGINS_DIR=$TCPLUGINS;}\
+\nelsif (!$PLUGINS_DIR && $ROOT_INSTALL){$PLUGINS\
+_DIR=\"/usr/local/bin/\";}\n\nif (!$INSTALL_DIR\
+ && !$ROOT_INSTALL){$INSTALL_DIR=\"$HOME/bin/\";mk\
+path ($INSTALL_DIR);}\nelsif (!$INSTALL_DIR && $R\
+OOT_INSTALL){$INSTALL_DIR=\"/usr/local/bin/\";}\n\\
+nif (-d \"mcoffee\"){`cp mcoffee/* $TCM`;}\n\n\nou\
+r $ENV_FILE=\"$TCDIR/t_coffee_env\";\n&env_file2pu\
+tenv ($ENV_FILE);\n&set_proxy($proxy);\nmy ($targe\
+t, $p, $r);\n$target=$p;\n\nforeach $p ( ((keys (\
+%PG)),(keys(%MODE)),(@smode)) )\n {\n if ($ARG\
+V[0] eq $p && $target eq \"\"){$target=$p;}\n }\n\
+if ($target eq \"\"){exit ($EXIT_FAILURE);}\n\n\nf\
+oreach $r (@required_applications)\n {\n my @a\
+pp_list;\n my $i;\n $i=0;\n \n @app_li\
+st=split (/_OR_/, $r);\n foreach my $pg (@app_l\
+ist)\n {\n $i+=&pg_is_installed ($pg);\n \
+ }\n if ($i==0)\n {\n print \"One of \
+the following packages must be installed to procee\
+d: \";\n foreach my $pg (@app_list)\n {\n p\
+rint (\"$pg \");\n }\n die;\n }\n }\n\n\n\
+\n\n\n\n&sign_license_ni();\n\n\n$PG{C}{compiler}=\
+get_C_compiler($CC);\n$PG{Fortran}{compiler}=get_F\
+_compiler($FC);\n$PG{CXX}{compiler}=$PG{CPP}{compi\
+ler}=$PG{GPP}{compiler}=get_CXX_compiler($CXX);\ni\
+f ($CXXFLAGS){$PG{CPP}{options}=$PG{GPP}{options}=\
+$PG{CXX}{options}=$CXXFLAGS;}\nif ($CFLAGS ne \"\"\
+ ){$PG{C}{options}=$CFLAGS;}\nforeach my $c (keys(\
+%PG))\n {\n my $arguments;\n if ($PG{$c}{co\
+mpiler})\n {\n $arguments=\"$PG{$c}{compiler_\
+flag}=$PG{$c}{compiler} \";\n if ($PG{$c}{options}\
+)\n {\n $arguments.=\"$PG{$c}{options_flag}=\
+'\" . $PG{$c}{options} . \"' \";\n }\n $PG{$c}{a\
+rguments}=$arguments;\n }\n }\n\nif ($PG{$ta\
+rget}){$PG{$target}{install}=1;}\nelse\n {\n f\
+oreach my $pg (keys(%PG))\n {\n if ( $target \
+eq \"all\" || ($PG{$pg}{mode}=~/$target/))\n {\n\
+ $PG{$pg} {install}=1;\n }\n }\n }\n\n\
+foreach my $pg (keys(%PG))\n {\n if (!$PG{$pg}\
+{update_action}){$PG{$pg}{update_action}=$default_\
+update_action;}\n elsif ($PG{$pg}{update_action\
+} eq \"never\"){$PG{$pg}{install}=0;}\n if ( $f\
+orce && $PG{$pg}{install})\n {\n `rm $BIN/$pg\
+ $BIN/$pg.exe $SILENT`;\n }\n if ($PG{$pg}\
+{update_action} eq \"update\" && $PG{$pg}{install}\
+){$PG{$pg}{update}=1;}\n }\n\nif (($target=~/clea\
+n/))\n {\n print \"------- cleaning executable\
+s -----\\n\";\n `rm bin/* $SILENT`;\n exit (\
+$EXIT_SUCCESS);\n }\n\nif ( !$PG{$target}){print \
+\"------- Installing T-Coffee Modes\\n\";}\n\nfore\
+ach my $m (keys(%MODE))\n {\n if ( $target eq \
+\"all\" || $target eq $m)\n {\n print \"\\n--\
+----- The installer will now install the $m compon\
+ents $MODE{$m}{description}\\n\";\n foreach my $pg\
+ (keys(%PG))\n {\n if ( $PG{$pg}{mode} =~/$m\
+/ && $PG{$pg}{install})\n {\n if ($PG{$pg}{\
+touched}){print \"------- $PG{$pg}{dname}: already\
+ processed\\n\";}\n else {$PG{$pg}{success}=&inst\
+all_pg($pg);$PG{$pg}{touched}=1;}\n }\n }\\
+n }\n }\n\nif ( $PG{$target}){print \"------\
+- Installing Individual Package\\n\";}\nforeach my\
+ $pg (keys (%PG))\n {\n \n if ( $PG{$pg}{in\
+stall} && !$PG{$pg}{touched})\n {\n print \"\\
+\n------- Install $pg\\n\";\n $PG{$pg}{success}=&i\
+nstall_pg($pg);$PG{$pg}{touched}=1;\n }\n }\\
+nprint \"------- Finishing The installation\\n\";\\
+nmy $final_report=&install ($INSTALL_DIR);\n\nprin\
+t \"\\n\";\nprint \"******************************\
+***************************************\\n\";\npri\
+nt \"******** INSTALLATION SUMMARY \
+ *****************\\n\";\nprint \"**********\
**************************************************\
-********\\n\";\nprint \"------- SUMMARY package In\
-stallation:\\n\";\nprint \"------- Executable In\
-stalled in: $PLUGINS_DIR\\n\";\n\nforeach my $pg (\
-keys(%PG))\n {\n if ( $PG{$pg}{install})\n \
- {\n my $bin_status=($PG{$pg}{from_binary} && $PG\
-{$pg}{success})?\"[from binary]\":\"\";\n if (\
- $PG{$pg}{new} && !$PG{$pg}{old}) \
- {print \"*------ $PG{$pg}{dname}: insta\
-lled $bin_status\\n\"; $PG{$pg}{status}=1;}\n elsi\
-f ( $PG{$pg}{new} && $PG{$pg}{old}) \
- {print \"*------ $PG{$pg}{dname}: u\
-pdated $bin_status\\n\" ; $PG{$pg}{status}=1;} \n\
- elsif (!$PG{$pg}{new} && $PG{$pg}{old} && !$PG{\
-$pg}{update}){print \"*------ $PG{$pg}{dnam\
-e}: previous\\n\" ; $PG{$pg}{status}=1;}\n elsif \
-(!$PG{$pg}{new} && $PG{$pg}{old} && $PG{$pg}{upd\
-ate}){print \"*------ $PG{$pg}{dname}: fail\
-ed update (previous installation available)\\n\";$\
-PG{$pg}{status}=0;}\n else \
- {print \"*------\
- $PG{$pg}{dname}: failed installation\\n\";\
-$PG{$pg}{status}=0;}\n }\n }\nmy $failure;\n\
-\nif ( !$PG{$target}){print \"*------ SUMMARY mode\
- Installation:\\n\";}\nforeach my $m (keys(%MODE))\
-\n {\n \n if ( $target eq \"all\" || $target \
-eq $m)\n {\n my $succesful=1;\n foreach my $p\
-g (keys(%PG))\n {\n if (($PG{$pg}{mode}=~/$m\
-/) && $PG{$pg}{install} && $PG{$pg}{status}==0)\n \
- {\n $succesful=0;\n print \"*!!!!!! \
-$PG{$pg}{dname}: Missing\\n\";\n }\n }\n i\
-f ( $succesful)\n {\n $MODE{$m}{status}=1;\n\
- print \"*------ MODE $MODE{$m}{dname} S\
-UCCESSFULLY installed\\n\";\n }\n else\n {\n \
- $failure++;\n $MODE{$m}{status}=0;\n pr\
-int \"*!!!!!! MODE $MODE{$m}{dname} UNSUCCES\
-SFULLY installed\\n\";\n }\n }\n }\n\n \
-\n \nif ($clean==1 && ($BASE=~/install4tcoffe\
-e/) ){print \"*------ Clean Installation Directory\
-: $BASE\\n\";`rm -rf $BASE`;}\nforeach my $pg (key\
-s(%PG)){if ($PG{$pg}{install} && $PG{$pg}{status}=\
-=0){exit ($EXIT_FAILURE);}}\n\nif ($failure)\n {\\
-n print \"*************************************\
-********************************\\n\";\n print \
-\"******** SOME PACKAGES FAILED TO INSTALL \
- *****************\\n\";\n print \"*********\
+*********\\n\";\nprint \"------- SUMMARY package I\
+nstallation:\\n\";\nprint \"------- Executable I\
+nstalled in: $PLUGINS_DIR\\n\";\n\nforeach my $pg \
+(keys(%PG))\n {\n if ( $PG{$pg}{install})\n \
+ {\n my $bin_status=($PG{$pg}{from_binary} && $P\
+G{$pg}{success})?\"[from binary]\":\"\";\n if \
+( $PG{$pg}{new} && !$PG{$pg}{old}) \
+ {print \"*------ $PG{$pg}{dname}: inst\
+alled $bin_status\\n\"; $PG{$pg}{status}=1;}\n els\
+if ( $PG{$pg}{new} && $PG{$pg}{old}) \
+ {print \"*------ $PG{$pg}{dname}: \
+updated $bin_status\\n\" ; $PG{$pg}{status}=1;} \\
+n elsif (!$PG{$pg}{new} && $PG{$pg}{old} && !$PG\
+{$pg}{update}){print \"*------ $PG{$pg}{dna\
+me}: previous\\n\" ; $PG{$pg}{status}=1;}\n elsif \
+ (!$PG{$pg}{new} && $PG{$pg}{old} && $PG{$pg}{up\
+date}){print \"*------ $PG{$pg}{dname}: fai\
+led update (previous installation available)\\n\";\
+$PG{$pg}{status}=0;}\n else \
+ {print \"*-----\
+- $PG{$pg}{dname}: failed installation\\n\"\
+;$PG{$pg}{status}=0;}\n }\n }\nmy $failure;\\
+n\nif ( !$PG{$target}){print \"*------ SUMMARY mod\
+e Installation:\\n\";}\nforeach my $m (keys(%MODE)\
+)\n {\n \n if ( $target eq \"all\" || $target\
+ eq $m)\n {\n my $succesful=1;\n foreach my $\
+pg (keys(%PG))\n {\n if (($PG{$pg}{mode}=~/$\
+m/) && $PG{$pg}{install} && $PG{$pg}{status}==0)\n\
+ {\n $succesful=0;\n print \"*!!!!!! \
+ $PG{$pg}{dname}: Missing\\n\";\n }\n }\n \
+if ( $succesful)\n {\n $MODE{$m}{status}=1;\\
+n print \"*------ MODE $MODE{$m}{dname} \
+SUCCESSFULLY installed\\n\";\n }\n else\n {\n \
+ $failure++;\n $MODE{$m}{status}=0;\n p\
+rint \"*!!!!!! MODE $MODE{$m}{dname} UNSUCCE\
+SSFULLY installed\\n\";\n }\n }\n }\n\n \
+ \n \nif ($clean==1 && ($BASE=~/install4tcoff\
+ee/) ){print \"*------ Clean Installation Director\
+y: $BASE\\n\";`rm -rf $BASE`;}\nforeach my $pg (ke\
+ys(%PG)){if ($PG{$pg}{install} && $PG{$pg}{status}\
+==0){exit ($EXIT_FAILURE);}}\n\nif ($failure)\n {\
+\n print \"************************************\
+*********************************\\n\";\n print\
+ \"******** SOME PACKAGES FAILED TO INSTALL \
+ *****************\\n\";\n print \"********\
**************************************************\
-**********\\n\";\n print \"\\nSome of the repor\
-ted failures may be due to connectivity problems\"\
-;\n print \"\\nRerun the installation and the i\
-nstaller will specifically try to install the miss\
-ing packages\";\n print \"\\nIf this Fails, go \
-to the original website and install the package ma\
-nually\";\n }\n\nprint \"************************\
-*********************************************\\n\"\
-;\nprint \"******** FINALIZE YOUR INS\
-TALLATION *****************\\n\";\nprint \"****\
+***********\\n\";\n print \"\\nSome of the repo\
+rted failures may be due to connectivity problems\\
+";\n print \"\\nRerun the installation and the \
+installer will specifically try to install the mis\
+sing packages\";\n print \"\\nIf this Fails, go\
+ to the original website and install the package m\
+anually\";\n }\n\nprint \"***********************\
+**********************************************\\n\\
+";\nprint \"******** FINALIZE YOUR IN\
+STALLATION *****************\\n\";\nprint \"***\
**************************************************\
-***************\\n\";\nprint \"------- Your execut\
-ables are in:\\n\"; \nprint \"------- $PLUGI\
-NS_DIR:\\n\";\nprint \"------- Add this directory \
-to your path with the following command:\\n\";\npr\
-int \"------- export PATH=$PLUGINS_DIR:\\$PA\
-TH\\n\";\nprint \"------- Make this permanent by a\
-dding this line to the file:\\n\";\nprint \"------\
-- $HOME/.bashrc\\n\";\nexit ($EXIT_SUCCESS);\
- \n \nsub get_CXX_compiler\n {\n my $c=@_[0]\
-;\n my (@clist)=(\"g++\");\n \n return ge\
-t_compil ($c, @clist);\n }\nsub get_C_compiler\n \
-{\n my $c=@_[0];\n my (@clist)=(\"gcc\", \"c\
-c\", \"icc\");\n \n return get_compil ($c, @\
-clist);\n }\n\nsub get_F_compiler\n {\n my ($c\
-)=@_[0];\n my @clist=(\"f77\", \"g77\",\"g95\",\
- \"gfortran\", \"ifort\");\n return get_compil \
-($c, @clist);\n } \n \nsub get_compil\n {\\
-n my ($fav,@clist)=(@_);\n \n #return the\
- first compiler found installed in the system. Che\
-ck first the favorite\n foreach my $c ($fav,@cl\
-ist)\n {\n if (&pg_is_installed ($c)){return\
- $c;}\n }\n return \"\";\n }\nsub exit_if\
-_pg_not_installed\n {\n my (@arg)=(@_);\n \\
-n foreach my $p (@arg)\n {\n if ( !&pg_is_\
-installed ($p))\n {\n print \"!!!!!!!! The $\
-p utility must be installed for this installation \
-to proceed [FATAL]\\n\";\n die;\n }\n }\
-\n return 1;\n }\nsub set_proxy\n {\n my (\
-$proxy)=(@_);\n my (@list,$p);\n \n @list\
-= (\"HTTP_proxy\", \"http_proxy\", \"HTTP_PROXY\",\
- \"ALL_proxy\", \"all_proxy\",\"HTTP_proxy_4_TCOFF\
-EE\",\"http_proxy_4_TCOFFEE\");\n \n if (!$p\
-roxy)\n {\n foreach my $p (@list)\n {\n \
- if ( ($ENV_SET{$p}) || $ENV{$p}){$proxy=$ENV{$p};\
-}\n }\n }\n foreach my $p(@list){$ENV{$p\
-}=$proxy;}\n }\n \nsub check_internet_connection\\
-n {\n my $internet;\n \n if ( -e \"x\"){\
-unlink (\"x\");}\n if (&pg_is_installed \
-(\"wget\")){`wget www.google.com -Ox >/dev/null 2>\
-/dev/null`;}\n elsif (&pg_is_installed (\"c\
-url\")){`curl www.google.com -ox >/dev/null 2>/dev\
-/null`;}\n else\n {\n printf stderr \"\\nE\
-RROR: No pg for remote file fetching [wget or curl\
-][FATAL]\\n\";\n exit ($EXIT_FAILURE);\n }\n \
- \n if ( !-e \"x\" || -s \"x\" < 10){$interne\
-t=0;}\n else {$internet=1;}\n if (-e \"x\"){\
-unlink \"x\";}\n return $internet;\n }\nsub ur\
-l2file\n {\n my ($cmd, $file,$wget_arg, $curl_\
-arg)=(@_);\n my ($exit,$flag, $pg, $arg);\n \
-\n if ($INTERNET || check_internet_connection (\
-)){$INTERNET=1;}\n else\n {\n print STDERR\
- \"ERROR: No Internet Connection [FATAL:install.pl\
-]\\n\";\n exit ($EXIT_FAILURE);\n }\n \n \
- if (&pg_is_installed (\"wget\")){$pg=\"wg\
-et\"; $flag=\"-O\";$arg=\"--tries=2 --connect-time\
-out=10 $wget_arg\";}\n elsif (&pg_is_installed\
- (\"curl\")){$pg=\"curl\"; $flag=\"-o\";$arg=$c\
-url_arg;}\n else\n {\n printf stderr \"\\n\
+****************\\n\";\nprint \"------- Your execu\
+tables are in:\\n\"; \nprint \"------- $PLUG\
+INS_DIR:\\n\";\nprint \"------- Add this directory\
+ to your path with the following command:\\n\";\np\
+rint \"------- export PATH=$PLUGINS_DIR:\\$P\
+ATH\\n\";\nprint \"------- Make this permanent by \
+adding this line to the file:\\n\";\nprint \"-----\
+-- $HOME/.bashrc\\n\";\nexit ($EXIT_SUCCESS)\
+; \n \nsub get_CXX_compiler\n {\n my $c=@_[0\
+];\n my (@clist)=(\"g++\");\n \n return g\
+et_compil ($c, @clist);\n }\nsub get_C_compiler\n \
+ {\n my $c=@_[0];\n my (@clist)=(\"gcc\", \"\
+cc\", \"icc\");\n \n return get_compil ($c, \
+@clist);\n }\n\nsub get_F_compiler\n {\n my ($\
+c)=@_[0];\n my @clist=(\"f77\", \"g77\",\"g95\"\
+, \"gfortran\", \"ifort\");\n return get_compil\
+ ($c, @clist);\n } \n \nsub get_compil\n {\
+\n my ($fav,@clist)=(@_);\n \n #return th\
+e first compiler found installed in the system. Ch\
+eck first the favorite\n foreach my $c ($fav,@c\
+list)\n {\n if (&pg_is_installed ($c)){retur\
+n $c;}\n }\n return \"\";\n }\nsub exit_i\
+f_pg_not_installed\n {\n my (@arg)=(@_);\n \
+\n foreach my $p (@arg)\n {\n if ( !&pg_is\
+_installed ($p))\n {\n print \"!!!!!!!! The \
+$p utility must be installed for this installation\
+ to proceed [FATAL]\\n\";\n die;\n }\n \
+}\n return 1;\n }\nsub set_proxy\n {\n my \
+($proxy)=(@_);\n my (@list,$p);\n \n @lis\
+t= (\"HTTP_proxy\", \"http_proxy\", \"HTTP_PROXY\"\
+, \"ALL_proxy\", \"all_proxy\",\"HTTP_proxy_4_TCOF\
+FEE\",\"http_proxy_4_TCOFFEE\");\n \n if (!$\
+proxy)\n {\n foreach my $p (@list)\n {\n \
+ if ( ($ENV_SET{$p}) || $ENV{$p}){$proxy=$ENV{$p}\
+;}\n }\n }\n foreach my $p(@list){$ENV{$\
+p}=$proxy;}\n }\n \nsub check_internet_connection\
+\n {\n my $internet;\n \n if ( -e \"x\")\
+{unlink (\"x\");}\n if (&pg_is_installed \
+ (\"wget\")){`wget www.google.com -Ox >/dev/null 2\
+>/dev/null`;}\n elsif (&pg_is_installed (\"\
+curl\")){`curl www.google.com -ox >/dev/null 2>/de\
+v/null`;}\n else\n {\n printf stderr \"\\n\
ERROR: No pg for remote file fetching [wget or cur\
l][FATAL]\\n\";\n exit ($EXIT_FAILURE);\n }\n\
- \n \n if (-e $file){unlink($file);}\n \
- $exit=system \"$pg $cmd $flag$file $arg\";\n r\
-eturn $exit;\n }\n\nsub pg_is_installed\n {\n \
- my ($p, $dir)=(@_);\n my ($r,$m, $ret);\n m\
-y ($supported, $language, $compil);\n \n \n \
- if ( $PG{$p})\n {\n $language=$PG{$p}{langua\
-ge2};\n $compil=$PG{$language}{compiler};\n }\
-\n \n if ( $compil eq \"CPAN\")\n {\n i\
-f ( system (\"perl -M$p -e 1\")==$EXIT_SUCCESS){$r\
-et=1;}\n else {$ret=0;}\n }\n elsif ($dir)\
-\n {\n if (-e \"$dir/$p\" || -e \"$dir/$p\\.e\
-xe\"){$ret=1;}\n else {$ret=0;}\n }\n elsi\
-f (-e \"$PLUGINS_DIR/$p\" || -e \"$PLUGINS_DIR/$p.\
-exe\"){$ret=1;}\n else\n {\n $r=`which $p \
-2>/dev/null`;\n if ($r eq \"\"){$ret=0;}\n else {$\
-ret=1;}\n }\n \n return $ret;\n }\nsub \
-install\n {\n my ($new_bin)=(@_);\n my ($co\
-pied, $report);\n\n \n if (!$ROOT_INSTALL)\n\
- {\n \n if (-e \"$BIN/t_coffee\"){`$CP $BIN/t\
-_coffee $INSTALL_DIR`};\n `cp $BIN/* $PLUGINS_DIR`\
-;\n $copied=1;\n }\n else\n {\n $copi\
-ed=&root_run (\"You must be root to finalize the i\
-nstallation\", \"$CP $BIN/* $INSTALL_DIR $SILENT\"\
-);\n }\n \n \n if ( !$copied)\n {\\
-n $report=\"*!!!!!! Installation unsuccesful.\
- The executables have been left in $BASE/bin\\n\";\
-\n }\n elsif ( $copied && $ROOT)\n {\n \
- $report=\"*------ Installation succesful. Your ex\
-ecutables have been copied in $new_bin and are on \
-your PATH\\n\";\n }\n elsif ( $copied && !$ROO\
-T)\n {\n $report= \"*!!!!!! T-Coffee and a\
-ssociated packages have been copied in: $new_bin\\\
-n\";\n $report.=\"*!!!!!! This address is NOT\
- in your PATH sytem variable\\n\";\n $report.\
-=\"*!!!!!! You can do so by adding the following l\
-ine in your ~/.bashrc file:\\n\";\n $report.=\
-\"*!!!!!! export PATH=$new_bin:\\$PATH\\n\";\n \
-}\n return $report;\n}\n\nsub sign_license_ni\n \
-{\n my $F=new FileHandle;\n open ($F, \"lice\
-nse.txt\");\n while (<$F>)\n {\n print \"$\
-_\";\n }\n close ($F);\n \n return;\\
-n }\n\nsub install_pg\n {\n my ($pg)=(@_);\n \
- my ($report, $previous, $language, $compiler, $\
-return);\n \n if (!$PG{$pg}{install}){return\
- 1;}\n \n $previous=&pg_is_installed ($pg);\\
-n \n if ($PG{$pg}{update_action} eq \"no_upd\
-ate\" && $previous)\n {\n $PG{$pg}{old}=1;\n \
-$PG{$pg}{new}=0;\n $return=1;\n }\n else\n\
- {\n $PG{$pg}{old}=$previous;\n \n if ($PG{$p\
-g} {language2} eq \"Perl\"){&install_perl_package \
-($pg);}\n elsif ($BINARIES_ONLY && &install_binary\
-_package ($pg)){$PG{$pg}{from_binary}=1;}\n elsif \
-(&install_source_package ($pg)){;}\n else \n {\n\
- \n if (!&supported_os($OS))\n {\n \
-print \"!!!!!!!! $pg compilation failed, binary un\
-supported for $OS\\n\"; \n }\n elsif (!(\
-$PG{$pg}{from_binary}=&install_binary_package ($pg\
-)))\n {\n print \"!!!!!!!! $pg compilation \
-and binary installation failed\\n\";\n }\n \
- }\n $PG{$pg}{new}=$return=&pg_is_installed ($pg,\
-$BIN);\n }\n\n \n return $return;\n }\\
-nsub install_perl_package\n {\n my ($pg)=(@_);\
-\n my ($report, $language, $compiler);\n \n \
- $language=$PG{$pg} {language2};\n $compiler=\
-$PG{$language}{compiler};\n \n if (!&pg_is_i\
-nstalled ($pg))\n {\n if ( $OS eq \"windows\"\
-){`perl -M$compiler -e 'install $pg'`;}\n elsif ( \
-$ROOT eq \"sudo\"){system (\"sudo perl -M$compiler\
- -e 'install $pg'\");}\n else {system (\"su root -\
-c perl -M$compiler -e 'install $pg'\");}\n }\\
-n return &pg_is_installed ($pg);\n }\n\n\n\nsu\
-b install_source_package\n {\n my ($pg)=(@_);\\
-n my ($report, $download, $arguments, $language\
-, $address, $name, $ext, $main_dir, $distrib);\n \
- my $wget_tmp=\"$TMP/wget.tmp\";\n my (@fl);\n\
- if ( -e \"$BIN/$pg\" || -e \"$BIN/$pg.exe\"){r\
-eturn 1;}\n \n #\n # check if the module \
-exists in the repository cache \n #\n if( repo_\
-load($pg) ) {\n return 1;\n }\n \n if ($pg \
-eq \"t_coffee\") {return &install_t_coffee ($pg\
-);}\n elsif ($pg eq \"TMalign\"){return &inst\
-all_TMalign ($pg);}\n \n chdir $DISTRIBUTION\
-S;\n \n $download=$PG{$pg}{source};\n \n \
- if (($download =~/tgz/))\n {\n ($address,$\
-name,$ext)=($download=~/(.+\\/)([^\\/]+)(\\.tgz).*\
-/);\n }\n elsif (($download=~/tar\\.gz/))\\
-n {\n ($address,$name,$ext)=($download=~/(.+\\
-\/)([^\\/]+)(\\.tar\\.gz).*/);\n }\n elsif\
- (($download=~/tar/))\n {\n ($address,$name,$\
-ext)=($download=~/(.+\\/)([^\\/]+)(\\.tar).*/);\n \
- }\n else\n {\n ($address,$name)=($dow\
-nload=~/(.+\\/)([^\\/]+)/);\n $ext=\"\";\n }\\
-n $distrib=\"$name$ext\";\n \n if ( !-d $\
-pg){mkdir $pg;}\n chdir $pg;\n \n #get the\
- distribution if available\n if ( -e \"$DOWNLOA\
-D_DIR/$distrib\")\n {\n `$CP $DOWNLOAD_DIR/$d\
-istrib .`;\n }\n #UNTAR and Prepare everyt\
-hing\n if (!-e \"$name.tar\" && !-e \"$name\")\\
-n {\n &check_rm ($wget_tmp);\n print \"\\n---\
----- Downloading/Installing $pg\\n\";\n \n if (!-e\
- $distrib && &url2file (\"$download\", \"$wget_tmp\
-\")==$EXIT_SUCCESS)\n {\n \n `mv $wget_t\
-mp $distrib`;\n `$CP $distrib $DOWNLOAD_DIR/`;\
-\n }\n\n if (!-e $distrib)\n {\n print \"!\
-!!!!!! Download of $pg distribution failed\\n\";\n\
- print \"!!!!!!! Check Address: $PG{$pg}{sourc\
-e}\\n\";\n return 0;\n }\n print \"\\n------\
-- unzipping/untaring $name\\n\";\n if (($ext =~/z/\
-))\n { \n &flush_command (\"gunzip $name$ext\
-\");\n \n }\n if (($ext =~/tar/) || ($ext =~\
-/tgz/))\n {\n &flush_command(\"tar -xvf $nam\
-e.tar\");\n }\n }\n #Guess and enter the\
- distribution directory\n @fl=ls($p);\n fore\
-ach my $f (@fl)\n {\n if (-d $f)\n {\n \
-$main_dir=$f;\n }\n }\n if (-d $main_dir\
-)\n \n {\n chdir $main_dir;}\n else\n \
- {\n print \"Error: $main_dir does not exist\";\\
-n }\n print \"\\n------- Compiling/Install\
-ing $pg\\n\";\n `make clean $SILENT`;\n \n \
- \n #\n # SAP module\n #\n if ($pg eq\
- \"sap\")\n {\n if (-e \"./configure\")\n {\
-\n #new sap distribution\n if ($OS eq \"ma\
-cosx\")\n {\n &replace_line_in_file (\"./sr\
-c/galloc.h\", \"malloc.h\", \"\");\n &replace_li\
-ne_in_file (\"./src/pdbprot.h\", \"malloc.h\", \"\\
-");\n &replace_line_in_file (\"./src/pdbprot.c\",\
- \"malloc.h\", \"\");\n }\n \n &flus\
-h_command (\"./configure\");\n &flush_command \
-(\"make clean\");\n &flush_command (\"make\");\
-\n &check_cp (\"./src/$pg\", \"$BIN\");\n \
-repo_store(\"./src/$pg\");\n }\n else\n {\n \
- #old style distribution\n `rm *.o sap sap.e\
-xe ./util/aa/*.o ./util/wt/.o $SILENT`;\n &fl\
-ush_command (\"make $arguments sap\");\n &chec\
-k_cp ($pg, \"$BIN\");\n repo_store($pg);\n }\
-\n }\n \n #\n # CLUSTALW2 module\n \
- #\n elsif ($pg eq \"clustalw2\")\n {\n &\
-flush_command(\"./configure\");\n &flush_command(\\
-"make $arguments\");\n &check_cp (\"./src/$pg\", \\
-"$BIN\");\n repo_store(\"./src/$pg\");\n }\n \
- \n #\n # FSA module\n # \n elsif ($\
-pg eq \"fsa\")\n {\n &flush_command(\"./confi\
-gure --prefix=$BIN\");\n &flush_command(\"make $ar\
-guments\");\n &flush_command (\"make install\");\n\
-\n repo_store(\"fsa\", \"$BIN/bin\");\n `mv $BIN/b\
-in/* $BIN`;\n `rmdir $BIN/bin`;\n }\n \n \
- #\n # CLUSTALW module\n #\n elsif ($pg \
-eq \"clustalw\")\n {\n &flush_command(\"make \
-$arguments clustalw\");\n `$CP $pg $BIN $SILENT`;\\
-n repo_store($pg);\n }\n \n #\n # MA\
-FFT module\n #\n elsif ($pg eq \"mafft\")\n \
- {\n my $base=cwd();\n my $c;\n \n #compile co\
-re\n mkpath (\"./mafft/bin\");\n mkpath (\"./mafft\
-/lib\");\n chdir \"$base/core\";\n `make clean $SI\
-LENT`;\n &flush_command (\"make $arguments\");\n &\
-flush_command (\"make install LIBDIR=../mafft/lib \
-BINDIR=../mafft/bin\");\n \n #compile extension\n \
-chdir \"$base/extensions\";\n `make clean $SILENT`\
-;\n &flush_command (\"make $arguments\");\n &flush\
-_command (\"make install LIBDIR=../mafft/lib BINDI\
-R=../mafft/bin\");\n \n #put everything in mafft a\
-nd copy the compiled stuff in bin\n chdir \"$base\\
-";\n if ($ROOT_INSTALL)\n {\n &root_run (\"Y\
-ou Must be Root to Install MAFFT\\n\", \"mkdir /us\
-r/local/mafft/;$CP mafft/lib/* /usr/local/mafft;$C\
-P mafft/lib/mafft* /usr/local/bin ;$CP mafft/bin/m\
-afft /usr/local/bin/; \");\n }\n else\n {\n \
- `$CP mafft/lib/* $BIN`;\n `$CP mafft/bin/ma\
-fft $BIN`;\n }\n `tar -cvf mafft.tar mafft`;\n \
-`gzip mafft.tar`;\n `mv mafft.tar.gz $BIN`;\n \n r\
-epo_store(\"mafft/bin/mafft\", \"mafft/lib/\", \"$\
-BIN/mafft.tar.gz\");\n }\n \n #\n \
-# DIALIGN-TX module\n #\n elsif ( $pg eq \"d\
-ialign-tx\" )\n {\n my $f;\n my $base=cwd();\\
-n\n chdir \"./source\";\n if ($OS eq \"macosx\"){&\
-flush_command (\"cp makefile.MAC_OS makefile\");}\\
-n\n &flush_command (\" make CPPFLAGS='-O3 -funroll\
--loops' all\");\n \n chdir \"..\";\n &check_cp (\"\
-./source/$pg\", \"$BIN\");\n repo_store(\"./source\
-/$pg\");\n }\n \n #\n # DIALIGN-T \
-module \n # (is the same as dialign-tx, but it \
-is mantained for backward name compatibility with \
-tcoffee)\n #\n elsif ( $pg eq \"dialign-t\" \
-)\n {\n my $f;\n my $base=cwd();\n\n chdir \"\
-./source\";\n if ($OS eq \"macosx\"){&flush_comman\
-d (\"cp makefile.MAC_OS makefile\");}\n\n &flush_c\
-ommand (\" make CPPFLAGS='-O3 -funroll-loops' all\\
-");\n \n chdir \"..\";\n &check_cp (\"./source/dia\
-lign-tx\", \"$BIN/dialign-t\");\n repo_store(\"$BI\
-N/dialign-t\"); \n } \n \n #\n \
- # POA module\n #\n elsif ($pg eq \"poa\")\\
-n {\n &flush_command (\"make $arguments poa\"\
-);\n &check_cp (\"$pg\", \"$BIN\");\n repo_store(\\
-"$pg\");\n }\n \n \n #\n # PROB\
-CONS module\n #\n elsif ( $pg eq \"probcons\\
-")\n {\n &add_C_libraries(\"./ProbabilisticMo\
-del.h\", \"list\", \"cstring\");\n \n `rm *.exe $S\
-ILENT`;\n &flush_command (\"make $arguments probco\
-ns\");\n &check_cp(\"$pg\", \"$BIN/$pg\");\n repo_\
-store(\"$pg\");\n }\n \n #\n # PRO\
-BCONS RNA module\n #\n elsif ( $pg eq \"prob\
-consRNA\")\n {\n &add_C_libraries(\"./Probabi\
-listicModel.h\", \"list\", \"cstring\");\n &add_C_\
-libraries(\"./Main.cc\", \"iomanip\", \"cstring\",\
-\"climits\");\n `rm *.exe $SILENT`;\n &flush_comma\
-nd (\"make $arguments probcons\");\n &check_cp(\"p\
-robcons\", \"$BIN/$pg\");\n repo_store(\"$BIN/$pg\\
-");\n }\n\n #\n # MUSCLE module\n #\n elsi\
-f ( $pg eq \"muscle\")\n { \n `rm *.o muscle\
- muscle.exe $SILENT`;\n if ($OS eq \"macosx\" || $\
-OS eq \"linux\")\n {\n &replace_line_in_file\
- (\"./Makefile\", \"LDLIBS = -lm -static\", \"LDL\
-IBS = -lm\");\n }\n elsif ($OS eq \"windows\")\n\
- {\n &replace_line_in_file (\"./intmath.cpp\\
-", \"double log2e\", \"double cedric_log\");\
-\n &replace_line_in_file (\"./intmath.cpp\", \
-\"double log2\", \"double log_notuse\");\n \
- &replace_line_in_file (\"./intmath.cpp\", \"do\
-uble cedric_log\", \"double log2e\");\n }\n &flu\
-sh_command (\"make $arguments all\");\n &check_cp(\
-\"$pg\", \"$BIN\");\n repo_store(\"$pg\"); \n \
- }\n \n #\n # MUS4 module\n #\n \
- elsif ( $pg eq \"mus4\")\n {\n `rm *.o mu\
-scle muscle.exe $SILENT`;\n &flush_command (\"./mk\
-\");\n &check_cp(\"$pg\", \"$BIN\");\n repo_store(\
-\"$pg\"); \n }\n \n #\n # PCMA mod\
-ule\n #\n elsif ( $pg eq \"pcma\")\n {\\
-n if ($OS eq \"macosx\")\n {\n &replace_line\
-_in_file (\"./alcomp2.c\", \"malloc.h\", \"\");\n\
- }\n &flush_command (\"make $arguments pcma\");\\
-n &check_cp(\"$pg\", \"$BIN\");\n repo_store(\"$pg\
-\"); \n }\n \n #\n # KALIGN module\
-\n #\n elsif ($pg eq \"kalign\")\n {\n \
-&flush_command (\"./configure\");\n &flush_command\
-(\"make $arguments\");\n &check_cp (\"$pg\",$BIN);\
-\n repo_store(\"$pg\"); \n }\n \n #\n\
- # AMAP module\n #\n elsif ( $pg eq \"ama\
-p\")\n {\n &add_C_libraries(\"./Amap.cc\", \"\
-iomanip\", \"cstring\",\"climits\"); \n `make clea\
-n $SILENT`;\n &flush_command (\"make $arguments al\
-l\");\n &check_cp (\"$pg\", $BIN);\n repo_store(\"\
-$pg\"); \n }\n \n #\n # PRODA modu\
-le\n #\n elsif ( $pg eq \"proda\")\n {\\
-n &add_C_libraries(\"AlignedFragment.h\", \"vector\
-\", \"iostream\", \"cstring\",\"cstdlib\");\n &add\
-_C_libraries(\"Main.cc\", \"vector\", \"climits\")\
-; \n &add_C_libraries(\"Sequence.cc\", \"stdlib.h\\
-", \"cstdio\"); \n &flush_command (\"make $argumen\
-ts all\");\n &check_cp (\"$pg\", $BIN);\n repo_sto\
-re(\"$pg\"); \n }\n \n #\n # PRANK\
- module\n #\n elsif ( $pg eq \"prank\")\n \
- {\n &flush_command (\"make $arguments all\");\n\
- &check_cp (\"$pg\", $BIN);\n repo_store(\"$pg\");\
- \n }\n \n #\n # !!!! MUSTANG modu\
-le\n #\n elsif ( $pg eq \"mustang\")\n \
- {\n &flush_command (\"rm ./bin/*\");\n &flush_com\
-mand (\"make $arguments all\");\n\n if ( $OS=~/win\
-dows/){&flush_command(\"cp ./bin/* $BIN/mustang.ex\
-e\");}\n else {&flush_command(\"cp ./bin/* $BIN/mu\
-stang\");}\n \n repo_store(\"$BIN/mustang\");\n \
- }\n\n #\n # RNAplfold module\n #\n elsif ( $\
-pg eq \"RNAplfold\")\n {\n &flush_command(\".\
-/configure\");\n &flush_command (\"make $arguments\
- all\");\n &check_cp(\"./Progs/RNAplfold\", \"$BIN\
-\");\n &check_cp(\"./Progs/RNAalifold\", \"$BIN\")\
-;\n &check_cp(\"./Progs/RNAfold\", \"$BIN\");\n \n\
- repo_store(\"./Progs/RNAplfold\", \"./Progs/RNAal\
-ifold\", \"./Progs/RNAfold\");\n }\n \n \
- #\n # !!! RETREE module\n #\n elsif ( \
-$pg eq \"retree\")\n {\n chdir \"src\";\n &fl\
-ush_command (\"make $arguments all\");\n &flush_co\
-mmand (\"make put\");\n system \"cp ../exe/* $BIN\\
-";\n \n repo_store(\"retree\", \"../exe\");\n \
- }\n \n chdir $CDIR;\n return &pg_is_install\
-ed ($pg, $BIN);\n }\n\nsub install_t_coffee\n {\\
-n my ($pg)=(@_);\n my ($report,$cflags, $arg\
-uments, $language, $compiler) ;\n #1-Install T-\
-Coffee\n chdir \"t_coffee_source\";\n &flush\
-_command (\"make clean\");\n print \"\\n-------\
- Compiling T-Coffee\\n\";\n $language=$PG{$pg} \
-{language2};\n $arguments=$PG{$language}{argume\
-nts};\n if (!($arguments =~/CFLAGS/)){$argument\
-s .= \" CFLAGS=-O2 \";}\n\n if ( $CC ne \"\"){&\
-flush_command (\"make -i $arguments t_coffee\");}\\
-n &check_cp ($pg, $BIN);\n \n chdir $CDIR\
+ \n if ( !-e \"x\" || -s \"x\" < 10){$intern\
+et=0;}\n else {$internet=1;}\n if (-e \"x\")\
+{unlink \"x\";}\n return $internet;\n }\nsub u\
+rl2file\n {\n my ($cmd, $file,$wget_arg, $curl\
+_arg)=(@_);\n my ($exit,$flag, $pg, $arg);\n \
+ \n if ($INTERNET || check_internet_connection \
+()){$INTERNET=1;}\n else\n {\n print STDER\
+R \"ERROR: No Internet Connection [FATAL:install.p\
+l]\\n\";\n exit ($EXIT_FAILURE);\n }\n \n \
+ if (&pg_is_installed (\"wget\")){$pg=\"w\
+get\"; $flag=\"-O\";$arg=\"--tries=2 --connect-tim\
+eout=10 $wget_arg\";}\n elsif (&pg_is_installe\
+d (\"curl\")){$pg=\"curl\"; $flag=\"-o\";$arg=$\
+curl_arg;}\n else\n {\n printf stderr \"\\\
+nERROR: No pg for remote file fetching [wget or cu\
+rl][FATAL]\\n\";\n exit ($EXIT_FAILURE);\n }\\
+n \n \n if (-e $file){unlink($file);}\n \
+ $exit=system \"$pg $cmd $flag$file $arg\";\n \
+return $exit;\n }\n\nsub pg_is_installed\n {\n \
+ my ($p, $dir)=(@_);\n my ($r,$m, $ret);\n \
+my ($supported, $language, $compil);\n \n \n \
+ if ( $PG{$p})\n {\n $language=$PG{$p}{langu\
+age2};\n $compil=$PG{$language}{compiler};\n \
+}\n \n if ( $compil eq \"CPAN\")\n {\n \
+if ( system (\"perl -M$p -e 1\")==$EXIT_SUCCESS){$\
+ret=1;}\n else {$ret=0;}\n }\n elsif ($dir\
+)\n {\n if (-e \"$dir/$p\" || -e \"$dir/$p\\.\
+exe\"){$ret=1;}\n else {$ret=0;}\n }\n els\
+if (-e \"$PLUGINS_DIR/$p\" || -e \"$PLUGINS_DIR/$p\
+.exe\"){$ret=1;}\n else\n {\n $r=`which $p\
+ 2>/dev/null`;\n if ($r eq \"\"){$ret=0;}\n else {\
+$ret=1;}\n }\n \n return $ret;\n }\nsub\
+ install\n {\n my ($new_bin)=(@_);\n my ($c\
+opied, $report);\n\n \n if (!$ROOT_INSTALL)\\
+n {\n \n if (-e \"$BIN/t_coffee\"){`$CP $BIN/\
+t_coffee $INSTALL_DIR`};\n `cp $BIN/* $PLUGINS_DIR\
+`;\n $copied=1;\n }\n else\n {\n $cop\
+ied=&root_run (\"You must be root to finalize the \
+installation\", \"$CP $BIN/* $INSTALL_DIR $SILENT\\
+");\n }\n \n \n if ( !$copied)\n {\
+\n $report=\"*!!!!!! Installation unsuccesful\
+. The executables have been left in $BASE/bin\\n\"\
+;\n }\n elsif ( $copied && $ROOT)\n {\n \
+ $report=\"*------ Installation succesful. Your e\
+xecutables have been copied in $new_bin and are on\
+ your PATH\\n\";\n }\n elsif ( $copied && !$RO\
+OT)\n {\n $report= \"*!!!!!! T-Coffee and \
+associated packages have been copied in: $new_bin\\
+\n\";\n $report.=\"*!!!!!! This address is NO\
+T in your PATH sytem variable\\n\";\n $report\
+.=\"*!!!!!! You can do so by adding the following \
+line in your ~/.bashrc file:\\n\";\n $report.\
+=\"*!!!!!! export PATH=$new_bin:\\$PATH\\n\";\n \
+ }\n return $report;\n}\n\nsub sign_license_ni\n \
+ {\n my $F=new FileHandle;\n open ($F, \"lic\
+ense.txt\");\n while (<$F>)\n {\n print \"\
+$_\";\n }\n close ($F);\n \n return;\
+\n }\n\nsub install_pg\n {\n my ($pg)=(@_);\n\
+ my ($report, $previous, $language, $compiler, \
+$return);\n \n if (!$PG{$pg}{install}){retur\
+n 1;}\n \n $previous=&pg_is_installed ($pg);\
+\n \n if ($PG{$pg}{update_action} eq \"no_up\
+date\" && $previous)\n {\n $PG{$pg}{old}=1;\n\
+ $PG{$pg}{new}=0;\n $return=1;\n }\n else\\
+n {\n $PG{$pg}{old}=$previous;\n \n if ($PG{$\
+pg} {language2} eq \"Perl\"){&install_perl_package\
+ ($pg);}\n elsif ($BINARIES_ONLY && &install_binar\
+y_package ($pg)){$PG{$pg}{from_binary}=1;}\n elsif\
+ (&install_source_package ($pg)){;}\n else \n {\\
+n \n if (!&supported_os($OS))\n {\n \
+ print \"!!!!!!!! $pg compilation failed, binary u\
+nsupported for $OS\\n\"; \n }\n elsif (!\
+($PG{$pg}{from_binary}=&install_binary_package ($p\
+g)))\n {\n print \"!!!!!!!! $pg compilation\
+ and binary installation failed\\n\";\n }\n\
+ }\n $PG{$pg}{new}=$return=&pg_is_installed ($pg\
+,$BIN);\n }\n\n \n return $return;\n }\
+\nsub install_perl_package\n {\n my ($pg)=(@_)\
+;\n my ($report, $language, $compiler);\n \n\
+ $language=$PG{$pg} {language2};\n $compiler\
+=$PG{$language}{compiler};\n \n if (!&pg_is_\
+installed ($pg))\n {\n if ( $OS eq \"windows\\
+"){`perl -M$compiler -e 'install $pg'`;}\n elsif (\
+ $ROOT eq \"sudo\"){system (\"sudo perl -M$compile\
+r -e 'install $pg'\");}\n else {system (\"su root \
+-c perl -M$compiler -e 'install $pg'\");}\n }\
+\n return &pg_is_installed ($pg);\n }\n\n\n\ns\
+ub install_source_package\n {\n my ($pg)=(@_);\
+\n my ($report, $download, $arguments, $languag\
+e, $address, $name, $ext, $main_dir, $distrib);\n \
+ my $wget_tmp=\"$TMP/wget.tmp\";\n my (@fl);\\
+n if ( -e \"$BIN/$pg\" || -e \"$BIN/$pg.exe\"){\
+return 1;}\n \n #\n # check if the module\
+ exists in the repository cache \n #\n if( repo\
+_load($pg) ) {\n return 1;\n }\n \n if ($pg\
+ eq \"t_coffee\") {return &install_t_coffee ($p\
+g);}\n elsif ($pg eq \"TMalign\"){return &ins\
+tall_TMalign ($pg);}\n \n chdir $DISTRIBUTIO\
+NS;\n \n $download=$PG{$pg}{source};\n \n\
+ if (($download =~/tgz/))\n {\n ($address,\
+$name,$ext)=($download=~/(.+\\/)([^\\/]+)(\\.tgz).\
+*/);\n }\n elsif (($download=~/tar\\.gz/))\
+\n {\n ($address,$name,$ext)=($download=~/(.+\
+\\/)([^\\/]+)(\\.tar\\.gz).*/);\n }\n elsi\
+f (($download=~/tar/))\n {\n ($address,$name,\
+$ext)=($download=~/(.+\\/)([^\\/]+)(\\.tar).*/);\n\
+ }\n else\n {\n ($address,$name)=($do\
+wnload=~/(.+\\/)([^\\/]+)/);\n $ext=\"\";\n }\
+\n $distrib=\"$name$ext\";\n \n if ( !-d \
+$pg){mkdir $pg;}\n chdir $pg;\n \n #get th\
+e distribution if available\n if ( -e \"$DOWNLO\
+AD_DIR/$distrib\")\n {\n `$CP $DOWNLOAD_DIR/$\
+distrib .`;\n }\n #UNTAR and Prepare every\
+thing\n if (!-e \"$name.tar\" && !-e \"$name\")\
+\n {\n &check_rm ($wget_tmp);\n print \"\\n--\
+----- Downloading/Installing $pg\\n\";\n \n if (!-\
+e $distrib && &url2file (\"$download\", \"$wget_tm\
+p\")==$EXIT_SUCCESS)\n {\n \n `mv $wget_\
+tmp $distrib`;\n `$CP $distrib $DOWNLOAD_DIR/`\
+;\n }\n\n if (!-e $distrib)\n {\n print \"\
+!!!!!!! Download of $pg distribution failed\\n\";\\
+n print \"!!!!!!! Check Address: $PG{$pg}{sour\
+ce}\\n\";\n return 0;\n }\n print \"\\n-----\
+-- unzipping/untaring $name\\n\";\n if (($ext =~/z\
+/))\n { \n &flush_command (\"gunzip $name$ex\
+t\");\n \n }\n if (($ext =~/tar/) || ($ext =\
+~/tgz/))\n {\n &flush_command(\"tar -xvf $na\
+me.tar\");\n }\n }\n #Guess and enter th\
+e distribution directory\n @fl=ls($p);\n for\
+each my $f (@fl)\n {\n if (-d $f)\n {\n \
+ $main_dir=$f;\n }\n }\n if (-d $main_di\
+r)\n \n {\n chdir $main_dir;}\n else\n \
+ {\n print \"Error: $main_dir does not exist\";\
+\n }\n print \"\\n------- Compiling/Instal\
+ling $pg\\n\";\n `make clean $SILENT`;\n \n \
+ \n #\n # SAP module\n #\n if ($pg e\
+q \"sap\")\n {\n if (-e \"./configure\")\n \
+{\n #new sap distribution\n \n &flush_\
+command (\"./configure\");\n &flush_command (\\
+"make clean\");\n &flush_command (\"make\");\n\
+ &check_cp (\"./src/$pg\", \"$BIN\");\n re\
+po_store(\"./src/$pg\");\n }\n else\n {\n \
+#old style distribution\n `rm *.o sap sap.exe\
+ ./util/aa/*.o ./util/wt/.o $SILENT`;\n &flus\
+h_command (\"make $arguments sap\");\n &check_\
+cp ($pg, \"$BIN\");\n repo_store($pg);\n }\n\
+ }\n \n #\n # CLUSTALW2 module\n \
+#\n elsif ($pg eq \"clustalw2\")\n {\n &fl\
+ush_command(\"./configure\");\n &flush_command(\"m\
+ake $arguments\");\n &check_cp (\"./src/$pg\", \"$\
+BIN\");\n repo_store(\"./src/$pg\");\n }\n\n \
+ #\n # CLUSTAL-OMEGA module\n #\n elsif\
+ ($pg eq \"clustalo\")\n {\n &flush_command(\\
+"./configure\");\n &flush_command(\"make $argument\
+s\");\n &check_cp (\"./src/$pg\", \"$BIN\");\n rep\
+o_store(\"./src/$pg\");\n }\n\n #\n # S\
+TRIKE module\n #\n elsif ($pg eq \"strike\")\
+\n {\n &flush_command(\"make $arguments\");\n\
+ &check_cp (\"./bin/$pg\", \"$BIN\");\n repo_store\
+(\"./bin/$pg\");\n }\n \n #\n # FSA \
+module\n # \n elsif ($pg eq \"fsa\")\n \
+{\n &flush_command(\"./configure --prefix=$BIN\");\
+\n &flush_command(\"make $arguments\");\n &flush_c\
+ommand (\"make install\");\n\n repo_store(\"fsa\",\
+ \"$BIN/bin\");\n `mv $BIN/bin/* $BIN`;\n `rmdir $\
+BIN/bin`;\n }\n \n #\n # CLUSTALW mo\
+dule\n #\n elsif ($pg eq \"clustalw\")\n \
+ {\n &flush_command(\"make $arguments clustalw\")\
+;\n `$CP $pg $BIN $SILENT`;\n repo_store($pg);\n \
+ }\n \n #\n # MAFFT module\n #\n \
+ elsif ($pg eq \"mafft\")\n {\n my $base=cwd(\
+);\n my $c;\n \n #compile core\n mkpath (\"./mafft\
+/bin\");\n mkpath (\"./mafft/lib\");\n chdir \"$ba\
+se/core\";\n `make clean $SILENT`;\n &flush_comman\
+d (\"make $arguments\");\n &flush_command (\"make \
+install LIBDIR=../mafft/lib BINDIR=../mafft/bin\")\
+;\n \n #compile extension\n chdir \"$base/extensio\
+ns\";\n `make clean $SILENT`;\n &flush_command (\"\
+make $arguments\");\n &flush_command (\"make insta\
+ll LIBDIR=../mafft/lib BINDIR=../mafft/bin\");\n \\
+n #put everything in mafft and copy the compiled s\
+tuff in bin\n chdir \"$base\";\n if ($ROOT_INSTALL\
+)\n {\n &root_run (\"You Must be Root to Ins\
+tall MAFFT\\n\", \"mkdir /usr/local/mafft/;$CP maf\
+ft/lib/* /usr/local/mafft;$CP mafft/lib/mafft* /us\
+r/local/bin ;$CP mafft/bin/mafft /usr/local/bin/; \
+\");\n }\n else\n {\n `$CP mafft/lib/* $B\
+IN`;\n `$CP mafft/bin/mafft $BIN`;\n }\n `t\
+ar -cvf mafft.tar mafft`;\n `gzip mafft.tar`;\n `m\
+v mafft.tar.gz $BIN`;\n \n repo_store(\"mafft/bin/\
+mafft\", \"mafft/lib/\", \"$BIN/mafft.tar.gz\");\n\
+ }\n \n #\n # DIALIGN-TX module\n \
+ #\n elsif ( $pg eq \"dialign-tx\" )\n {\
+\n my $f;\n my $base=cwd();\n\n chdir \"./source\"\
+;\n if ($OS eq \"macosx\"){&flush_command (\"cp ma\
+kefile.MAC_OS makefile\");}\n\n &flush_command (\"\
+ make CPPFLAGS='-O3 -funroll-loops' all\");\n \n c\
+hdir \"..\";\n &check_cp (\"./source/$pg\", \"$BIN\
+\");\n repo_store(\"./source/$pg\");\n }\n \
+ \n #\n # DIALIGN-T module \n # (is the\
+ same as dialign-tx, but it is mantained for backw\
+ard name compatibility with tcoffee)\n #\n e\
+lsif ( $pg eq \"dialign-t\" )\n {\n my $f;\n \
+my $base=cwd();\n\n chdir \"./source\";\n if ($OS \
+eq \"macosx\"){&flush_command (\"cp makefile.MAC_O\
+S makefile\");}\n\n &flush_command (\" make CPPFLA\
+GS='-O3 -funroll-loops' all\");\n \n chdir \"..\";\
+\n &check_cp (\"./source/dialign-tx\", \"$BIN/dial\
+ign-t\");\n repo_store(\"$BIN/dialign-t\"); \n \
+ } \n \n #\n # POA module\n #\\
+n elsif ($pg eq \"poa\")\n {\n &flush_comm\
+and (\"make $arguments poa\");\n &check_cp (\"$pg\\
+", \"$BIN\");\n repo_store(\"$pg\");\n }\n \
+ \n \n #\n # PROBCONS module\n #\n \
+ elsif ( $pg eq \"probcons\")\n {\n &add_C_l\
+ibraries(\"./ProbabilisticModel.h\", \"list\", \"c\
+string\");\n \n `rm *.exe $SILENT`;\n &flush_comma\
+nd (\"make $arguments probcons\");\n &check_cp(\"$\
+pg\", \"$BIN/$pg\");\n repo_store(\"$pg\");\n \
+ }\n \n #\n # PROBCONS RNA module\n \
+#\n elsif ( $pg eq \"probconsRNA\")\n {\n \
+&add_C_libraries(\"./ProbabilisticModel.h\", \"lis\
+t\", \"cstring\");\n &add_C_libraries(\"./Main.cc\\
+", \"iomanip\", \"cstring\",\"climits\");\n `rm *.\
+exe $SILENT`;\n &flush_command (\"make $arguments \
+probcons\");\n &check_cp(\"probcons\", \"$BIN/$pg\\
+");\n repo_store(\"$BIN/$pg\");\n }\n\n #\n #\
+ MUSCLE module\n #\n elsif ( $pg eq \"muscle\"\
+)\n { \n `rm *.o muscle muscle.exe $SILENT`;\\
+n if ($OS eq \"macosx\" || $OS eq \"linux\")\n {\
+\n &replace_line_in_file (\"./Makefile\", \"LD\
+LIBS = -lm -static\", \"LDLIBS = -lm\");\n }\n \
+elsif ($OS eq \"windows\")\n {\n &replace_li\
+ne_in_file (\"./intmath.cpp\", \"double log2e\", \
+ \"double cedric_log\");\n &replace_line_i\
+n_file (\"./intmath.cpp\", \"double log2\", \
+ \"double log_notuse\");\n &replace_line_in_fi\
+le (\"./intmath.cpp\", \"double cedric_log\", \"d\
+ouble log2e\");\n }\n &flush_command (\"make $ar\
+guments all\");\n &check_cp(\"$pg\", \"$BIN\");\n \
+repo_store(\"$pg\"); \n }\n \n #\n \
+ # MUS4 module\n #\n elsif ( $pg eq \"m\
+us4\")\n {\n `rm *.o muscle muscle.exe $SILEN\
+T`;\n &flush_command (\"./mk\");\n &check_cp(\"$pg\
+\", \"$BIN\");\n repo_store(\"$pg\"); \n }\n \
+ \n #\n # PCMA module\n #\n elsif \
+( $pg eq \"pcma\")\n {\n if ($OS eq \"macosx\\
+")\n {\n &replace_line_in_file (\"./alcomp2.\
+c\", \"malloc.h\", \"\");\n }\n &flush_command \
+(\"make $arguments pcma\");\n &check_cp(\"$pg\", \\
+"$BIN\");\n repo_store(\"$pg\"); \n }\n \
+\n #\n # KALIGN module\n #\n elsif ($p\
+g eq \"kalign\")\n {\n &flush_command (\"./co\
+nfigure\");\n &flush_command(\"make $arguments\");\
+\n &check_cp (\"$pg\",$BIN);\n repo_store(\"$pg\")\
+; \n }\n \n #\n # AMAP module\n \
+ #\n elsif ( $pg eq \"amap\")\n {\n &add_C\
+_libraries(\"./Amap.cc\", \"iomanip\", \"cstring\"\
+,\"climits\"); \n `make clean $SILENT`;\n &flush_c\
+ommand (\"make $arguments all\");\n &check_cp (\"$\
+pg\", $BIN);\n repo_store(\"$pg\"); \n }\n \
+ \n #\n # PRODA module\n #\n elsif (\
+ $pg eq \"proda\")\n {\n &add_C_libraries(\"A\
+lignedFragment.h\", \"vector\", \"iostream\", \"cs\
+tring\",\"cstdlib\");\n &add_C_libraries(\"Main.cc\
+\", \"vector\", \"climits\"); \n &add_C_libraries(\
+\"Sequence.cc\", \"stdlib.h\", \"cstdio\"); \n &fl\
+ush_command (\"make $arguments all\");\n &check_cp\
+ (\"$pg\", $BIN);\n repo_store(\"$pg\"); \n }\
+\n \n #\n # PRANK module\n #\n el\
+sif ( $pg eq \"prank\")\n {\n &flush_command \
+(\"make $arguments all\");\n &check_cp (\"$pg\", $\
+BIN);\n repo_store(\"$pg\"); \n }\n \n \
+ #\n # !!!! MUSTANG module\n #\n elsif \
+( $pg eq \"mustang\")\n {\n &flush_command (\\
+"rm ./bin/*\");\n &flush_command (\"make $argument\
+s all\");\n\n if ( $OS=~/windows/){&flush_command(\
+\"cp ./bin/* $BIN/mustang.exe\");}\n else {&flush_\
+command(\"cp ./bin/* $BIN/mustang\");}\n \n repo_s\
+tore(\"$BIN/mustang\");\n }\n\n #\n # RNAplfo\
+ld module\n #\n elsif ( $pg eq \"RNAplfold\")\n\
+ {\n &flush_command(\"./configure\");\n &flus\
+h_command (\"make $arguments all\");\n &check_cp(\\
+"./Progs/RNAplfold\", \"$BIN\");\n &check_cp(\"./P\
+rogs/RNAalifold\", \"$BIN\");\n &check_cp(\"./Prog\
+s/RNAfold\", \"$BIN\");\n \n repo_store(\"./Progs/\
+RNAplfold\", \"./Progs/RNAalifold\", \"./Progs/RNA\
+fold\");\n }\n \n #\n # !!! RETREE\
+ module\n #\n elsif ( $pg eq \"retree\")\n \
+ {\n chdir \"src\";\n &flush_command (\"make $a\
+rguments all\");\n &flush_command (\"make put\");\\
+n system \"cp ../exe/* $BIN\";\n \n repo_store(\"r\
+etree\", \"../exe\");\n }\n \n chdir $CDIR\
;\n return &pg_is_installed ($pg, $BIN);\n }\n\
-sub install_TMalign\n {\n my ($pg)=(@_);\n \
-my $report;\n chdir \"t_coffee_source\";\n p\
-rint \"\\n------- Compiling TMalign\\n\";\n `rm\
- TMalign TMalign.exe $SILENT`;\n if ( $FC ne \"\
-\"){&flush_command (\"make -i $PG{Fortran}{argumen\
-ts} TMalign\");}\n &check_cp ($pg, $BIN);\n \
-repo_store($pg);\n\n if ( !-e \"$BIN/$pg\" && p\
-g_has_binary_distrib ($pg))\n {\n print \"!!!\
-!!!! Compilation of $pg impossible. Will try to in\
-stall from binary\\n\";\n return &install_binary_p\
-ackage ($pg);\n }\n chdir $CDIR;\n retu\
-rn &pg_is_installed ($pg, $BIN);\n }\n\nsub pg_ha\
-s_binary_distrib\n {\n my ($pg)=(@_);\n if \
-($PG{$pg}{windows}){return 1;}\n elsif ($PG{$pg\
-}{osx}){return 1;}\n elsif ($PG{$pg}{linux}){re\
-turn 1;}\n return 0;\n }\nsub install_binary_p\
-ackage\n {\n my ($pg)=(@_);\n my ($base,$re\
-port,$name, $download, $arguments, $language, $dir\
-);\n my $isdir;\n &input_os();\n \n if\
- (!&supported_os($OS)){return 0;}\n if ( $PG{$p\
-g}{binary}){$name=$PG{$pg}{binary};}\n else \n \
- {\n $name=$pg;\n if ( $OS eq \"windows\"){$na\
-me.=\".exe\";}\n }\n \n $download=\"$WE\
-B_BASE/Packages/Binaries/$OS/$name\";\n \n $\
-base=cwd();\n chdir $TMP;\n \n if (!-e $n\
-ame)\n {\n `rm x $SILENT`;\n if ( url2file(\"\
-$download\",\"x\")==$EXIT_SUCCESS)\n {\n `mv\
- x $name`;\n }\n }\n \n if (!-e $name\
-)\n {\n print \"!!!!!!! $PG{$pg}{dname}: Down\
-load of $pg binary failed\\n\";\n print \"!!!!!!! \
-$PG{$pg}{dname}: Check Address: $download\\n\";\n \
-return 0;\n }\n print \"\\n------- Install\
-ing $pg\\n\";\n \n if ($name =~/tar\\.gz/)\n\
- {\n `gunzip $name`;\n `tar -xvf $pg.tar`;\n\
- chdir $pg;\n if ( $pg eq \"mafft\")\n {\n i\
-f ($ROOT_INSTALL)\n {\n &root_run (\"You Mu\
-st be Roor to Install MAFFT\\n\", \"$CP mafft/bin/\
-* /usr/local/mafft;mkdir /usr/local/mafft/; $CP ma\
-fft/lib/* /usr/local/bin/\");\n }\n else\
-\n {\n `$CP $TMP/$pg/bin/* $BIN $SILENT`;\n\
- `$CP $TMP/$pg/lib/* $BIN $SILENT`;\n }\n \
- }\n else\n {\n if (-e \"$TMP/$pg/data\"){`$\
-CP $TMP/$pg/data/* $TCM $SILENT`;}\n if (!($pg\
-=~/\\*/)){`rm -rf $pg`;}\n }\n }\n else\\
-n {\n &check_cp (\"$pg\", \"$BIN\");\n `chmod\
- u+x $BIN/$pg`; \n unlink ($pg);\n }\n chd\
-ir $base;\n $PG{$pg}{from_binary}=1;\n retur\
-n &pg_is_installed ($pg, $BIN);\n }\n\nsub add_di\
-r \n {\n my $dir=@_[0];\n \n if (!-e $di\
-r && !-d $dir)\n {\n my @l;\n umask (0000);\n\
- @l=mkpath ($dir,{mode => 0777});\n \n }\n \
- else\n {\n return 0;\n }\n }\nsub chec\
-k_rm \n {\n my ($file)=(@_);\n \n if ( -\
-e $file)\n {\n return unlink($file);\n }\
-\n return 0;\n }\nsub check_cp\n {\n my ($\
-from, $to)=(@_);\n if ( !-e $from && -e \"$from\
-\\.exe\"){$from=\"$from\\.exe\";}\n if ( !-e $f\
-rom){return 0;}\n \n `$CP $from $to`;\n \
- return 1;\n }\n\nsub repo_store \n{\n # chec\
-k that all required data are available\n if( $RE\
-PO_ROOT eq \"\" ) { return; }\n\n\n # extract t\
-he package name from the specified path\n my $p\
-g =`basename $_[0]`;\n chomp($pg);\n \n my $\
-VER = $PG{$pg}{version};\n my $CACHE = \"$REPO_\
-ROOT/$pg/$VER/$OSNAME-$OSARCH\"; \n \n print\
- \"-------- Storing package: \\\"$pg\\\" to path: \
-$CACHE\\n\";\n \n # clean the cache path if \
-exists and create it again\n `rm -rf $CACHE`;\n\
- `mkdir -p $CACHE`;\n \n for my $path (@_) \
-{\n\n # check if it is a single file \n if( \
--f $path ) {\n `cp $path $CACHE`;\n }\n # .\
-. or a directory, in this case copy all the conten\
-t \n elsif( -d $path ) {\n opendir(IMD, $path);\
-\n my @thefiles= readdir(IMD);\n closedir(IMD)\
-;\n \n for my $_file (@thefiles) {\n if( $_\
-file ne \".\" && $_file ne \"..\") {\n `cp \
-$path/$_file $CACHE`;\n }\n }\n } \n } \n\
- \n \n} \n\nsub repo_load \n{\n my ($pg)=(\
-@_);\n\n # check that all required data are ava\
-ilable\n if( $REPO_ROOT eq \"\" ) { return 0; }\
-\n\n my $VER = $PG{$pg}{version};\n my $CACH\
+\nsub install_t_coffee\n {\n my ($pg)=(@_);\n \
+ my ($report,$cflags, $arguments, $language, $co\
+mpiler) ;\n #1-Install T-Coffee\n chdir \"t_\
+coffee_source\";\n &flush_command (\"make clean\
+\");\n print \"\\n------- Compiling T-Coffee\\n\
+\";\n $language=$PG{$pg} {language2};\n $arg\
+uments=$PG{$language}{arguments};\n\n if ( $CC \
+ne \"\"){\n print \"make -i $arguments t_coff\
+ee \\n\";\n &flush_command (\"make -i $argume\
+nts t_coffee\");\n }\n &check_cp ($pg, $BIN)\
+;\n \n chdir $CDIR;\n return &pg_is_insta\
+lled ($pg, $BIN);\n }\nsub install_TMalign\n {\n\
+ my ($pg)=(@_);\n my $report;\n chdir \"t\
+_coffee_source\";\n print \"\\n------- Compilin\
+g TMalign\\n\";\n `rm TMalign TMalign.exe $SILE\
+NT`;\n if ( $FC ne \"\"){&flush_command (\"make\
+ -i $PG{Fortran}{arguments} TMalign\");}\n &che\
+ck_cp ($pg, $BIN);\n repo_store($pg);\n\n if\
+ ( !-e \"$BIN/$pg\" && pg_has_binary_distrib ($pg)\
+)\n {\n print \"!!!!!!! Compilation of $pg im\
+possible. Will try to install from binary\\n\";\n \
+return &install_binary_package ($pg);\n }\n \
+ chdir $CDIR;\n return &pg_is_installed ($pg, \
+$BIN);\n }\n\nsub pg_has_binary_distrib\n {\n \
+ my ($pg)=(@_);\n if ($PG{$pg}{windows}){return\
+ 1;}\n elsif ($PG{$pg}{osx}){return 1;}\n el\
+sif ($PG{$pg}{linux}){return 1;}\n return 0;\n \
+ }\nsub install_binary_package\n {\n my ($pg)=\
+(@_);\n my ($base,$report,$name, $download, $ar\
+guments, $language, $dir);\n my $isdir;\n &i\
+nput_os();\n \n #\n # - paolodt - Check i\
+f the module exists in the repository cache \n \
+#\n if( repo_load($pg) ) {\n $PG{$pg}{from_bin\
+ary}=1;\n return 1;\n }\n # - paolodt - end \n\
+ \n if (!&supported_os($OS)){return 0;}\n \
+ if ( $PG{$pg}{binary}){$name=$PG{$pg}{binary};}\n\
+ else \n {\n $name=$pg;\n if ( $OS eq \"wi\
+ndows\"){$name.=\".exe\";}\n }\n \n $do\
+wnload=\"$WEB_BASE/Packages/Binaries/$OS/$name\";\\
+n \n $base=cwd();\n chdir $TMP;\n \n \
+ if (!-e $name)\n {\n `rm x $SILENT`;\n if (\
+ url2file(\"$download\",\"x\")==$EXIT_SUCCESS)\n \
+ {\n `mv x $name`;\n }\n }\n \n i\
+f (!-e $name)\n {\n print \"!!!!!!! $PG{$pg}{\
+dname}: Download of $pg binary failed\\n\";\n prin\
+t \"!!!!!!! $PG{$pg}{dname}: Check Address: $downl\
+oad\\n\";\n return 0;\n }\n print \"\\n---\
+---- Installing $pg\\n\";\n \n if ($name =~/\
+tar\\.gz/)\n {\n `gunzip $name`;\n `tar -xvf\
+ $pg.tar`;\n chdir $pg;\n if ( $pg eq \"mafft\")\n\
+ {\n if ($ROOT_INSTALL)\n {\n &root_r\
+un (\"You Must be Roor to Install MAFFT\\n\", \"$C\
+P mafft/bin/* /usr/local/mafft;mkdir /usr/local/ma\
+fft/; $CP mafft/lib/* /usr/local/bin/\");\n \
+}\n else\n {\n `$CP $TMP/$pg/bin/* $BIN\
+ $SILENT`;\n `$CP $TMP/$pg/lib/* $BIN $SILENT`;\n\
+ }\n }\n else\n {\n if (-e \"$TMP/$p\
+g/data\"){`$CP $TMP/$pg/data/* $TCM $SILENT`;}\n \
+ if (!($pg=~/\\*/)){`rm -rf $pg`;}\n }\n \
+}\n else\n {\n &check_cp (\"$pg\", \"$BIN\\
+");\n `chmod u+x $BIN/$pg`; \n unlink ($pg);\n \
+ }\n chdir $base;\n $PG{$pg}{from_binary}=1\
+;\n return &pg_is_installed ($pg, $BIN);\n }\n\
+\nsub add_dir \n {\n my $dir=@_[0];\n \n \
+ if (!-e $dir && !-d $dir)\n {\n my @l;\n uma\
+sk (0000);\n @l=mkpath ($dir,{mode => 0777});\n \n\
+ }\n else\n {\n return 0;\n }\n \
+ }\nsub check_rm \n {\n my ($file)=(@_);\n \
+\n if ( -e $file)\n {\n return unlink($fil\
+e);\n }\n return 0;\n }\nsub check_cp\n \
+{\n my ($from, $to)=(@_);\n if ( !-e $from &\
+& -e \"$from\\.exe\"){$from=\"$from\\.exe\";}\n \
+ if ( !-e $from){return 0;}\n \n `$CP $f\
+rom $to`;\n return 1;\n }\n\nsub repo_store \n\
+{\n # check that all required data are available\
+\n if( $REPO_ROOT eq \"\" ) { return; }\n\n\n \
+ # extract the package name from the specified pat\
+h\n my $pg =`basename $_[0]`;\n chomp($pg);\\
+n \n my $VER = $PG{$pg}{version};\n my $CACH\
E = \"$REPO_ROOT/$pg/$VER/$OSNAME-$OSARCH\"; \n \
- if( !-e \"$CACHE/$pg\" ) {\n print \"-------\
-- Module \\\"$pg\\\" NOT found on repository cache\
-.\\n\";\n return 0;\n }\n \n print \"\
--------- Module \\\"$pg\\\" found on repository ca\
-che. Using copy on path: $CACHE\\n\";\n `cp $CA\
-CHE/* $BIN`;\n return 1;\n}\n\nsub check_file_l\
-ist_exists \n {\n my ($base, @flist)=(@_);\n \
- my $f;\n\n foreach $f (@flist)\n {\n if \
-( !-e \"$base/$f\"){return 0;}\n }\n retur\
-n 1;\n }\nsub ls\n {\n my $f=@_[0];\n my @\
-fl;\n chomp(@fl=`ls -1 $f`);\n return @fl;\n\
- }\nsub flush_command\n {\n my $command=@_[0]\
-;\n my $F=new FileHandle;\n open ($F, \"$com\
-mand|\");\n while (<$F>){print \" --- $_\";}\
-\n close ($F);\n } \n\nsub input_installati\
-on_directory\n {\n my $dir=@_[0];\n my $new\
-;\n \n print \"------- The current installat\
-ion directory is: [$dir]\\n\";\n print \"??????\
-? Return to keep the default or new value:\";\n \
-\n if ($NO_QUESTION==0)\n {\n chomp ($new=\
-<stdin>);\n while ( $new ne \"\" && !input_yes (\"\
-You have entered $new. Is this correct? ([y]/n):\"\
-))\n {\n print \"???????New installation dir\
-ectory:\";\n chomp ($new=<stdin>);\n }\n $di\
-r=($new eq \"\")?$dir:$new;\n $dir=~s/\\/$//;\n \
- }\n \n if ( -d $dir){return $dir;}\n e\
-lsif (&root_run (\"You must be root to create $dir\
-\",\"mkdir $dir\")==$EXIT_SUCCESS){return $dir;}\n\
- else\n {\n print \"!!!!!!! $dir could not\
- be created\\n\";\n if ( $NO_QUESTION)\n {\n \
- return \"\";\n }\n elsif ( &input_yes (\"??????\
-? Do you want to provide a new directory([y]/n)?:\\
-"))\n {\n return input_installation_director\
-y ($dir);\n }\n else\n {\n return \"\";\n \
- }\n }\n \n }\nsub input_yes\n {\n m\
-y $question =@_[0];\n my $answer;\n\n if ($N\
-O_QUESTION==1){return 1;}\n \n if ($question\
- eq \"\"){$question=\"??????? Do you wish to proce\
-ed ([y]/n)?:\";}\n print $question;\n chomp(\
-$answer=lc(<STDIN>));\n if (($answer=~/^y/) || \
-$answer eq \"\"){return 1;}\n elsif ( ($answer=\
-~/^n/)){return 0;}\n else\n {\n return inp\
-ut_yes($question);\n }\n }\nsub root_run\n \
-{\n my ($txt, $cmd)=(@_);\n \n if ( syste\
-m ($cmd)==$EXIT_SUCCESS){return $EXIT_SUCCESS;}\n \
- else \n {\n print \"------- $txt\\n\";\n i\
-f ( $ROOT eq \"sudo\"){return system (\"sudo $cmd\\
-");}\n else {return system (\"su root -c \\\"$cmd\\
-\\"\");}\n }\n }\nsub get_root\n {\n if \
-(&pg_is_installed (\"sudo\")){return \"sudo\";}\n \
- else {return \"su\";}\n }\n\nsub get_os\n {\n\
- my $raw_os=`uname`;\n my $os;\n\n $raw_o\
-s=lc ($raw_os);\n \n if ($raw_os =~/cygwin/)\
-{$os=\"windows\";}\n elsif ($raw_os =~/linux/){\
-$os=\"linux\";}\n elsif ($raw_os =~/osx/){$os=\\
-"macosx\";}\n elsif ($raw_os =~/darwin/){$os=\"\
-macosx\";}\n else\n {\n $os=$raw_os;\n \
- }\n return $os;\n }\nsub input_os\n {\n \
-my $answer;\n if ($OS) {return $OS;}\n \n \
- print \"??????? which os do you use: [w]indows, [\
-l]inux, [m]acosx:?\";\n $answer=lc(<STDIN>);\n\\
-n if (($answer=~/^m/)){$OS=\"macosx\";}\n el\
-sif ( ($answer=~/^w/)){$OS=\"windows\";}\n elsi\
-f ( ($answer=~/^linux/)){$OS=\"linux\";}\n \n \
- else\n {\n return &input_os();\n }\n \
- return $OS;\n }\n\nsub supported_os\n {\n m\
-y ($os)=(@_[0]);\n return $SUPPORTED_OS{$os};\n\
- }\n \n \n\n\nsub update_tclinkdb \n {\n \
- my $file =@_[0];\n my $name;\n my $F=new F\
-ileHandle;\n my ($download, $address, $name, $l\
-, $db);\n \n if ( $file eq \"update\"){$file\
-=$TCLINKDB_ADDRESS;}\n \n if ( $file =~/http\
-:\\/\\// || $file =~/ftp:\\/\\//)\n {\n ($add\
-ress, $name)=($download=~/(.*)\\/([^\\/]+)$/);\n `\
-rm x $SILENT`;\n if (&url2file ($file,\"x\")==$EXI\
-T_SUCCESS)\n {\n print \"------- Susscessful\
- upload of $name\";\n `mv x $name`;\n $fil\
-e=$name;\n }\n }\n open ($F, \"$file\");\
-\n while (<$F>)\n {\n my $l=$_;\n if (($l \
-=~/^\\/\\//) || ($db=~/^#/)){;}\n elsif ( !($l =~/\
-\\w/)){;}\n else\n {\n my @v=split (/\\s+/, \
-$l);\n if ( $l=~/^MODE/)\n {\n $MODE{$v\
-[1]}{$v[2]}=$v[3];\n }\n elsif ($l=~/^PG\
-/)\n {\n $PG{$v[1]}{$v[2]}=$v[3];\n }\
-\n }\n }\n close ($F);\n &post_proces\
-s_PG();\n return;\n }\n\n\n\nsub initialize_PG\
-\n {\n\n$PG{\"t_coffee\"}{\"4_TCOFFEE\"}=\"TCOFFE\
-E\";\n$PG{\"t_coffee\"}{\"type\"}=\"sequence_multi\
-ple_aligner\";\n$PG{\"t_coffee\"}{\"ADDRESS\"}=\"h\
-ttp://www.tcoffee.org\";\n$PG{\"t_coffee\"}{\"lang\
-uage\"}=\"C\";\n$PG{\"t_coffee\"}{\"language2\"}=\\
-"C\";\n$PG{\"t_coffee\"}{\"source\"}=\"http://www.\
-tcoffee.org/Packages/T-COFFEE_distribution.tar.gz\\
-";\n$PG{\"t_coffee\"}{\"update_action\"}=\"always\\
-";\n$PG{\"t_coffee\"}{\"mode\"}=\"tcoffee,mcoffee,\
-rcoffee,expresso,3dcoffee\";\n$PG{\"clustalw2\"}{\\
-"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"clustalw2\"}{\\
-"type\"}=\"sequence_multiple_aligner\";\n$PG{\"clu\
-stalw2\"}{\"ADDRESS\"}=\"http://www.clustal.org\";\
-\n$PG{\"clustalw2\"}{\"language\"}=\"C++\";\n$PG{\\
-"clustalw2\"}{\"language2\"}=\"CXX\";\n$PG{\"clust\
-alw2\"}{\"source\"}=\"http://www.clustal.org/downl\
-oad/2.0.10/clustalw-2.0.10-src.tar.gz\";\n$PG{\"cl\
-ustalw2\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\"c\
-lustalw2\"}{\"version\"}=\"2.0.10\";\n$PG{\"clusta\
-lw\"}{\"4_TCOFFEE\"}=\"CLUSTALW\";\n$PG{\"clustalw\
-\"}{\"type\"}=\"sequence_multiple_aligner\";\n$PG{\
-\"clustalw\"}{\"ADDRESS\"}=\"http://www.clustal.or\
-g\";\n$PG{\"clustalw\"}{\"language\"}=\"C\";\n$PG{\
-\"clustalw\"}{\"language2\"}=\"C\";\n$PG{\"clustal\
-w\"}{\"source\"}=\"http://www.clustal.org/download\
-/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1\
-.82.UNIX.tar.gz\";\n$PG{\"clustalw\"}{\"mode\"}=\"\
-mcoffee,rcoffee\";\n$PG{\"clustalw\"}{\"version\"}\
-=\"1.82\";\n$PG{\"dialign-t\"}{\"4_TCOFFEE\"}=\"DI\
-ALIGNT\";\n$PG{\"dialign-t\"}{\"type\"}=\"sequence\
-_multiple_aligner\";\n$PG{\"dialign-t\"}{\"ADDRESS\
-\"}=\"http://dialign-tx.gobics.de/\";\n$PG{\"diali\
-gn-t\"}{\"DIR\"}=\"/usr/share/dialign-tx/\";\n$PG{\
-\"dialign-t\"}{\"language\"}=\"C\";\n$PG{\"dialign\
--t\"}{\"language2\"}=\"C\";\n$PG{\"dialign-t\"}{\"\
-source\"}=\"http://dialign-tx.gobics.de/DIALIGN-TX\
-_1.0.2.tar.gz\";\n$PG{\"dialign-t\"}{\"mode\"}=\"m\
-coffee\";\n$PG{\"dialign-t\"}{\"binary\"}=\"dialig\
-n-t\";\n$PG{\"dialign-t\"}{\"version\"}=\"1.0.2\";\
-\n$PG{\"dialign-tx\"}{\"4_TCOFFEE\"}=\"DIALIGNTX\"\
-;\n$PG{\"dialign-tx\"}{\"type\"}=\"sequence_multip\
-le_aligner\";\n$PG{\"dialign-tx\"}{\"ADDRESS\"}=\"\
-http://dialign-tx.gobics.de/\";\n$PG{\"dialign-tx\\
-"}{\"DIR\"}=\"/usr/share/dialign-tx/\";\n$PG{\"dia\
-lign-tx\"}{\"language\"}=\"C\";\n$PG{\"dialign-tx\\
-"}{\"language2\"}=\"C\";\n$PG{\"dialign-tx\"}{\"so\
-urce\"}=\"http://dialign-tx.gobics.de/DIALIGN-TX_1\
-.0.2.tar.gz\";\n$PG{\"dialign-tx\"}{\"mode\"}=\"mc\
-offee\";\n$PG{\"dialign-tx\"}{\"binary\"}=\"dialig\
-n-tx\";\n$PG{\"dialign-tx\"}{\"version\"}=\"1.0.2\\
-";\n$PG{\"poa\"}{\"4_TCOFFEE\"}=\"POA\";\n$PG{\"po\
-a\"}{\"type\"}=\"sequence_multiple_aligner\";\n$PG\
-{\"poa\"}{\"ADDRESS\"}=\"http://www.bioinformatics\
-.ucla.edu/poa/\";\n$PG{\"poa\"}{\"language\"}=\"C\\
-";\n$PG{\"poa\"}{\"language2\"}=\"C\";\n$PG{\"poa\\
-"}{\"source\"}=\"http://downloads.sourceforge.net/\
-poamsa/poaV2.tar.gz\";\n$PG{\"poa\"}{\"DIR\"}=\"/u\
-sr/share/\";\n$PG{\"poa\"}{\"FILE1\"}=\"blosum80.m\
-at\";\n$PG{\"poa\"}{\"mode\"}=\"mcoffee\";\n$PG{\"\
-poa\"}{\"binary\"}=\"poa\";\n$PG{\"poa\"}{\"versio\
-n\"}=\"2.0\";\n$PG{\"probcons\"}{\"4_TCOFFEE\"}=\"\
-PROBCONS\";\n$PG{\"probcons\"}{\"type\"}=\"sequenc\
-e_multiple_aligner\";\n$PG{\"probcons\"}{\"ADDRESS\
-\"}=\"http://probcons.stanford.edu/\";\n$PG{\"prob\
-cons\"}{\"language2\"}=\"CXX\";\n$PG{\"probcons\"}\
-{\"language\"}=\"C++\";\n$PG{\"probcons\"}{\"sourc\
-e\"}=\"http://probcons.stanford.edu/probcons_v1_12\
-.tar.gz\";\n$PG{\"probcons\"}{\"mode\"}=\"mcoffee\\
-";\n$PG{\"probcons\"}{\"binary\"}=\"probcons\";\n$\
-PG{\"probcons\"}{\"version\"}=\"1.12\";\n$PG{\"maf\
-ft\"}{\"4_TCOFFEE\"}=\"MAFFT\";\n$PG{\"mafft\"}{\"\
-type\"}=\"sequence_multiple_aligner\";\n$PG{\"maff\
-t\"}{\"ADDRESS\"}=\"http://align.bmr.kyushu-u.ac.j\
-p/mafft/online/server/\";\n$PG{\"mafft\"}{\"langua\
-ge\"}=\"C\";\n$PG{\"mafft\"}{\"language\"}=\"C\";\\
-n$PG{\"mafft\"}{\"source\"}=\"http://align.bmr.kyu\
-shu-u.ac.jp/mafft/software/mafft-6.603-with-extens\
-ions-src.tgz\";\n$PG{\"mafft\"}{\"windows\"}=\"htt\
-p://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-\
-6.603-mingw.tar\";\n$PG{\"mafft\"}{\"mode\"}=\"mco\
-ffee,rcoffee\";\n$PG{\"mafft\"}{\"binary\"}=\"maff\
-t.tar.gz\";\n$PG{\"mafft\"}{\"version\"}=\"6.603\"\
-;\n$PG{\"muscle\"}{\"4_TCOFFEE\"}=\"MUSCLE\";\n$PG\
-{\"muscle\"}{\"type\"}=\"sequence_multiple_aligner\
-\";\n$PG{\"muscle\"}{\"ADDRESS\"}=\"http://www.dri\
-ve5.com/muscle/\";\n$PG{\"muscle\"}{\"language\"}=\
-\"C++\";\n$PG{\"muscle\"}{\"language2\"}=\"GPP\";\\
-n$PG{\"muscle\"}{\"source\"}=\"http://www.drive5.c\
-om/muscle/downloads3.7/muscle3.7_src.tar.gz\";\n$P\
-G{\"muscle\"}{\"windows\"}=\"http://www.drive5.com\
-/muscle/downloads3.7/muscle3.7_win32.zip\";\n$PG{\\
-"muscle\"}{\"linux\"}=\"http://www.drive5.com/musc\
-le/downloads3.7/muscle3.7_linux_ia32.tar.gz\";\n$P\
-G{\"muscle\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\
-\"muscle\"}{\"version\"}=\"3.7\";\n$PG{\"mus4\"}{\\
-"4_TCOFFEE\"}=\"MUS4\";\n$PG{\"mus4\"}{\"type\"}=\\
-"sequence_multiple_aligner\";\n$PG{\"mus4\"}{\"ADD\
-RESS\"}=\"http://www.drive5.com/muscle/\";\n$PG{\"\
-mus4\"}{\"language\"}=\"C++\";\n$PG{\"mus4\"}{\"la\
-nguage2\"}=\"GPP\";\n$PG{\"mus4\"}{\"source\"}=\"h\
-ttp://www.drive5.com/muscle/muscle4.0_src.tar.gz\"\
-;\n$PG{\"mus4\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$\
-PG{\"mus4\"}{\"version\"}=\"4.0\";\n$PG{\"pcma\"}{\
-\"4_TCOFFEE\"}=\"PCMA\";\n$PG{\"pcma\"}{\"type\"}=\
-\"sequence_multiple_aligner\";\n$PG{\"pcma\"}{\"AD\
-DRESS\"}=\"ftp://iole.swmed.edu/pub/PCMA/\";\n$PG{\
-\"pcma\"}{\"language\"}=\"C\";\n$PG{\"pcma\"}{\"la\
-nguage2\"}=\"C\";\n$PG{\"pcma\"}{\"source\"}=\"ftp\
-://iole.swmed.edu/pub/PCMA/pcma.tar.gz\";\n$PG{\"p\
-cma\"}{\"mode\"}=\"mcoffee\";\n$PG{\"pcma\"}{\"ver\
-sion\"}=\"1.0\";\n$PG{\"kalign\"}{\"4_TCOFFEE\"}=\\
-"KALIGN\";\n$PG{\"kalign\"}{\"type\"}=\"sequence_m\
-ultiple_aligner\";\n$PG{\"kalign\"}{\"ADDRESS\"}=\\
-"http://msa.cgb.ki.se\";\n$PG{\"kalign\"}{\"langua\
-ge\"}=\"C\";\n$PG{\"kalign\"}{\"language2\"}=\"C\"\
-;\n$PG{\"kalign\"}{\"source\"}=\"http://msa.cgb.ki\
-.se/downloads/kalign/current.tar.gz\";\n$PG{\"kali\
-gn\"}{\"mode\"}=\"mcoffee\";\n$PG{\"kalign\"}{\"ve\
-rsion\"}=\"1.0\";\n$PG{\"amap\"}{\"4_TCOFFEE\"}=\"\
-AMAP\";\n$PG{\"amap\"}{\"type\"}=\"sequence_multip\
-le_aligner\";\n$PG{\"amap\"}{\"ADDRESS\"}=\"http:/\
-/bio.math.berkeley.edu/amap/\";\n$PG{\"amap\"}{\"l\
-anguage\"}=\"C++\";\n$PG{\"amap\"}{\"language2\"}=\
-\"CXX\";\n$PG{\"amap\"}{\"source\"}=\"http://amap-\
-align.googlecode.com/files/amap.2.0.tar.gz\";\n$PG\
-{\"amap\"}{\"mode\"}=\"mcoffee\";\n$PG{\"amap\"}{\\
-"version\"}=\"2.0\";\n$PG{\"proda\"}{\"4_TCOFFEE\"\
-}=\"PRODA\";\n$PG{\"proda\"}{\"type\"}=\"sequence_\
-multiple_aligner\";\n$PG{\"proda\"}{\"ADDRESS\"}=\\
-"http://proda.stanford.edu\";\n$PG{\"proda\"}{\"la\
-nguage\"}=\"C++\";\n$PG{\"proda\"}{\"language2\"}=\
-\"CXX\";\n$PG{\"proda\"}{\"source\"}=\"http://prod\
-a.stanford.edu/proda_1_0.tar.gz\";\n$PG{\"proda\"}\
-{\"mode\"}=\"mcoffee\";\n$PG{\"proda\"}{\"version\\
-"}=\"1.0\";\n$PG{\"fsa\"}{\"4_TCOFFEE\"}=\"FSA\";\\
-n$PG{\"fsa\"}{\"type\"}=\"sequence_multiple_aligne\
-r\";\n$PG{\"fsa\"}{\"ADDRESS\"}=\"http://fsa.sourc\
-eforge.net/\";\n$PG{\"fsa\"}{\"language\"}=\"C++\"\
-;\n$PG{\"fsa\"}{\"language2\"}=\"CXX\";\n$PG{\"fsa\
-\"}{\"source\"}=\"http://sourceforge.net/projects/\
-fsa/files/fsa-1.15.3.tar.gz/download/\";\n$PG{\"fs\
-a\"}{\"mode\"}=\"mcoffee\";\n$PG{\"fsa\"}{\"versio\
-n\"}=\"1.15.3\";\n$PG{\"prank\"}{\"4_TCOFFEE\"}=\"\
-PRANK\";\n$PG{\"prank\"}{\"type\"}=\"sequence_mult\
-iple_aligner\";\n$PG{\"prank\"}{\"ADDRESS\"}=\"htt\
-p://www.ebi.ac.uk/goldman-srv/prank/\";\n$PG{\"pra\
-nk\"}{\"language\"}=\"C++\";\n$PG{\"prank\"}{\"lan\
-guage2\"}=\"CXX\";\n$PG{\"prank\"}{\"source\"}=\"h\
-ttp://www.ebi.ac.uk/goldman-srv/prank/src/prank/pr\
-ank.src.100303.tgz\";\n$PG{\"prank\"}{\"mode\"}=\"\
-mcoffee\";\n$PG{\"prank\"}{\"version\"}=\"100303\"\
-;\n$PG{\"sap\"}{\"4_TCOFFEE\"}=\"SAP\";\n$PG{\"sap\
-\"}{\"type\"}=\"structure_pairwise_aligner\";\n$PG\
-{\"sap\"}{\"ADDRESS\"}=\"http://mathbio.nimr.mrc.a\
-c.uk/wiki/Software\";\n$PG{\"sap\"}{\"language\"}=\
-\"C\";\n$PG{\"sap\"}{\"language2\"}=\"C\";\n$PG{\"\
-sap\"}{\"source\"}=\"http://mathbio.nimr.mrc.ac.uk\
-/download/sap-1.1.1.tar.gz\";\n$PG{\"sap\"}{\"mode\
-\"}=\"expresso,3dcoffee\";\n$PG{\"sap\"}{\"version\
-\"}=\"1.1.1\";\n$PG{\"TMalign\"}{\"4_TCOFFEE\"}=\"\
-TMALIGN\";\n$PG{\"TMalign\"}{\"type\"}=\"structure\
-_pairwise_aligner\";\n$PG{\"TMalign\"}{\"ADDRESS\"\
-}=\"http://zhang.bioinformatics.ku.edu/TM-align/TM\
-align.f\";\n$PG{\"TMalign\"}{\"language\"}=\"Fortr\
-an\";\n$PG{\"TMalign\"}{\"language2\"}=\"Fortran\"\
-;\n$PG{\"TMalign\"}{\"source\"}=\"http://zhang.bio\
-informatics.ku.edu/TM-align/TMalign.f\";\n$PG{\"TM\
-align\"}{\"linux\"}=\"http://zhang.bioinformatics.\
-ku.edu/TM-align/TMalign_32.gz\";\n$PG{\"TMalign\"}\
-{\"mode\"}=\"expresso,3dcoffee\";\n$PG{\"TMalign\"\
-}{\"version\"}=\"1.0\";\n$PG{\"mustang\"}{\"4_TCOF\
-FEE\"}=\"MUSTANG\";\n$PG{\"mustang\"}{\"type\"}=\"\
-structure_pairwise_aligner\";\n$PG{\"mustang\"}{\"\
-ADDRESS\"}=\"http://www.cs.mu.oz.au/~arun/mustang\\
-";\n$PG{\"mustang\"}{\"language\"}=\"C++\";\n$PG{\\
-"mustang\"}{\"language2\"}=\"CXX\";\n$PG{\"mustang\
-\"}{\"source\"}=\"http://ww2.cs.mu.oz.au/~arun/mus\
-tang/mustang_v3.2.1.tgz\";\n$PG{\"mustang\"}{\"mod\
-e\"}=\"expresso,3dcoffee\";\n$PG{\"mustang\"}{\"ve\
-rsion\"}=\"3.2.1\";\n$PG{\"lsqman\"}{\"4_TCOFFEE\"\
-}=\"LSQMAN\";\n$PG{\"lsqman\"}{\"type\"}=\"structu\
-re_pairwise_aligner\";\n$PG{\"lsqman\"}{\"ADDRESS\\
-"}=\"empty\";\n$PG{\"lsqman\"}{\"language\"}=\"emp\
-ty\";\n$PG{\"lsqman\"}{\"language2\"}=\"empty\";\n\
-$PG{\"lsqman\"}{\"source\"}=\"empty\";\n$PG{\"lsqm\
-an\"}{\"update_action\"}=\"never\";\n$PG{\"lsqman\\
-"}{\"mode\"}=\"expresso,3dcoffee\";\n$PG{\"align_p\
-db\"}{\"4_TCOFFEE\"}=\"ALIGN_PDB\";\n$PG{\"align_p\
-db\"}{\"type\"}=\"structure_pairwise_aligner\";\n$\
-PG{\"align_pdb\"}{\"ADDRESS\"}=\"empty\";\n$PG{\"a\
-lign_pdb\"}{\"language\"}=\"empty\";\n$PG{\"align_\
-pdb\"}{\"language2\"}=\"empty\";\n$PG{\"align_pdb\\
-"}{\"source\"}=\"empty\";\n$PG{\"align_pdb\"}{\"up\
-date_action\"}=\"never\";\n$PG{\"align_pdb\"}{\"mo\
-de\"}=\"expresso,3dcoffee\";\n$PG{\"fugueali\"}{\"\
-4_TCOFFEE\"}=\"FUGUE\";\n$PG{\"fugueali\"}{\"type\\
-"}=\"structure_pairwise_aligner\";\n$PG{\"fugueali\
-\"}{\"ADDRESS\"}=\"http://www-cryst.bioc.cam.ac.uk\
-/fugue/download.html\";\n$PG{\"fugueali\"}{\"langu\
-age\"}=\"empty\";\n$PG{\"fugueali\"}{\"language2\"\
-}=\"empty\";\n$PG{\"fugueali\"}{\"source\"}=\"empt\
-y\";\n$PG{\"fugueali\"}{\"update_action\"}=\"never\
-\";\n$PG{\"fugueali\"}{\"mode\"}=\"expresso,3dcoff\
-ee\";\n$PG{\"dalilite.pl\"}{\"4_TCOFFEE\"}=\"DALIL\
-ITEc\";\n$PG{\"dalilite.pl\"}{\"type\"}=\"structur\
-e_pairwise_aligner\";\n$PG{\"dalilite.pl\"}{\"ADDR\
-ESS\"}=\"built_in\";\n$PG{\"dalilite.pl\"}{\"ADDRE\
-SS2\"}=\"http://www.ebi.ac.uk/Tools/webservices/se\
-rvices/dalilite\";\n$PG{\"dalilite.pl\"}{\"languag\
-e\"}=\"Perl\";\n$PG{\"dalilite.pl\"}{\"language2\"\
-}=\"Perl\";\n$PG{\"dalilite.pl\"}{\"source\"}=\"em\
-pty\";\n$PG{\"dalilite.pl\"}{\"update_action\"}=\"\
-never\";\n$PG{\"dalilite.pl\"}{\"mode\"}=\"express\
-o,3dcoffee\";\n$PG{\"probconsRNA\"}{\"4_TCOFFEE\"}\
-=\"PROBCONSRNA\";\n$PG{\"probconsRNA\"}{\"type\"}=\
-\"RNA_multiple_aligner\";\n$PG{\"probconsRNA\"}{\"\
-ADDRESS\"}=\"http://probcons.stanford.edu/\";\n$PG\
-{\"probconsRNA\"}{\"language\"}=\"C++\";\n$PG{\"pr\
-obconsRNA\"}{\"language2\"}=\"CXX\";\n$PG{\"probco\
-nsRNA\"}{\"source\"}=\"http://probcons.stanford.ed\
-u/probconsRNA.tar.gz\";\n$PG{\"probconsRNA\"}{\"mo\
-de\"}=\"mcoffee,rcoffee\";\n$PG{\"probconsRNA\"}{\\
-"version\"}=\"1.0\";\n$PG{\"sfold\"}{\"4_TCOFFEE\"\
-}=\"CONSAN\";\n$PG{\"sfold\"}{\"type\"}=\"RNA_pair\
-wise_aligner\";\n$PG{\"sfold\"}{\"ADDRESS\"}=\"htt\
-p://selab.janelia.org/software/consan/\";\n$PG{\"s\
-fold\"}{\"language\"}=\"empty\";\n$PG{\"sfold\"}{\\
-"language2\"}=\"empty\";\n$PG{\"sfold\"}{\"source\\
-"}=\"empty\";\n$PG{\"sfold\"}{\"update_action\"}=\\
-"never\";\n$PG{\"sfold\"}{\"mode\"}=\"rcoffee\";\n\
-$PG{\"RNAplfold\"}{\"4_TCOFFEE\"}=\"RNAPLFOLD\";\n\
-$PG{\"RNAplfold\"}{\"type\"}=\"RNA_secondarystruct\
-ure_predictor\";\n$PG{\"RNAplfold\"}{\"ADDRESS\"}=\
-\"http://www.tbi.univie.ac.at/~ivo/RNA/\";\n$PG{\"\
-RNAplfold\"}{\"language\"}=\"C\";\n$PG{\"RNAplfold\
-\"}{\"language2\"}=\"C\";\n$PG{\"RNAplfold\"}{\"so\
-urce\"}=\"http://www.tbi.univie.ac.at/~ivo/RNA/Vie\
-nnaRNA-1.7.2.tar.gz\";\n$PG{\"RNAplfold\"}{\"mode\\
-"}=\"rcoffee,\";\n$PG{\"RNAplfold\"}{\"version\"}=\
-\"1.7.2\";\n$PG{\"retree\"}{\"4_TCOFFEE\"}=\"PHYLI\
-P\";\n$PG{\"retree\"}{\"type\"}=\"RNA_secondarystr\
-ucture_predictor\";\n$PG{\"retree\"}{\"ADDRESS\"}=\
-\"http://evolution.gs.washington.edu/phylip/\";\n$\
-PG{\"retree\"}{\"language\"}=\"C\";\n$PG{\"retree\\
-"}{\"language2\"}=\"C\";\n$PG{\"retree\"}{\"source\
-\"}=\"http://evolution.gs.washington.edu/phylip/do\
-wnload/phylip-3.69.tar.gz\";\n$PG{\"retree\"}{\"mo\
-de\"}=\"trmsd,\";\n$PG{\"retree\"}{\"version\"}=\"\
-3.69\";\n$PG{\"hmmtop\"}{\"4_TCOFFEE\"}=\"HMMTOP\"\
-;\n$PG{\"hmmtop\"}{\"type\"}=\"protein_secondaryst\
-ructure_predictor\";\n$PG{\"hmmtop\"}{\"ADDRESS\"}\
-=\"www.enzim.hu/hmmtop/\";\n$PG{\"hmmtop\"}{\"lang\
-uage\"}=\"C\";\n$PG{\"hmmtop\"}{\"language2\"}=\"C\
-\";\n$PG{\"hmmtop\"}{\"source\"}=\"empty\";\n$PG{\\
-"hmmtop\"}{\"update_action\"}=\"never\";\n$PG{\"hm\
-mtop\"}{\"mode\"}=\"tcoffee\";\n$PG{\"gorIV\"}{\"4\
-_TCOFFEE\"}=\"GOR4\";\n$PG{\"gorIV\"}{\"type\"}=\"\
-protein_secondarystructure_predictor\";\n$PG{\"gor\
-IV\"}{\"ADDRESS\"}=\"http://mig.jouy.inra.fr/logic\
-iels/gorIV/\";\n$PG{\"gorIV\"}{\"language\"}=\"C\"\
-;\n$PG{\"gorIV\"}{\"language2\"}=\"C\";\n$PG{\"gor\
-IV\"}{\"source\"}=\"http://mig.jouy.inra.fr/logici\
-els/gorIV/GOR_IV.tar.gz\";\n$PG{\"gorIV\"}{\"updat\
-e_action\"}=\"never\";\n$PG{\"gorIV\"}{\"mode\"}=\\
-"tcoffee\";\n$PG{\"wublast.pl\"}{\"4_TCOFFEE\"}=\"\
-EBIWUBLASTc\";\n$PG{\"wublast.pl\"}{\"type\"}=\"pr\
-otein_homology_predictor\";\n$PG{\"wublast.pl\"}{\\
-"ADDRESS\"}=\"built_in\";\n$PG{\"wublast.pl\"}{\"A\
-DDRESS2\"}=\"http://www.ebi.ac.uk/Tools/webservice\
-s/services/wublast\";\n$PG{\"wublast.pl\"}{\"langu\
-age\"}=\"Perl\";\n$PG{\"wublast.pl\"}{\"language2\\
-"}=\"Perl\";\n$PG{\"wublast.pl\"}{\"source\"}=\"em\
-pty\";\n$PG{\"wublast.pl\"}{\"update_action\"}=\"n\
-ever\";\n$PG{\"wublast.pl\"}{\"mode\"}=\"psicoffee\
-,expresso,accurate\";\n$PG{\"blastpgp.pl\"}{\"4_TC\
-OFFEE\"}=\"EBIBLASTPGPc\";\n$PG{\"blastpgp.pl\"}{\\
-"type\"}=\"protein_homology_predictor\";\n$PG{\"bl\
-astpgp.pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\"bla\
-stpgp.pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.uk/T\
-ools/webservices/services/blastpgp\";\n$PG{\"blast\
-pgp.pl\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp.\
-pl\"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\\
-"}{\"source\"}=\"empty\";\n$PG{\"blastpgp.pl\"}{\"\
-update_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\
-\"mode\"}=\"psicoffee,expresso,accurate\";\n$PG{\"\
-blastcl3\"}{\"4_TCOFFEE\"}=\"NCBIWEBBLAST\";\n$PG{\
-\"blastcl3\"}{\"type\"}=\"protein_homology_predict\
-or\";\n$PG{\"blastcl3\"}{\"ADDRESS\"}=\"ftp://ftp.\
-ncbi.nih.gov/blast/executables/LATEST\";\n$PG{\"bl\
-astcl3\"}{\"language\"}=\"C\";\n$PG{\"blastcl3\"}{\
-\"language2\"}=\"C\";\n$PG{\"blastcl3\"}{\"source\\
-"}=\"empty\";\n$PG{\"blastcl3\"}{\"update_action\"\
-}=\"never\";\n$PG{\"blastcl3\"}{\"mode\"}=\"psicof\
-fee,expresso,3dcoffee\";\n$PG{\"blastpgp\"}{\"4_TC\
-OFFEE\"}=\"NCBIBLAST\";\n$PG{\"blastpgp\"}{\"type\\
+ \n print \"-------- Storing package: \\\"$pg\\\
+\" to path: $CACHE\\n\";\n \n # clean the ca\
+che path if exists and create it again\n `rm -r\
+f $CACHE`;\n `mkdir -p $CACHE`;\n \n for my\
+ $path (@_) {\n\n # check if it is a single fi\
+le \n if( -f $path ) {\n `cp $path $CACHE`;\
+\n }\n # .. or a directory, in this case copy al\
+l the content \n elsif( -d $path ) {\n opendir(\
+IMD, $path);\n my @thefiles= readdir(IMD);\n c\
+losedir(IMD);\n \n for my $_file (@thefiles) {\
+\n if( $_file ne \".\" && $_file ne \"..\") {\n\
+ `cp $path/$_file $CACHE`;\n }\n }\n \
+} \n } \n \n \n} \n\nsub repo_load \n{\n \
+ my ($pg)=(@_);\n\n # check that all required \
+data are available\n if( $REPO_ROOT eq \"\" ) {\
+ return 0; }\n\n my $VER = $PG{$pg}{version};\n\
+ my $CACHE = \"$REPO_ROOT/$pg/$VER/$OSNAME-$OSA\
+RCH\"; \n if( !-e \"$CACHE/$pg\" ) {\n pri\
+nt \"-------- Module \\\"$pg\\\" NOT found on repo\
+sitory cache.\\n\";\n return 0;\n }\n \n\
+ print \"-------- Module \\\"$pg\\\" found on r\
+epository cache. Using copy on path: $CACHE\\n\";\\
+n `cp $CACHE/* $BIN`;\n return 1;\n}\n\nsub \
+check_file_list_exists \n {\n my ($base, @flis\
+t)=(@_);\n my $f;\n\n foreach $f (@flist)\n \
+ {\n if ( !-e \"$base/$f\"){return 0;}\n \
+}\n return 1;\n }\nsub ls\n {\n my $f=@_[0\
+];\n my @fl;\n chomp(@fl=`ls -1 $f`);\n r\
+eturn @fl;\n }\nsub flush_command\n {\n my $c\
+ommand=@_[0];\n my $F=new FileHandle;\n open\
+ ($F, \"$command|\");\n while (<$F>){print \" \
+ --- $_\";}\n close ($F);\n } \n\nsub inpu\
+t_installation_directory\n {\n my $dir=@_[0];\\
+n my $new;\n \n print \"------- The curre\
+nt installation directory is: [$dir]\\n\";\n pr\
+int \"??????? Return to keep the default or new va\
+lue:\";\n \n if ($NO_QUESTION==0)\n {\n \
+chomp ($new=<stdin>);\n while ( $new ne \"\" && !i\
+nput_yes (\"You have entered $new. Is this correct\
+? ([y]/n):\"))\n {\n print \"???????New inst\
+allation directory:\";\n chomp ($new=<stdin>);\
+\n }\n $dir=($new eq \"\")?$dir:$new;\n $dir=~s/\
+\\/$//;\n }\n \n if ( -d $dir){return $\
+dir;}\n elsif (&root_run (\"You must be root to\
+ create $dir\",\"mkdir $dir\")==$EXIT_SUCCESS){ret\
+urn $dir;}\n else\n {\n print \"!!!!!!! $d\
+ir could not be created\\n\";\n if ( $NO_QUESTION)\
+\n {\n return \"\";\n }\n elsif ( &input_y\
+es (\"??????? Do you want to provide a new directo\
+ry([y]/n)?:\"))\n {\n return input_installat\
+ion_directory ($dir);\n }\n else\n {\n ret\
+urn \"\";\n }\n }\n \n }\nsub input_yes\
+\n {\n my $question =@_[0];\n my $answer;\n\
+\n if ($NO_QUESTION==1){return 1;}\n \n i\
+f ($question eq \"\"){$question=\"??????? Do you w\
+ish to proceed ([y]/n)?:\";}\n print $question;\
+\n chomp($answer=lc(<STDIN>));\n if (($answe\
+r=~/^y/) || $answer eq \"\"){return 1;}\n elsif\
+ ( ($answer=~/^n/)){return 0;}\n else\n {\\
+n return input_yes($question);\n }\n }\nsub \
+root_run\n {\n my ($txt, $cmd)=(@_);\n \n \
+ if ( system ($cmd)==$EXIT_SUCCESS){return $EXIT_\
+SUCCESS;}\n else \n {\n print \"------- $t\
+xt\\n\";\n if ( $ROOT eq \"sudo\"){return system (\
+\"sudo $cmd\");}\n else {return system (\"su root \
+-c \\\"$cmd\\\"\");}\n }\n }\nsub get_root\n\
+ {\n if (&pg_is_installed (\"sudo\")){return \\
+"sudo\";}\n else {return \"su\";}\n }\n\nsub g\
+et_os\n {\n my $raw_os=`uname`;\n my $os;\n\
+\n $raw_os=lc ($raw_os);\n \n if ($raw_os\
+ =~/cygwin/){$os=\"windows\";}\n elsif ($raw_os\
+ =~/linux/){$os=\"linux\";}\n elsif ($raw_os =~\
+/osx/){$os=\"macosx\";}\n elsif ($raw_os =~/dar\
+win/){$os=\"macosx\";}\n else\n {\n $os=$r\
+aw_os;\n }\n return $os;\n }\nsub input_o\
+s\n {\n my $answer;\n if ($OS) {return $OS;\
+}\n \n print \"??????? which os do you use: \
+[w]indows, [l]inux, [m]acosx:?\";\n $answer=lc(\
+<STDIN>);\n\n if (($answer=~/^m/)){$OS=\"macosx\
+\";}\n elsif ( ($answer=~/^w/)){$OS=\"windows\"\
+;}\n elsif ( ($answer=~/^linux/)){$OS=\"linux\"\
+;}\n \n else\n {\n return &input_os();\\
+n }\n return $OS;\n }\n\nsub supported_os\
+\n {\n my ($os)=(@_[0]);\n return $SUPPORTE\
+D_OS{$os};\n }\n \n \n\n\nsub update_tclink\
+db \n {\n my $file =@_[0];\n my $name;\n \
+ my $F=new FileHandle;\n my ($download, $addres\
+s, $name, $l, $db);\n \n if ( $file eq \"upd\
+ate\"){$file=$TCLINKDB_ADDRESS;}\n \n if ( $\
+file =~/http:\\/\\// || $file =~/ftp:\\/\\//)\n \
+ {\n ($address, $name)=($download=~/(.*)\\/([^\\\
+/]+)$/);\n `rm x $SILENT`;\n if (&url2file ($file,\
+\"x\")==$EXIT_SUCCESS)\n {\n print \"-------\
+ Susscessful upload of $name\";\n `mv x $name`\
+;\n $file=$name;\n }\n }\n open ($F,\
+ \"$file\");\n while (<$F>)\n {\n my $l=$_\
+;\n if (($l =~/^\\/\\//) || ($db=~/^#/)){;}\n elsi\
+f ( !($l =~/\\w/)){;}\n else\n {\n my @v=spl\
+it (/\\s+/, $l);\n if ( $l=~/^MODE/)\n {\
+\n $MODE{$v[1]}{$v[2]}=$v[3];\n }\n els\
+if ($l=~/^PG/)\n {\n $PG{$v[1]}{$v[2]}=$v[3\
+];\n }\n }\n }\n close ($F);\n \
+&post_process_PG();\n return;\n }\n\n\n\nsub i\
+nitialize_PG\n {\n\n$PG{\"t_coffee\"}{\"4_TCOFFEE\
+\"}=\"TCOFFEE\";\n$PG{\"t_coffee\"}{\"type\"}=\"se\
+quence_multiple_aligner\";\n$PG{\"t_coffee\"}{\"AD\
+DRESS\"}=\"http://www.tcoffee.org\";\n$PG{\"t_coff\
+ee\"}{\"language\"}=\"C++\";\n$PG{\"t_coffee\"}{\"\
+language2\"}=\"CXX\";\n$PG{\"t_coffee\"}{\"source\\
+"}=\"http://www.tcoffee.org/Packages/T-COFFEE_dist\
+ribution.tar.gz\";\n$PG{\"t_coffee\"}{\"update_act\
+ion\"}=\"always\";\n$PG{\"t_coffee\"}{\"mode\"}=\"\
+tcoffee,mcoffee,rcoffee,expresso,3dcoffee\";\n$PG{\
+\"clustalo\"}{\"4_TCOFFEE\"}=\"CLUSTALO\";\n$PG{\"\
+clustalo\"}{\"type\"}=\"sequence_multiple_aligner\\
+";\n$PG{\"clustalo\"}{\"ADDRESS\"}=\"http://www.cl\
+ustal.org/omega/\";\n$PG{\"clustalo\"}{\"language\\
+"}=\"C++\";\n$PG{\"clustalo\"}{\"language2\"}=\"C+\
++\";\n$PG{\"clustalo\"}{\"source\"}=\"http://www.c\
+lustal.org/omega/clustal-omega-1.1.0.tar.gz\";\n$P\
+G{\"clustalo\"}{\"mode\"}=\"mcoffee\";\n$PG{\"clus\
+talo\"}{\"version\"}=\"1.1.0\";\n$PG{\"strike\"}{\\
+"4_TCOFFEE\"}=\"STRIKE\";\n$PG{\"strike\"}{\"type\\
+"}=\"sequence_alignment_scoring\";\n$PG{\"strike\"\
+}{\"ADDRESS\"}=\"http://www.tcoffee.org/Projects/s\
+trike/index.html\";\n$PG{\"strike\"}{\"language\"}\
+=\"C++\";\n$PG{\"strike\"}{\"language2\"}=\"CXX\";\
+\n$PG{\"strike\"}{\"source\"}=\"http://www.tcoffee\
+.org/Projects/strike/strike_v1.2.tar.bz2\";\n$PG{\\
+"strike\"}{\"mode\"}=\"tcoffee,expresso\";\n$PG{\"\
+strike\"}{\"version\"}=\"1.2\";\n$PG{\"clustalw2\"\
+}{\"4_TCOFFEE\"}=\"CLUSTALW2\";\n$PG{\"clustalw2\"\
+}{\"type\"}=\"sequence_multiple_aligner\";\n$PG{\"\
+clustalw2\"}{\"ADDRESS\"}=\"http://www.clustal.org\
+\";\n$PG{\"clustalw2\"}{\"language\"}=\"C++\";\n$P\
+G{\"clustalw2\"}{\"language2\"}=\"CXX\";\n$PG{\"cl\
+ustalw2\"}{\"source\"}=\"http://www.clustal.org/do\
+wnload/2.0.10/clustalw-2.0.10-src.tar.gz\";\n$PG{\\
+"clustalw2\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\
+\"clustalw2\"}{\"version\"}=\"2.0.10\";\n$PG{\"clu\
+stalw\"}{\"4_TCOFFEE\"}=\"CLUSTALW\";\n$PG{\"clust\
+alw\"}{\"type\"}=\"sequence_multiple_aligner\";\n$\
+PG{\"clustalw\"}{\"ADDRESS\"}=\"http://www.clustal\
+.org\";\n$PG{\"clustalw\"}{\"language\"}=\"C\";\n$\
+PG{\"clustalw\"}{\"language2\"}=\"C\";\n$PG{\"clus\
+talw\"}{\"source\"}=\"http://www.clustal.org/downl\
+oad/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clusta\
+lw1.82.UNIX.tar.gz\";\n$PG{\"clustalw\"}{\"mode\"}\
+=\"mcoffee,rcoffee\";\n$PG{\"clustalw\"}{\"version\
+\"}=\"1.82\";\n$PG{\"dialign-t\"}{\"4_TCOFFEE\"}=\\
+"DIALIGNT\";\n$PG{\"dialign-t\"}{\"type\"}=\"seque\
+nce_multiple_aligner\";\n$PG{\"dialign-t\"}{\"ADDR\
+ESS\"}=\"http://dialign-tx.gobics.de/\";\n$PG{\"di\
+align-t\"}{\"DIR\"}=\"/usr/share/dialign-tx/\";\n$\
+PG{\"dialign-t\"}{\"language\"}=\"C\";\n$PG{\"dial\
+ign-t\"}{\"language2\"}=\"C\";\n$PG{\"dialign-t\"}\
+{\"source\"}=\"http://dialign-tx.gobics.de/DIALIGN\
+-TX_1.0.2.tar.gz\";\n$PG{\"dialign-t\"}{\"mode\"}=\
+\"mcoffee\";\n$PG{\"dialign-t\"}{\"binary\"}=\"dia\
+lign-t\";\n$PG{\"dialign-t\"}{\"version\"}=\"1.0.2\
+\";\n$PG{\"dialign-tx\"}{\"4_TCOFFEE\"}=\"DIALIGNT\
+X\";\n$PG{\"dialign-tx\"}{\"type\"}=\"sequence_mul\
+tiple_aligner\";\n$PG{\"dialign-tx\"}{\"ADDRESS\"}\
+=\"http://dialign-tx.gobics.de/\";\n$PG{\"dialign-\
+tx\"}{\"DIR\"}=\"/usr/share/dialign-tx/\";\n$PG{\"\
+dialign-tx\"}{\"language\"}=\"C\";\n$PG{\"dialign-\
+tx\"}{\"language2\"}=\"C\";\n$PG{\"dialign-tx\"}{\\
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-o}{description}=\" for very accurate structure bas\
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-ee\"}{description}=\" for multiple structure align\
-ments\";\n$MODE{mcoffee} {description}=\" for comb\
-ining alternative multiple sequence alignment pack\
-ages\\n------- into a unique meta-package. The ins\
-taller will upload several MSA packages and compil\
-e them\\n\n\";\n\n\n&post_process_PG();\nreturn;\n\
-}\n\nsub post_process_PG\n {\n my $p;\n \n \
- %PG=&name2dname (%PG);\n %MODE=&name2dname(%\
-MODE);\n foreach $p (keys(%PG)){if ( $PG{$p}{ty\
-pe} eq \"compiler\"){$PG{$p}{update_action}=\"neve\
-r\";}}\n \n }\n\nsub name2dname\n {\n my (\
-%L)=(@_);\n my ($l, $ml);\n \n foreach my\
- $pg (keys(%L))\n {\n $l=length ($pg);\n if (\
- $l>$ml){$ml=$l;}\n }\n $ml+=1;\n forea\
-ch my $pg (keys(%L))\n {\n my $name;\n $l=$ml\
--length ($pg);\n $name=$pg;\n for ( $b=0; $b<$l; $\
-b++)\n {\n $name .=\" \";\n }\n $L{$pg}{dn\
-ame}=$name;\n }\n return %L;\n }\n\nsub e\
-nv_file2putenv\n {\n my $f=@_[0];\n my $F=n\
-ew FileHandle;\n my $n;\n \n open ($F, \"\
-$f\");\n while (<$F>)\n {\n my $line=$_;\n\
- my($var, $value)=($_=~/(\\S+)\\=(\\S*)/);\n $ENV{\
-$var}=$value;\n $ENV_SET{$var}=1;\n $n++;\n }\
-\n close ($F);\n return $n;\n }\n\nsub repl\
-ace_line_in_file\n {\n my ($file, $wordin, $wo\
-rdout)=@_;\n my $O=new FileHandle;\n my $I=n\
-ew FileHandle;\n my $l;\n if (!-e $file){ret\
-urn;}\n \n system (\"mv $file $file.old\");\\
-n open ($O, \">$file\");\n open ($I, \"$file\
-.old\");\n while (<$I>)\n {\n $l=$_;\n if \
-(!($l=~/$wordin/)){print $O \"$l\";}\n elsif ( $wo\
-rdout ne \"\"){$l=~s/$wordin/$wordout/g;print $O \\
-"$l\";}\n }\n close ($O);\n close ($I);\
-\n return;\n }\n\nsub add_C_libraries\n {\n \
- my ($file,$first,@list)=@_;\n \n my $O=new F\
-ileHandle;\n my $I=new FileHandle;\n my ($l,\
-$anchor);\n if (!-e $file){return;}\n \n $\
-anchor=\"#include <$first>\";\n \n system (\"m\
-v $file $file.old\");\n open ($O, \">$file\");\\
-n open ($I, \"$file.old\");\n while (<$I>)\n\
- {\n $l=$_;\n print $O \"$l\";\n if (!($l=~/$\
-anchor/))\n {\n \n foreach my $lib (@li\
-st)\n {\n print $O \"#incl\
-ude <$lib>\\n\";\n }\n }\n }\
-\n close ($O);\n close ($I);\n return;\n \
- }\n","use Env;\nuse Cwd;\n@suffix=(\"tmp\", \"t\
-emp\", \"cache\", \"t_coffee\", \"core\", \"tcoffe\
-e\");\n\nif ($#ARGV==-1)\n {\n print \"clean_c\
-ache.pl -file <file to add in -dir> -dir=<dir> -si\
-ze=<value in Mb>\\n0: unlimited -1 always.\\nWill \
-only clean directories matching:[\";\n foreach \
-$k(@suffix){print \"*$k* \";}\n print \"]\\n\";\
-\n exit (EXIT_FAILURE);\n }\n\n$cl=join (\" \"\
-,@ARGV);\nif (($cl=~/\\-no_action/))\n {\n exi\
-t (EXIT_SUCCESS);\n }\n\nif (($cl=~/\\-debug/))\n\
- {\n $DEBUG=1;\n }\nelse\n {\n $DEBUG=0;\\
-n }\n\nif (($cl=~/\\-dir=(\\S+)/))\n {\n $dir\
-=$1;\n }\nelse\n {\n $dir=\"./\";\n }\n\nif \
-($cl=~/\\-file=(\\S+)/)\n {\n $file=$1;\n }\n\
-else\n {\n $file=0;\n }\n\nif ($cl=~/\\-size=\
-(\\S+)/)\n {\n $max_size=$1;\n }\nelse\n {\n\
- $max_size=0;#unlimited\n }\nif ($cl=~/\\-forc\
-e/)\n {\n $force=1;\n }\nelse\n {\n $forc\
-e=0;\n }\n\nif ($cl=~/\\-age=(\\S+)/)\n {\n $\
-max_age=$1;\n }\nelse\n {\n $max_age=0;#unlim\
-ited\n }\n\n$max_size*=1000000;\nif ( ! -d $dir)\\
-n {\n print STDERR \"\\nCannot process $dir: d\
-oes not exist \\n\";\n exit (EXIT_FAILURE);\n \
-}\n\nif ( !($dir=~/^\\//))\n {\n $base=cwd();\\
-n $dir=\"$base/$dir\";\n }\n\n$proceed=0;\nfor\
-each $s (@suffix)\n {\n \n if (($dir=~/$s/)\
-){$proceed=1;}\n $s=uc ($s);\n if (($dir=~/$\
-s/)){$proceed=1;}\n }\nif ( $proceed==0)\n {\n \
- print STDERR \"Clean_cache.pl can only clean dir\
-ectories whose absolute path name contains the fol\
-lowing strings:\";\n foreach $w (@suffix) {prin\
-t STDERR \"$w \";$w=lc($w); print STDERR \"$w \";}\
-\n print STDERR \"\\nCannot process $dir\\n\";\\
-n exit (EXIT_FAILURE);\n }\n\n$name_file=\"$di\
-r/name_file.txt\";\n$size_file=\"$dir/size_file.tx\
-t\";\nif ( $force){&create_ref_file ($dir,$name_fi\
-le,$size_file);}\nif ($file){&add_file ($dir, $nam\
-e_file, $size_file, $file);}\n&clean_dir ($dir, $n\
-ame_file, $size_file, $max_size,$max_age);\nexit (\
-EXIT_SUCCESS);\n\nsub clean_dir \n {\n my ($di\
-r, $name_file, $size_file, $max_size, $max_age)=@_\
-;\n my ($tot_size, $size, $f, $s);\n\n \n $\
-tot_size=&get_tot_size ($dir, $name_file, $size_fi\
-le);\n\n if ( $tot_size<=$max_size){return ;}\n\
- else {$max_size/=2;}\n \n #recreate the \
-name file in case some temprary files have not bee\
-n properly registered\n &create_ref_file ($dir,\
- $name_file, $size_file, $max_age);\n \n $new_\
-name_file=&vtmpnam();\n open (R, \"$name_file\"\
-);\n open (W, \">$new_name_file\");\n while \
-(<R>)\n {\n my $line=$_;\n \n ($f, $s)=($line\
-=~/(\\S+) (\\S+)/);\n if ( !($f=~/\\S/)){next;}\n \
-\n elsif ($max_size && $tot_size>=$max_size && !($\
-f=~/name_file/))\n {\n remove ( \"$dir/$f\")\
-;\n $tot_size-=$s;\n }\n elsif ( $max_age &&\
- -M(\"$dir/$f\")>=$max_age)\n {\n remove ( \\
-"$dir/$f\");\n $tot_size-=$s;\n }\n else\n \
- {\n print W \"$f $s\\n\";\n }\n }\n \
- close (R);\n close (W);\n open (F, \">$size\
-_file\");\n print F \"$tot_size\";\n if ( -e\
- $new_name_file){`mv $new_name_file $name_file`;}\\
-n close (F);\n }\nsub get_tot_size\n {\n m\
-y ($dir, $name_file, $size_file)=@_;\n my $size\
-;\n \n if ( !-d $dir){return 0;}\n if ( !\
--e $name_file)\n {\n \n &create_ref_file ($di\
-r, $name_file, $size_file);\n }\n open (F,\
- \"$size_file\");\n $size=<F>;\n close (F);\\
-n chomp ($size);\n return $size;\n }\nsub s\
-ize \n {\n my $f=@_[0];\n\n if ( !-d $f){re\
-turn -s($f);}\n else {return &dir2size($f);}\n \
- }\nsub dir2size\n {\n my $d=@_[0];\n my ($\
-s, $f);\n \n if ( !-d $d) {return 0;}\n \\
-n foreach $f (&dir2list ($d))\n {\n if ( -\
-d $f){$s+=&dir2size (\"$d/$f\");}\n else {$s+= -s \
-\"$dir/$f\";}\n }\n return $s;\n }\n\nsub\
- remove \n {\n my $file=@_[0];\n my ($f);\n\
- \n debug_print( \"--- $file ---\\n\");\n \
- if (($file eq \".\") || ($file eq \"..\") || ($fi\
-le=~/\\*/)){return EXIT_FAILURE;}\n elsif ( !-d\
- $file)\n {\n debug_print (\"unlink $file\\n\\
-");\n if (-e $file){unlink ($file);}\n }\n \
- elsif ( -d $file)\n {\n debug_print (\"+++++\
-+++ $file +++++++\\n\");\n foreach $f (&dir2list($\
-file))\n {\n &remove (\"$file/$f\");\n }\n\
- debug_print (\"rmdir $file\\n\");\n rmdir $file;\\
-n }\n else\n {\n debug_print (\"?????\
-???? $file ????????\\n\");\n }\n return EX\
-IT_SUCCESS;\n }\n\nsub dir2list\n {\n my $dir\
-=@_[0];\n my (@list1, @list2,@list3, $l);\n\n \
- opendir (DIR,$dir);\n @list1=readdir (DIR);\n\
- closedir (DIR);\n \n foreach $l (@list1)\
-\n {\n if ( $l ne \".\" && $l ne \"..\"){@lis\
-t2=(@list2, $l);}\n }\n @list3 = sort { (-\
-M \"$dir/$list2[$b]\") <=> (-M \"$dir/$list2[$a]\"\
-)} @list2;\n return @list3;\n \n }\n\nsub d\
-ebug_print\n {\n \n if ($DEBUG==1){print @_\
-;}\n \n }\nsub create_ref_file\n {\n my ($\
-dir,$name_file,$size_file)=@_;\n my ($f, $s, $t\
-ot_size, @l);\n \n if ( !-d $dir){return;}\n\
- \n @l=&dir2list ($dir);\n open (F, \">$n\
-ame_file\");\n foreach $f (@l)\n {\n $s=&s\
-ize(\"$dir/$f\");\n $tot_size+=$s;\n print F \"$f \
-$s\\n\";\n }\n &myecho ($tot_size, \">$siz\
-e_file\");\n close (F);\n }\nsub add_file \n \
-{\n my ($dir,$name_file,$size_file,$file)=@_;\n\
- my ($s, $tot_size);\n \n if ( !-d $dir) \
- {return;}\n if ( !-e \"$dir/$file\" ) {return\
-;}\n if ( !-e $name_file){&create_ref_file ($di\
-r,$name_file,$size_file);}\n \n $s=&siz\
-e(\"$dir/$file\");\n open (F, \">>$name_file\")\
-;\n print F \"$file\\n\";\n close (F);\n\n \
- $tot_size=&get_tot_size ($dir,$name_file,$size_f\
-ile);\n $tot_size+=$s;\n &myecho ($tot_size,\
- \">$size_file\");\n \n }\n \nsub myecho\n {\\
-n my ($string, $file)=@_;\n open (ECHO, $fil\
-e) || die;\n print ECHO \"$string\";\n close\
- (ECHO);\n }\n \n \n \nsub vtmpnam\n {\n \
-my $tmp_file_name;\n $tmp_name_counter++;\n \
-$tmp_file_name=\"tmp_file_for_clean_cache_pdb$$.$t\
-mp_name_counter\";\n $tmp_file_list[$ntmp_file+\
-+]=$tmp_file_name;\n if ( -e $tmp_file_name) {r\
-eturn &vtmpnam ();}\n else {return $tmp_file_na\
-me;}\n }\n","\nmy $address=\"http://www.tcoffee.o\
-rg/Projects/Datasets/NatureMethodsDataset.tar.gz\"\
-;\nmy $out=\"NatureMethodsDataset.tar.gz\";\n&url2\
-file ($address,$out);\n\nif ( -e $out)\n {\n \\
-n system (\"gunzip NatureMethodsDataset.tar.gz\\
-");\n system (\"tar -xvf NatureMethodsDataset.t\
-ar\");\n \n print \"Your Data Set is in the \
-Folder NatureMethodsDataset\\n\";\n }\nelse \n {\
-\n print \"Could not Download Dataset --- Web s\
-ite may be down -- Try again later\\n\";\n }\n\n\\
-n\n\nsub url2file\n{\n my ($address, $out, $wge\
-t_arg, $curl_arg)=(@_);\n my ($pg, $flag, $r, $\
-arg, $count);\n \n if (!$CONFIGURATION){&che\
-ck_configuration (\"wget\", \"INTERNET\", \"gzip\"\
-);$CONFIGURATION=1;}\n \n if (&pg_is_install\
-ed (\"wget\")) {$pg=\"wget\"; $flag=\"-O\";$arg=\
-$wget_arg;}\n elsif (&pg_is_installed (\"curl\"\
-)){$pg=\"curl\"; $flag=\"-o\";$arg=$curl_arg;}\n \
- return system (\"$pg $address $flag $out>/dev/nu\
-ll 2>/dev/null\");\n\n}\n\nsub pg_is_installed\n \
-{\n my @ml=@_;\n my $r, $p, $m;\n my $sup\
-ported=0;\n \n my $p=shift (@ml);\n if ($\
-p=~/::/)\n {\n if (system (\"perl -M$p -e 1\"\
-)==$EXIT_SUCCESS){return 1;}\n else {return 0;}\n \
- }\n else\n {\n $r=`which $p 2>/dev/nu\
-ll`;\n if ($r eq \"\"){return 0;}\n else {return 1\
-;}\n }\n }\nsub check_configuration \n {\\
-n my @l=@_;\n my $v;\n foreach my $\
-p (@l)\n {\n \n if ( $p eq \"EMAIL\")\n \
-{ \n if ( !($EMAIL=~/@/))\n {\n exit (EX\
-IT_FAILURE);\n }\n }\n elsif( $p eq \"INTER\
-NET\")\n {\n if ( !&check_internet_conne\
-ction())\n {\n exit (EXIT_FAILURE);\n }\n \
- }\n elsif( $p eq \"wget\")\n {\n if (\
-!&pg_is_installed (\"wget\") && !&pg_is_installed \
-(\"curl\"))\n {\n exit (EXIT_FAILURE);\n }\n \
- }\n elsif( !(&pg_is_installed ($p)))\n {\
-\n exit (EXIT_FAILURE);\n }\n }\n r\
-eturn 1;\n }\nsub check_internet_connection\n \
-{\n my $internet;\n my $tmp;\n &check_con\
-figuration ( \"wget\"); \n \n $tmp=&vtmpnam \
-();\n \n if (&pg_is_installed (\"wget\
-\")){`wget www.google.com -O$tmp >/dev/null 2>/dev\
-/null`;}\n elsif (&pg_is_installed (\"curl\\
-")){`curl www.google.com -o$tmp >/dev/null 2>/dev/\
-null`;}\n \n if ( !-e $tmp || -s $tmp < 10){\
-$internet=0;}\n else {$internet=1;}\n if (-e\
- $tmp){unlink $tmp;}\n\n return $internet;\n }\
-\n\nsub vtmpnam\n {\n my $r=rand(100000);\n m\
-y $f=\"file.$r.$$\";\n while (-e $f)\n {\n $\
-f=vtmpnam();\n }\n push (@TMPFILE_LIST, $f);\n r\
-eturn $f;\n }\n\n","\n$t_coffee=\"t_coffee\";\
-\n\nforeach $value ( @ARGV)\n {\n $seq_file=$s\
-eq_file.\" \".$value;\n }\n\n$name=$ARGV[0];\n$na\
-me=~s/\\.[^\\.]*$//;\n$lib_name=\"$name.mocca_lib\\
-";\n$type=`t_coffee $seq_file -get_type -quiet`;\n\
-chop ($type);\n\nif ( $type eq \"PROTEIN\"){$lib_m\
-ode=\"lalign_rs_s_pair -lalign_n_top 20\";}\nelsif\
- ( $type eq\"DNA\"){$lib_mode=\"lalign_rs_s_dna_pa\
-ir -lalign_n_top 40\";}\n\nif ( !(-e $lib_name))\n\
- {\n \n $command=\"$t_coffee -mocca -seq_weigh\
-t=no -cosmetic_penalty=0 -mocca_interactive -in $l\
-ib_mode -out_lib $lib_name -infile $seq_file\";\n \
- \n }\nelsif ( (-e $lib_name))\n {\n $command=\\
-"$t_coffee -mocca -seq_weight=no -cosmetic_penalty\
-=0 -mocca_interactive -in $lib_name -infile $seq_f\
-ile\";\n \n }\n\nsystem ($command);\n\nexit;\n\n\
-","my $WSDL = 'http://www.ebi.ac.uk/Tools/webservi\
-ces/wsdl/WSDaliLite.wsdl';\n\nuse SOAP::Lite;\nuse\
- Data::Dumper;\nuse Getopt::Long qw(:config no_ign\
-ore_case bundling);\nuse File::Basename;\n\nmy $ch\
-eckInterval = 5;\n\nmy %params=(\n 'async' => \
-'1', # Use async mode and simulate sync mode in cl\
-ient\n );\nGetOptions(\n 'pdb1=s' => \\\
-$params{'sequence1'},\n 'chainid1=s' => \\$para\
-ms{'chainid1'},\n 'pdb2=s' => \\$params{'se\
-quence2'},\n 'chainid2=s' => \\$params{'chainid\
-2'},\n \"help|h\" => \\$help, # Usage info\n \
- \"async|a\" => \\$async, # Asynchronous submiss\
-ion\n \"polljob\" => \\$polljob, # Get results\
-\n \"status\" => \\$status, # Get status\n \
-\"jobid|j=s\" => \\$jobid, # JobId\n \"email|S\
-=s\" => \\$params{email}, # E-mail address\n \\
-"trace\" => \\$trace, # SOAP messages\n \"\
-sequence=s\" => \\$sequence, # Input PDB\n );\n\
-\nmy $scriptName = basename($0, ());\nif($help) {\\
-n &usage();\n exit(0);\n}\n\nif($trace) {\n \
- print \"Tracing active\\n\";\n SOAP::Lite->i\
-mport(+trace => 'debug');\n}\n\nmy $soap = SOAP::L\
-ite\n ->service($WSDL)\n ->on_fault(sub {\n \
+.pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\"blastpgp.\
+pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.uk/Tools/w\
+ebservices/services/blastpgp\";\n$PG{\"blastpgp.pl\
+\"}{\"language\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}{\
+\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\"}{\"s\
+ource\"}=\"empty\";\n$PG{\"blastpgp.pl\"}{\"update\
+_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\"mode\
+\"}=\"psicoffee,expresso,accurate\";\n$PG{\"blasta\
+ll\"}{\"4_TCOFFEE\"}=\"blastall\";\n$PG{\"blastall\
+\"}{\"type\"}=\"protein_homology_predictor\";\n$PG\
+{\"blastall\"}{\"ADDRESS\"}=\"ftp://ftp.ncbi.nih.g\
+ov/blast/executables/LATEST\";\n$PG{\"blastall\"}{\
+\"language\"}=\"C\";\n$PG{\"blastall\"}{\"language\
+2\"}=\"C\";\n$PG{\"blastall\"}{\"source\"}=\"empty\
+\";\n$PG{\"blastall\"}{\"update_action\"}=\"never\\
+";\n$PG{\"blastall\"}{\"mode\"}=\"psicoffee,expres\
+so,3dcoffee\";\n$PG{\"legacy_blast.pl\"}{\"4_TCOFF\
+EE\"}=\"NCBIBLAST\";\n$PG{\"legacy_blast.pl\"}{\"t\
+ype\"}=\"protein_homology_predictor\";\n$PG{\"lega\
+cy_blast.pl\"}{\"ADDRESS\"}=\"ftp://ftp.ncbi.nih.g\
+ov/blast/executables/LATEST\";\n$PG{\"legacy_blast\
+.pl\"}{\"language\"}=\"C\";\n$PG{\"legacy_blast.pl\
+\"}{\"language2\"}=\"C\";\n$PG{\"legacy_blast.pl\"\
+}{\"source\"}=\"empty\";\n$PG{\"legacy_blast.pl\"}\
+{\"update_action\"}=\"never\";\n$PG{\"legacy_blast\
+.pl\"}{\"mode\"}=\"psicoffee,expresso,3dcoffee\";\\
+n$PG{\"SOAP::Lite\"}{\"4_TCOFFEE\"}=\"SOAPLITE\";\\
+n$PG{\"SOAP::Lite\"}{\"type\"}=\"library\";\n$PG{\\
+"SOAP::Lite\"}{\"ADDRESS\"}=\"http://cpansearch.pe\
+rl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL\\
+";\n$PG{\"SOAP::Lite\"}{\"language\"}=\"Perl\";\n$\
+PG{\"SOAP::Lite\"}{\"language2\"}=\"Perl\";\n$PG{\\
+"SOAP::Lite\"}{\"source\"}=\"empty\";\n$PG{\"blast\
+pgp\"}{\"update_action\"}=\"never\";\n$PG{\"SOAP::\
+Lite\"}{\"mode\"}=\"none\";\n$PG{\"XML::Simple\"}{\
+\"4_TCOFFEE\"}=\"XMLSIMPLE\";\n$PG{\"XML::Simple\"\
+}{\"type\"}=\"library\";\n$PG{\"XML::Simple\"}{\"A\
+DDRESS\"}=\"http://search.cpan.org/~grantm/XML-Sim\
+ple-2.18/lib/XML/Simple.pm\";\n$PG{\"XML::Simple\"\
+}{\"language\"}=\"Perl\";\n$PG{\"XML::Simple\"}{\"\
+language2\"}=\"Perl\";\n$PG{\"XML::Simple\"}{\"sou\
+rce\"}=\"empty\";\n$PG{\"XML::Simple\"}{\"mode\"}=\
+\"psicoffee,expresso,accurate\";\n$MODE{\"tcoffee\\
+"}{\"name\"}=\"tcoffee\";\n$MODE{\"rcoffee\"}{\"na\
+me\"}=\"rcoffee\";\n$MODE{\"3dcoffee\"}{\"name\"}=\
+\"3dcoffee\";\n$MODE{\"mcoffee\"}{\"name\"}=\"mcof\
+fee\";\n$MODE{\"expresso\"}{\"name\"}=\"expresso\"\
+;\n$MODE{\"trmsd\"}{\"name\"}=\"trmsd\";\n$MODE{\"\
+accurate\"}{\"name\"}=\"accurate\";\n$MODE{\"seq_r\
+eformat\"}{\"name\"}=\"seq_reformat\";\n\n\n$PG{C}\
+{compiler}=\"gcc\";\n$PG{C}{compiler_flag}=\"CC\";\
+\n$PG{C}{options}=\"\";\n$PG{C}{options_flag}=\"CF\
+LAGS\";\n$PG{C}{type}=\"compiler\";\n\n$PG{\"CXX\"\
+}{compiler}=\"g++\";\n$PG{\"CXX\"}{compiler_flag}=\
+\"CXX\";\n$PG{\"CXX\"}{options}=\"\";\n$PG{\"CXX\"\
+}{options_flag}=\"CXXFLAGS\";\n$PG{CXX}{type}=\"co\
+mpiler\";\n\n$PG{\"CPP\"}{compiler}=\"g++\";\n$PG{\
+\"CPP\"}{compiler_flag}=\"CPP\";\n$PG{\"CPP\"}{opt\
+ions}=\"\";\n$PG{\"CPP\"}{options_flag}=\"CPPFLAGS\
+\";\n$PG{CPP}{type}=\"compiler\";\n\n$PG{\"GPP\"}{\
+compiler}=\"g++\";\n$PG{\"GPP\"}{compiler_flag}=\"\
+GPP\";\n$PG{\"GPP\"}{options}=\"\";\n$PG{\"GPP\"}{\
+options_flag}=\"CFLAGS\";\n$PG{GPP}{type}=\"compil\
+er\";\n\n$PG{Fortran}{compiler}=\"g77\";\n$PG{Fort\
+ran}{compiler_flag}=\"FCC\";\n$PG{Fortran}{type}=\\
+"compiler\";\n\n$PG{Perl}{compiler}=\"CPAN\";\n$PG\
+{Perl}{type}=\"compiler\";\n\n$SUPPORTED_OS{macox}\
+=\"Macintosh\";\n$SUPPORTED_OS{linux}=\"Linux\";\n\
+$SUPPORTED_OS{windows}=\"Cygwin\";\n\n\n\n$MODE{t_\
+coffee}{description}=\" for regular multiple seque\
+nce alignments\";\n$MODE{rcoffee} {description}=\"\
+ for RNA multiple sequence alignments\";\n\n$MODE{\
+psicoffee} {description}=\" for Homology Extended \
+multiple sequence alignments\";\n$MODE{expresso}{d\
+escription}=\" for very accurate structure based m\
+ultiple sequence alignments\";\n$MODE{\"3dcoffee\"\
+}{description}=\" for multiple structure alignment\
+s\";\n$MODE{mcoffee} {description}=\" for combinin\
+g alternative multiple sequence alignment packages\
+\\n------- into a unique meta-package. The install\
+er will upload several MSA packages and compile th\
+em\\n\n\";\n\n\n&post_process_PG();\nreturn;\n}\n\\
+nsub post_process_PG\n {\n my $p;\n \n %\
+PG=&name2dname (%PG);\n %MODE=&name2dname(%MODE\
+);\n foreach $p (keys(%PG)){if ( $PG{$p}{type} \
+eq \"compiler\"){$PG{$p}{update_action}=\"never\";\
+}}\n \n }\n\nsub name2dname\n {\n my (%L)=\
+(@_);\n my ($l, $ml);\n \n foreach my $pg\
+ (keys(%L))\n {\n $l=length ($pg);\n if ( $l>\
+$ml){$ml=$l;}\n }\n $ml+=1;\n foreach m\
+y $pg (keys(%L))\n {\n my $name;\n $l=$ml-len\
+gth ($pg);\n $name=$pg;\n for ( $b=0; $b<$l; $b++)\
+\n {\n $name .=\" \";\n }\n $L{$pg}{dname}\
+=$name;\n }\n return %L;\n }\n\nsub env_f\
+ile2putenv\n {\n my $f=@_[0];\n my $F=new F\
+ileHandle;\n my $n;\n \n open ($F, \"$f\"\
+);\n while (<$F>)\n {\n my $line=$_;\n my(\
+$var, $value)=($_=~/(\\S+)\\=(\\S*)/);\n $ENV{$var\
+}=$value;\n $ENV_SET{$var}=1;\n $n++;\n }\n \
+ close ($F);\n return $n;\n }\n\nsub replace_\
+line_in_file\n {\n my ($file, $wordin, $wordou\
+t)=@_;\n my $O=new FileHandle;\n my $I=new F\
+ileHandle;\n my $l;\n if (!-e $file){return;\
+}\n \n system (\"mv $file $file.old\");\n \
+ open ($O, \">$file\");\n open ($I, \"$file.old\
+\");\n while (<$I>)\n {\n $l=$_;\n if (!($\
+l=~/$wordin/)){print $O \"$l\";}\n elsif ( $wordou\
+t ne \"\"){$l=~s/$wordin/$wordout/g;print $O \"$l\\
+";}\n }\n close ($O);\n close ($I);\n \
+ return;\n }\n\nsub add_C_libraries\n {\n my \
+($file,$first,@list)=@_;\n \n my $O=new FileH\
+andle;\n my $I=new FileHandle;\n my ($l,$anc\
+hor);\n if (!-e $file){return;}\n \n $anch\
+or=\"#include <$first>\";\n \n system (\"mv $f\
+ile $file.old\");\n open ($O, \">$file\");\n \
+ open ($I, \"$file.old\");\n while (<$I>)\n \
+ {\n $l=$_;\n print $O \"$l\";\n if (!($l=~/$anch\
+or/))\n {\n \n foreach my $lib (@list)\\
+n {\n print $O \"#include \
+<$lib>\\n\";\n }\n }\n }\n \
+ close ($O);\n close ($I);\n return;\n }\
+\n","use Env;\nuse Cwd;\n@suffix=(\"tmp\", \"temp\\
+", \"cache\", \"t_coffee\", \"core\", \"tcoffee\")\
+;\n\nif ($#ARGV==-1)\n {\n print \"clean_cache\
+.pl -file <file to add in -dir> -dir=<dir> -size=<\
+value in Mb>\\n0: unlimited -1 always.\\nWill only\
+ clean directories matching:[\";\n foreach $k(@\
+suffix){print \"*$k* \";}\n print \"]\\n\";\n \
+ exit (EXIT_FAILURE);\n }\n\n$cl=join (\" \",@AR\
+GV);\nif (($cl=~/\\-no_action/))\n {\n exit (E\
+XIT_SUCCESS);\n }\n\nif (($cl=~/\\-debug/))\n {\\
+n $DEBUG=1;\n }\nelse\n {\n $DEBUG=0;\n }\
+\n\nif (($cl=~/\\-dir=(\\S+)/))\n {\n $dir=$1;\
+\n }\nelse\n {\n $dir=\"./\";\n }\n\nif ($cl\
+=~/\\-file=(\\S+)/)\n {\n $file=$1;\n }\nelse\
+\n {\n $file=0;\n }\n\nif ($cl=~/\\-size=(\\S\
++)/)\n {\n $max_size=$1;\n }\nelse\n {\n \
+$max_size=0;#unlimited\n }\nif ($cl=~/\\-force/)\\
+n {\n $force=1;\n }\nelse\n {\n $force=0;\
+\n }\n\nif ($cl=~/\\-age=(\\S+)/)\n {\n $max_\
+age=$1;\n }\nelse\n {\n $max_age=0;#unlimited\
+\n }\n\n$max_size*=1000000;\nif ( ! -d $dir)\n {\
+\n print STDERR \"\\nCannot process $dir: does \
+not exist \\n\";\n exit (EXIT_FAILURE);\n }\n\\
+nif ( !($dir=~/^\\//))\n {\n $base=cwd();\n \
+ $dir=\"$base/$dir\";\n }\n\n$proceed=0;\nforeach\
+ $s (@suffix)\n {\n \n if (($dir=~/$s/)){$p\
+roceed=1;}\n $s=uc ($s);\n if (($dir=~/$s/))\
+{$proceed=1;}\n }\nif ( $proceed==0)\n {\n pr\
+int STDERR \"Clean_cache.pl can only clean directo\
+ries whose absolute path name contains the followi\
+ng strings:\";\n foreach $w (@suffix) {print ST\
+DERR \"$w \";$w=lc($w); print STDERR \"$w \";}\n \
+ print STDERR \"\\nCannot process $dir\\n\";\n \
+ exit (EXIT_FAILURE);\n }\n\n$name_file=\"$dir/na\
+me_file.txt\";\n$size_file=\"$dir/size_file.txt\";\
+\nif ( $force){&create_ref_file ($dir,$name_file,$\
+size_file);}\nif ($file){&add_file ($dir, $name_fi\
+le, $size_file, $file);}\n&clean_dir ($dir, $name_\
+file, $size_file, $max_size,$max_age);\nexit (EXIT\
+_SUCCESS);\n\nsub clean_dir \n {\n my ($dir, $\
+name_file, $size_file, $max_size, $max_age)=@_;\n \
+ my ($tot_size, $size, $f, $s);\n\n \n $tot_\
+size=&get_tot_size ($dir, $name_file, $size_file);\
+\n\n if ( $tot_size<=$max_size){return ;}\n \
+else {$max_size/=2;}\n \n #recreate the name\
+ file in case some temprary files have not been pr\
+operly registered\n &create_ref_file ($dir, $na\
+me_file, $size_file, $max_age);\n \n $new_name\
+_file=&vtmpnam();\n open (R, \"$name_file\");\n\
+ open (W, \">$new_name_file\");\n while (<R>\
+)\n {\n my $line=$_;\n \n ($f, $s)=($line=~/(\
+\\S+) (\\S+)/);\n if ( !($f=~/\\S/)){next;}\n \n e\
+lsif ($max_size && $tot_size>=$max_size && !($f=~/\
+name_file/))\n {\n remove ( \"$dir/$f\");\n \
+ $tot_size-=$s;\n }\n elsif ( $max_age && -M(\
+\"$dir/$f\")>=$max_age)\n {\n remove ( \"$di\
+r/$f\");\n $tot_size-=$s;\n }\n else\n {\n\
+ print W \"$f $s\\n\";\n }\n }\n clo\
+se (R);\n close (W);\n open (F, \">$size_fil\
+e\");\n print F \"$tot_size\";\n if ( -e $ne\
+w_name_file){`mv $new_name_file $name_file`;}\n \
+ close (F);\n }\nsub get_tot_size\n {\n my ($\
+dir, $name_file, $size_file)=@_;\n my $size;\n \
+ \n if ( !-d $dir){return 0;}\n if ( !-e $\
+name_file)\n {\n \n &create_ref_file ($dir, $\
+name_file, $size_file);\n }\n open (F, \"$\
+size_file\");\n $size=<F>;\n close (F);\n \
+ chomp ($size);\n return $size;\n }\nsub size \
+\n {\n my $f=@_[0];\n\n if ( !-d $f){return\
+ -s($f);}\n else {return &dir2size($f);}\n }\n\
+sub dir2size\n {\n my $d=@_[0];\n my ($s, $\
+f);\n \n if ( !-d $d) {return 0;}\n \n \
+ foreach $f (&dir2list ($d))\n {\n if ( -d $f\
+){$s+=&dir2size (\"$d/$f\");}\n else {$s+= -s \"$d\
+ir/$f\";}\n }\n return $s;\n }\n\nsub rem\
+ove \n {\n my $file=@_[0];\n my ($f);\n \
+\n debug_print( \"--- $file ---\\n\");\n if \
+(($file eq \".\") || ($file eq \"..\") || ($file=~\
+/\\*/)){return EXIT_FAILURE;}\n elsif ( !-d $fi\
+le)\n {\n debug_print (\"unlink $file\\n\");\\
+n if (-e $file){unlink ($file);}\n }\n els\
+if ( -d $file)\n {\n debug_print (\"++++++++ \
+$file +++++++\\n\");\n foreach $f (&dir2list($file\
+))\n {\n &remove (\"$file/$f\");\n }\n deb\
+ug_print (\"rmdir $file\\n\");\n rmdir $file;\n \
+ }\n else\n {\n debug_print (\"?????????\
+ $file ????????\\n\");\n }\n return EXIT_S\
+UCCESS;\n }\n\nsub dir2list\n {\n my $dir=@_[\
+0];\n my (@list1, @list2,@list3, $l);\n\n op\
+endir (DIR,$dir);\n @list1=readdir (DIR);\n \
+closedir (DIR);\n \n foreach $l (@list1)\n \
+ {\n if ( $l ne \".\" && $l ne \"..\"){@list2=(\
+@list2, $l);}\n }\n @list3 = sort { (-M \"\
+$dir/$list2[$b]\") <=> (-M \"$dir/$list2[$a]\")} @\
+list2;\n return @list3;\n \n }\n\nsub debug\
+_print\n {\n \n if ($DEBUG==1){print @_;}\n\
+ \n }\nsub create_ref_file\n {\n my ($dir,\
+$name_file,$size_file)=@_;\n my ($f, $s, $tot_s\
+ize, @l);\n \n if ( !-d $dir){return;}\n \
+\n @l=&dir2list ($dir);\n open (F, \">$name_\
+file\");\n foreach $f (@l)\n {\n $s=&size(\
+\"$dir/$f\");\n $tot_size+=$s;\n print F \"$f $s\\\
+n\";\n }\n &myecho ($tot_size, \">$size_fi\
+le\");\n close (F);\n }\nsub add_file \n {\n \
+ my ($dir,$name_file,$size_file,$file)=@_;\n \
+my ($s, $tot_size);\n \n if ( !-d $dir) {r\
+eturn;}\n if ( !-e \"$dir/$file\" ) {return;}\n\
+ if ( !-e $name_file){&create_ref_file ($dir,$n\
+ame_file,$size_file);}\n \n $s=&size(\"\
+$dir/$file\");\n open (F, \">>$name_file\");\n \
+ print F \"$file\\n\";\n close (F);\n\n $t\
+ot_size=&get_tot_size ($dir,$name_file,$size_file)\
+;\n $tot_size+=$s;\n &myecho ($tot_size, \">\
+$size_file\");\n \n }\n \nsub myecho\n {\n \
+ my ($string, $file)=@_;\n open (ECHO, $file) |\
+| die;\n print ECHO \"$string\";\n close (EC\
+HO);\n }\n \n \n \nsub vtmpnam\n {\n my $\
+tmp_file_name;\n $tmp_name_counter++;\n $tmp\
+_file_name=\"tmp_file_for_clean_cache_pdb$$.$tmp_n\
+ame_counter\";\n $tmp_file_list[$ntmp_file++]=$\
+tmp_file_name;\n if ( -e $tmp_file_name) {retur\
+n &vtmpnam ();}\n else {return $tmp_file_name;}\
+\n }\n","\nmy $address=\"http://www.tcoffee.org/D\
+ata/Datasets/NatureProtocolsDataset.tar.gz\";\nmy \
+$out=\"NatureProtocolsDataset.tar.gz\";\n&url2file\
+ ($address,$out);\n\nif ( -e $out)\n {\n \n \
+ system (\"gunzip NatureProtocolsDataset.tar.gz\")\
+;\n system (\"tar -xvf NatureProtocolsDataset.t\
+ar\");\n system (\"rm -rf NatureProtocolsDataset\
+.tar\"); \n print \"Your Data Set is in the Fo\
+lder 'NatureProtocolsDataset'\\n\";\n }\nelse \n \
+ {\n print \"Could not Download Dataset --- Web\
+ site may be down -- Try again later\\n\";\n }\n\\
+n\n\n\nsub url2file\n{\n my ($address, $out, $w\
+get_arg, $curl_arg)=(@_);\n my ($pg, $flag, $r,\
+ $arg, $count);\n \n if (!$CONFIGURATION){&c\
+heck_configuration (\"wget\", \"INTERNET\", \"gzip\
+\");$CONFIGURATION=1;}\n \n if (&pg_is_insta\
+lled (\"wget\")) {$pg=\"wget\"; $flag=\"-O\";$ar\
+g=$wget_arg;}\n elsif (&pg_is_installed (\"curl\
+\")){$pg=\"curl\"; $flag=\"-o\";$arg=$curl_arg;}\n\
+ return system (\"$pg $address $flag $out>/dev/\
+null 2>/dev/null\");\n\n}\n\nsub pg_is_installed\n\
+ {\n my @ml=@_;\n my $r, $p, $m;\n my $s\
+upported=0;\n \n my $p=shift (@ml);\n if \
+($p=~/::/)\n {\n if (system (\"perl -M$p -e 1\
+\")==$EXIT_SUCCESS){return 1;}\n else {return 0;}\\
+n }\n else\n {\n $r=`which $p 2>/dev/\
+null`;\n if ($r eq \"\"){return 0;}\n else {return\
+ 1;}\n }\n }\nsub check_configuration \n \
+{\n my @l=@_;\n my $v;\n foreach my\
+ $p (@l)\n {\n \n if ( $p eq \"EMAIL\")\n \
+ { \n if ( !($EMAIL=~/@/))\n {\n exit (\
+EXIT_FAILURE);\n }\n }\n elsif( $p eq \"INT\
+ERNET\")\n {\n if ( !&check_internet_con\
+nection())\n {\n exit (EXIT_FAILURE);\n }\n \
+ }\n elsif( $p eq \"wget\")\n {\n if\
+ (!&pg_is_installed (\"wget\") && !&pg_is_installe\
+d (\"curl\"))\n {\n exit (EXIT_FAILURE);\n }\\
+n }\n elsif( !(&pg_is_installed ($p)))\n \
+ {\n exit (EXIT_FAILURE);\n }\n }\n \
+ return 1;\n }\nsub check_internet_connection\n\
+ {\n my $internet;\n my $tmp;\n &check_c\
+onfiguration ( \"wget\"); \n \n $tmp=&vtmpna\
+m ();\n \n if (&pg_is_installed (\"wg\
+et\")){`wget www.google.com -O$tmp >/dev/null 2>/d\
+ev/null`;}\n elsif (&pg_is_installed (\"cur\
+l\")){`curl www.google.com -o$tmp >/dev/null 2>/de\
+v/null`;}\n \n if ( !-e $tmp || -s $tmp < 10\
+){$internet=0;}\n else {$internet=1;}\n if (\
+-e $tmp){unlink $tmp;}\n\n return $internet;\n \
+ }\n\nsub vtmpnam\n {\n my $r=rand(100000);\n\
+ my $f=\"file.$r.$$\";\n while (-e $f)\n {\n \
+ $f=vtmpnam();\n }\n push (@TMPFILE_LIST, $f);\n\
+ return $f;\n }\n\n","\n$t_coffee=\"t_coffee\\
+";\n\nforeach $value ( @ARGV)\n {\n $seq_file=\
+$seq_file.\" \".$value;\n }\n\n$name=$ARGV[0];\n$\
+name=~s/\\.[^\\.]*$//;\n$lib_name=\"$name.mocca_li\
+b\";\n$type=`t_coffee $seq_file -get_type -quiet`;\
+\nchop ($type);\n\nif ( $type eq \"PROTEIN\"){$lib\
+_mode=\"lalign_rs_s_pair -lalign_n_top 20\";}\nels\
+if ( $type eq\"DNA\"){$lib_mode=\"lalign_rs_s_dna_\
+pair -lalign_n_top 40\";}\n\nif ( !(-e $lib_name))\
+\n {\n \n $command=\"$t_coffee -mocca -seq_wei\
+ght=no -cosmetic_penalty=0 -mocca_interactive -in \
+$lib_mode -out_lib $lib_name -infile $seq_file\";\\
+n \n }\nelsif ( (-e $lib_name))\n {\n $command\
+=\"$t_coffee -mocca -seq_weight=no -cosmetic_penal\
+ty=0 -mocca_interactive -in $lib_name -infile $seq\
+_file\";\n \n }\n\nsystem ($command);\n\nexit;\n\
+\n","my $WSDL = 'http://www.ebi.ac.uk/Tools/webser\
+vices/wsdl/WSDaliLite.wsdl';\n\nuse SOAP::Lite;\nu\
+se Data::Dumper;\nuse Getopt::Long qw(:config no_i\
+gnore_case bundling);\nuse File::Basename;\n\nmy $\
+checkInterval = 5;\n\nmy %params=(\n 'async' =\
+> '1', # Use async mode and simulate sync mode in \
+client\n );\nGetOptions(\n 'pdb1=s' => \
+\\$params{'sequence1'},\n 'chainid1=s' => \\$pa\
+rams{'chainid1'},\n 'pdb2=s' => \\$params{'\
+sequence2'},\n 'chainid2=s' => \\$params{'chain\
+id2'},\n \"help|h\" => \\$help, # Usage info\n\
+ \"async|a\" => \\$async, # Asynchronous submi\
+ssion\n \"polljob\" => \\$polljob, # Get resul\
+ts\n \"status\" => \\$status, # Get status\n \
+ \"jobid|j=s\" => \\$jobid, # JobId\n \"email\
+|S=s\" => \\$params{email}, # E-mail address\n \
+ \"trace\" => \\$trace, # SOAP messages\n \
+\"sequence=s\" => \\$sequence, # Input PDB\n );\
+\n\nmy $scriptName = basename($0, ());\nif($help) \
+{\n &usage();\n exit(0);\n}\n\nif($trace) {\\
+n print \"Tracing active\\n\";\n SOAP::Lite-\
+>import(+trace => 'debug');\n}\n\nmy $soap = SOAP:\
+:Lite\n ->service($WSDL)\n ->on_fault(sub {\\
+n my $soap = shift;\n my $res = shif\
+t;\n # Throw an exception for all faults\n \
+ if(ref($res) eq '') {\n die($res\
+);\n } else {\n die($res->faults\
+tring);\n }\n return new SOAP::SOM;\\
+n }\n );\n\nif( !($polljob || $st\
+atus) &&\n !( defined($params{'sequence1'}) && \
+defined($params{'sequence2'}) )\n ) {\n prin\
+t STDERR 'Error: bad option combination', \"\\n\";\
+\n &usage();\n exit(1);\n}\nelsif($polljob &\
+& defined($jobid)) {\n print \"Getting results \
+for job $jobid\\n\";\n getResults($jobid);\n}\n\
+elsif($status && defined($jobid)) {\n print STD\
+ERR \"Getting status for job $jobid\\n\";\n my \
+$result = $soap->checkStatus($jobid);\n print S\
+TDOUT \"$result\", \"\\n\";\n if($result eq 'DO\
+NE') {\n print STDERR \"To get results: $scriptNam\
+e --polljob --jobid $jobid\\n\";\n }\n}\nelse {\
+\n if(-f $params{'sequence1'}) {\n $params{'seq\
+uence1'} = read_file($params{'sequence1'});\n }\
+\n if(-f $params{'sequence2'}) {\n $params{'seq\
+uence2'} = read_file($params{'sequence2'});\n }\
+\n\n my $jobid;\n my $paramsData = SOAP::Dat\
+a->name('params')->type(map=>\\%params);\n # Fo\
+r SOAP::Lite 0.60 and earlier parameters are passe\
+d directly\n if($SOAP::Lite::VERSION eq '0.60' \
+|| $SOAP::Lite::VERSION =~ /0\\.[1-5]/) {\n \
+ $jobid = $soap->runDaliLite($paramsData);\n }\\
+n # For SOAP::Lite 0.69 and later parameter han\
+dling is different, so pass\n # undef's for tem\
+plated params, and then pass the formatted args.\n\
+ else {\n $jobid = $soap->runDaliLite(un\
+def,\n $paramsData);\n }\n\n if (def\
+ined($async)) {\n print STDOUT $jobid, \"\\n\";\n \
+ print STDERR \"To check status: $scriptName\
+ --status --jobid $jobid\\n\";\n } else { # Syn\
+chronous mode\n print STDERR \"JobId: $jobi\
+d\\n\";\n sleep 1;\n getResults($job\
+id);\n }\n}\n\nsub clientPoll($) {\n my $job\
+id = shift;\n my $result = 'PENDING';\n # Ch\
+eck status and wait if not finished\n #print ST\
+DERR \"Checking status: $jobid\\n\";\n while($r\
+esult eq 'RUNNING' || $result eq 'PENDING') {\n \
+ $result = $soap->checkStatus($jobid);\n \
+ print STDERR \"$result\\n\";\n if($result\
+ eq 'RUNNING' || $result eq 'PENDING') {\n \
+ # Wait before polling again.\n slee\
+p $checkInterval;\n }\n }\n}\n\nsub getR\
+esults($) {\n $jobid = shift;\n # Check stat\
+us, and wait if not finished\n clientPoll($jobi\
+d);\n # Use JobId if output file name is not de\
+fined\n unless(defined($outfile)) {\n $o\
+utfile=$jobid;\n }\n # Get list of data type\
+s\n my $resultTypes = $soap->getResults($jobid)\
+;\n # Get the data and write it to a file\n \
+if(defined($outformat)) { # Specified data type\n \
+ my $selResultType;\n foreach my $res\
+ultType (@$resultTypes) {\n if($resultT\
+ype->{type} eq $outformat) {\n $sel\
+ResultType = $resultType;\n }\n \
+}\n $res=$soap->poll($jobid, $selResultType\
+->{type});\n write_file($outfile.'.'.$selRe\
+sultType->{ext}, $res);\n } else { # Data types\
+ available\n # Write a file for each output\
+ type\n for my $resultType (@$resultTypes){\
+\n #print \"Getting $resultType->{type}\
+\\n\";\n $res=$soap->poll($jobid, $resu\
+ltType->{type});\n write_file($outfile.\
+'.'.$resultType->{ext}, $res);\n }\n }\n\
+}\n\nsub read_file($) {\n my $filename = shift;\
+\n open(FILE, $filename);\n my $content;\n \
+ my $buffer;\n while(sysread(FILE, $buffer, 10\
+24)) {\n $content.= $buffer;\n }\n close(FIL\
+E);\n return $content;\n}\n\nsub write_file($$)\
+ {\n my ($tmp,$entity) = @_;\n print STDERR \
+\"Creating result file: \".$tmp.\"\\n\";\n unle\
+ss(open (FILE, \">$tmp\")) {\n return 0;\n }\n \
+ syswrite(FILE, $entity);\n close (FILE);\n \
+ return 1;\n}\n\nsub usage {\n print STDERR <<\
+EOF\nDaliLite\n========\n\nPairwise comparison of \
+protein structures\n\n[Required]\n\n --pdb1 \
+ : str : PDB ID for structure 1\n --pdb\
+2 : str : PDB ID for structure 2\n\
+\n[Optional]\n\n --chain1 : str : C\
+hain identifer in structure 1\n --chain2 \
+ : str : Chain identifer in structure 2\n\n[G\
+eneral]\n\n -h, --help : : prints\
+ this help text\n -S, --email : str : \
+user email address\n -a, --async : \
+ : asynchronous submission\n --status \
+ : : poll for the status of a job\n --p\
+olljob : : poll for the results of a \
+job\n -j, --jobid : str : jobid for an\
+ asynchronous job\n -O, --outfile : str \
+: file name for results (default is jobid)\n \
+--trace : : show SOAP messages being \
+interchanged \n\nSynchronous job:\n\n The results\
+/errors are returned as soon as the job is finishe\
+d.\n Usage: $scriptName --email <your\\@email> [o\
+ptions] pdbFile [--outfile string]\n Returns: sav\
+es the results to disk\n\nAsynchronous job:\n\n U\
+se this if you want to retrieve the results at a l\
+ater time. The results \n are stored for up to 24\
+ hours. \n The asynchronous submission mode is re\
+commended when users are submitting \n batch jobs\
+ or large database searches \n Usage: $scriptName\
+ --email <your\\@email> --async [options] pdbFile\\
+n Returns: jobid\n\n Use the jobid to query for \
+the status of the job. \n Usage: $scriptName --st\
+atus --jobid <jobId>\n Returns: string indicating\
+ the status of the job:\n DONE - job has finish\
+ed\n RUNNING - job is running\n NOT_FOUND - \
+job cannot be found\n ERROR - the jobs has enco\
+untered an error\n\n When done, use the jobid to \
+retrieve the status of the job. \n Usage: $script\
+Name --polljob --jobid <jobId> [--outfile string]\\
+n\n[Help]\n\n For more detailed help information \
+refer to\n http://www.ebi.ac.uk/DaliLite/\nEOF\n;\
+\n}\n","my $WSDL = 'http://www.ebi.ac.uk/Tools/web\
+services/wsdl/WSWUBlast.wsdl';\n\nuse strict;\nuse\
+ SOAP::Lite;\nuse Getopt::Long qw(:config no_ignor\
+e_case bundling);\nuse File::Basename;\n\nmy $chec\
+kInterval = 15;\n\nmy $numOpts = scalar(@ARGV);\nm\
+y ($outfile, $outformat, $help, $async, $polljob, \
+$status, $ids, $jobid, $trace, $sequence);\nmy %pa\
+rams= ( # Defaults\n 'async' => 1, # Force i\
+nto async mode\n 'exp' => 10.0, # E-value th\
+reshold\n 'numal' => 50, # Maximum number of\
+ alignments\n 'scores' => 100, # Maximum num\
+ber of scores\n );\nGetOptions( # Map t\
+he options into variables\n \"program|p=s\" \
+ => \\$params{program}, # BLAST program\n \"dat\
+abase|D=s\" => \\$params{database}, # Search da\
+tabase\n \"matrix|m=s\" => \\$params{matri\
+x}, # Scoring matrix\n \"exp|E=f\" => \\
+\$params{exp}, # E-value threshold\n \"echofilt\
+er|e\" => \\$params{echofilter}, # Display filt\
+ered sequence\n \"filter|f=s\" => \\$param\
+s{filter}, # Low complexity filter name\n \"ali\
+gnments|b=i\" => \\$params{numal}, # Number of al\
+ignments\n \"scores|s=i\" => \\$params{sco\
+res}, # Number of scores\n \"sensitivity|S=s\" \
+=> \\$params{sensitivity}, # Search sensitivity\n \
+ \"sort|t=s\" => \\$params{sort}, # Sort h\
+its by...\n \"stats|T=s\" => \\$params{st\
+ats}, # Scoring statistic to use\n \"strand|d=s\
+\" => \\$params{strand}, # Strand to use in D\
+NA vs. DNA search\n \"topcombon|c=i\" => \\$p\
+arams{topcombon}, # Consistent sets of HSPs\n \\
+"outfile=s\" => \\$outfile, # Output file\n \
+ \"outformat|o=s\" => \\$outformat, # Output f\
+ormat\n \"help|h\" => \\$help, # Usage in\
+fo\n \"async|a\" => \\$async, # Asynchron\
+ous mode\n \"polljob\" => \\$polljob, # G\
+et results\n \"status\" => \\$status, # G\
+et job status\n \"ids\" => \\$ids, \
+# Get ids from result\n \"jobid|j=s\" => \
+\\$jobid, # JobId\n \"email=s\" => \\$p\
+arams{email}, # E-mail address\n \"trace\" \
+ => \\$trace, # SOAP trace\n \"sequence=s\\
+" => \\$sequence, # Query sequence\n );\n\\
+nmy $scriptName = basename($0, ());\nif($help || $\
+numOpts == 0) {\n &usage();\n exit(0);\n}\n\\
+nif($trace){\n print STDERR \"Tracing active\\n\
+\";\n SOAP::Lite->import(+trace => 'debug');\n}\
+\n\nmy $soap = SOAP::Lite\n ->service($WSDL)\n \
+ ->proxy('http://localhost/',\n #proxy => ['h\
+ttp' => 'http://your.proxy.server/'], # HTTP proxy\
+\n timeout => 600, # HTTP connection timeout\n \
+ )\n ->on_fault(sub { # SOAP fault handler\n \
my $soap = shift;\n my $res = shift;\
\n # Throw an exception for all faults\n \
if(ref($res) eq '') {\n die($res);\
\n } else {\n die($res->faultstr\
ing);\n }\n return new SOAP::SOM;\n \
}\n );\n\nif( !($polljob || $stat\
-us) &&\n !( defined($params{'sequence1'}) && de\
-fined($params{'sequence2'}) )\n ) {\n print \
-STDERR 'Error: bad option combination', \"\\n\";\n\
- &usage();\n exit(1);\n}\nelsif($polljob && \
-defined($jobid)) {\n print \"Getting results fo\
-r job $jobid\\n\";\n getResults($jobid);\n}\nel\
-sif($status && defined($jobid)) {\n print STDER\
-R \"Getting status for job $jobid\\n\";\n my $r\
-esult = $soap->checkStatus($jobid);\n print STD\
-OUT \"$result\", \"\\n\";\n if($result eq 'DONE\
-') {\n print STDERR \"To get results: $scriptName \
---polljob --jobid $jobid\\n\";\n }\n}\nelse {\n\
- if(-f $params{'sequence1'}) {\n $params{'seque\
-nce1'} = read_file($params{'sequence1'});\n }\n\
- if(-f $params{'sequence2'}) {\n $params{'seque\
-nce2'} = read_file($params{'sequence2'});\n }\n\
-\n my $jobid;\n my $paramsData = SOAP::Data-\
->name('params')->type(map=>\\%params);\n # For \
-SOAP::Lite 0.60 and earlier parameters are passed \
-directly\n if($SOAP::Lite::VERSION eq '0.60' ||\
- $SOAP::Lite::VERSION =~ /0\\.[1-5]/) {\n $\
-jobid = $soap->runDaliLite($paramsData);\n }\n \
- # For SOAP::Lite 0.69 and later parameter handl\
-ing is different, so pass\n # undef's for templ\
-ated params, and then pass the formatted args.\n \
- else {\n $jobid = $soap->runDaliLite(unde\
-f,\n $paramsData);\n }\n\n if (defin\
-ed($async)) {\n print STDOUT $jobid, \"\\n\";\n \
- print STDERR \"To check status: $scriptName -\
--status --jobid $jobid\\n\";\n } else { # Synch\
-ronous mode\n print STDERR \"JobId: $jobid\\
-\n\";\n sleep 1;\n getResults($jobid\
-);\n }\n}\n\nsub clientPoll($) {\n my $jobid\
+us || $ids) &&\n !( defined($ARGV[0]) || define\
+d($sequence) )\n ) {\n print STDERR 'Error: \
+bad option combination', \"\\n\";\n &usage();\n\
+ exit(1);\n}\nelsif($polljob && defined($jobid)\
+) {\n print \"Getting results for job $jobid\\n\
+\";\n getResults($jobid);\n}\nelsif($status && \
+defined($jobid)) {\n print STDERR \"Getting sta\
+tus for job $jobid\\n\";\n my $result = $soap->\
+checkStatus($jobid);\n print STDOUT \"$result\\\
+n\";\n if($result eq 'DONE') {\n print STDERR \\
+"To get results: $scriptName --polljob --jobid $jo\
+bid\\n\";\n }\n} \nelsif($ids && defined($jobi\
+d)) {\n print STDERR \"Getting ids from job $jo\
+bid\\n\";\n getIds($jobid);\n}\nelse {\n # P\
+repare input data\n my $content;\n my (@cont\
+ents) = ();\n if(-f $ARGV[0] || $ARGV[0] eq '-'\
+) { \n $content={type=>'sequence',content=>read_fi\
+le($ARGV[0])}; \n }\n if($sequence) { \n if(\
+-f $sequence || $sequence eq '-') { \n $conten\
+t={type=>'sequence',content=>read_file($ARGV[0])};\
+ \n } else {\n $content={type=>'sequence',cont\
+ent=>$sequence};\n }\n }\n push @contents, $\
+content;\n\n # Submit the job\n my $paramsDa\
+ta = SOAP::Data->name('params')->type(map=>\\%para\
+ms);\n my $contentData = SOAP::Data->name('cont\
+ent')->value(\\@contents);\n # For SOAP::Lite 0\
+.60 and earlier parameters are passed directly\n \
+ if($SOAP::Lite::VERSION eq '0.60' || $SOAP::Lite\
+::VERSION =~ /0\\.[1-5]/) {\n $jobid = $soa\
+p->runWUBlast($paramsData, $contentData);\n }\n\
+ # For SOAP::Lite 0.69 and later parameter hand\
+ling is different, so pass\n # undef's for temp\
+lated params, and then pass the formatted args.\n \
+ else {\n $jobid = $soap->runWUBlast(unde\
+f, undef,\n $paramsData, $contentData);\n \
+ }\n\n # Asynchronous mode: output jobid and ex\
+it.\n if (defined($async)) {\n print STDOUT $jo\
+bid, \"\\n\";\n print STDERR \"To check sta\
+tus: $scriptName --status --jobid $jobid\\n\";\n \
+ }\n # Synchronous mode: try to get results\n \
+ else {\n print STDERR \"JobId: $jobid\\n\
+\";\n sleep 1;\n getResults($jobid);\
+\n }\n}\n\nsub getIds($) {\n my $jobid = shi\
+ft;\n my $results = $soap->getIds($jobid);\n \
+ for my $result (@$results){\n print \"$result\\n\\
+";\n }\n}\n\nsub clientPoll($) {\n my $jobid\
= shift;\n my $result = 'PENDING';\n # Chec\
-k status and wait if not finished\n #print STDE\
-RR \"Checking status: $jobid\\n\";\n while($res\
-ult eq 'RUNNING' || $result eq 'PENDING') {\n \
- $result = $soap->checkStatus($jobid);\n \
-print STDERR \"$result\\n\";\n if($result e\
-q 'RUNNING' || $result eq 'PENDING') {\n \
- # Wait before polling again.\n sleep \
-$checkInterval;\n }\n }\n}\n\nsub getRes\
-ults($) {\n $jobid = shift;\n # Check status\
-, and wait if not finished\n clientPoll($jobid)\
-;\n # Use JobId if output file name is not defi\
-ned\n unless(defined($outfile)) {\n $out\
-file=$jobid;\n }\n # Get list of data types\\
-n my $resultTypes = $soap->getResults($jobid);\\
-n # Get the data and write it to a file\n if\
-(defined($outformat)) { # Specified data type\n \
- my $selResultType;\n foreach my $resul\
-tType (@$resultTypes) {\n if($resultTyp\
-e->{type} eq $outformat) {\n $selRe\
-sultType = $resultType;\n }\n }\\
-n $res=$soap->poll($jobid, $selResultType->\
-{type});\n write_file($outfile.'.'.$selResu\
-ltType->{ext}, $res);\n } else { # Data types a\
-vailable\n # Write a file for each output t\
-ype\n for my $resultType (@$resultTypes){\n\
- #print \"Getting $resultType->{type}\\\
-n\";\n $res=$soap->poll($jobid, $result\
-Type->{type});\n write_file($outfile.'.\
-'.$resultType->{ext}, $res);\n }\n }\n}\\
-n\nsub read_file($) {\n my $filename = shift;\n\
- open(FILE, $filename);\n my $content;\n \
-my $buffer;\n while(sysread(FILE, $buffer, 1024\
-)) {\n $content.= $buffer;\n }\n close(FILE)\
-;\n return $content;\n}\n\nsub write_file($$) {\
-\n my ($tmp,$entity) = @_;\n print STDERR \"\
-Creating result file: \".$tmp.\"\\n\";\n unless\
-(open (FILE, \">$tmp\")) {\n return 0;\n }\n \
- syswrite(FILE, $entity);\n close (FILE);\n \
-return 1;\n}\n\nsub usage {\n print STDERR <<EO\
-F\nDaliLite\n========\n\nPairwise comparison of pr\
-otein structures\n\n[Required]\n\n --pdb1 \
- : str : PDB ID for structure 1\n --pdb2 \
- : str : PDB ID for structure 2\n\n\
-[Optional]\n\n --chain1 : str : Cha\
-in identifer in structure 1\n --chain2 \
- : str : Chain identifer in structure 2\n\n[Gen\
-eral]\n\n -h, --help : : prints t\
-his help text\n -S, --email : str : us\
-er email address\n -a, --async : :\
- asynchronous submission\n --status \
-: : poll for the status of a job\n --pol\
-ljob : : poll for the results of a jo\
-b\n -j, --jobid : str : jobid for an a\
-synchronous job\n -O, --outfile : str : \
-file name for results (default is jobid)\n --\
-trace : : show SOAP messages being in\
-terchanged \n\nSynchronous job:\n\n The results/e\
-rrors are returned as soon as the job is finished.\
-\n Usage: $scriptName --email <your\\@email> [opt\
-ions] pdbFile [--outfile string]\n Returns: saves\
- the results to disk\n\nAsynchronous job:\n\n Use\
- this if you want to retrieve the results at a lat\
-er time. The results \n are stored for up to 24 h\
-ours. \n The asynchronous submission mode is reco\
-mmended when users are submitting \n batch jobs o\
-r large database searches \n Usage: $scriptName -\
--email <your\\@email> --async [options] pdbFile\n \
- Returns: jobid\n\n Use the jobid to query for th\
-e status of the job. \n Usage: $scriptName --stat\
-us --jobid <jobId>\n Returns: string indicating t\
+k status and wait if not finished\n while($resu\
+lt eq 'RUNNING' || $result eq 'PENDING') {\n \
+ $result = $soap->checkStatus($jobid);\n p\
+rint STDERR \"$result\\n\";\n if($result eq\
+ 'RUNNING' || $result eq 'PENDING') {\n \
+ # Wait before polling again.\n sleep $\
+checkInterval;\n }\n }\n}\n\nsub getResu\
+lts($) {\n my $jobid = shift;\n my $res;\n \
+ # Check status, and wait if not finished\n cl\
+ientPoll($jobid);\n # Use JobId if output file \
+name is not defined\n unless(defined($outfile))\
+ {\n $outfile=$jobid;\n }\n # Get lis\
+t of data types\n my $resultTypes = $soap->getR\
+esults($jobid);\n # Get the data and write it t\
+o a file\n if(defined($outformat)) { # Specifie\
+d data type\n if($outformat eq 'xml') {$outformat \
+= 'toolxml';}\n if($outformat eq 'txt') {$outforma\
+t = 'tooloutput';}\n my $selResultType;\n \
+ foreach my $resultType (@$resultTypes) {\n \
+ if($resultType->{type} eq $outformat) {\\
+n $selResultType = $resultType;\n \
+ }\n }\n $res=$soap->poll($\
+jobid, $selResultType->{type});\n if($outfile eq '\
+-') {\n write_file($outfile, $res);\n } else \
+{\n write_file($outfile.'.'.$selResultType->{e\
+xt}, $res);\n }\n } else { # Data types availab\
+le\n # Write a file for each output type\n \
+ for my $resultType (@$resultTypes){\n \
+ #print STDERR \"Getting $resultType->{type}\\
+\n\";\n $res=$soap->poll($jobid, $resul\
+tType->{type});\n if($outfile eq '-') {\n wri\
+te_file($outfile, $res);\n } else {\n write_f\
+ile($outfile.'.'.$resultType->{ext}, $res);\n \
+}\n }\n }\n}\n\nsub read_file($) {\n \
+my $filename = shift;\n my ($content, $buffer);\
+\n if($filename eq '-') {\n while(sysread(STDIN\
+, $buffer, 1024)) {\n $content .= $buffer;\n }\
+\n }\n else { # File\n open(FILE, $filename)\
+ or die \"Error: unable to open input file\";\n wh\
+ile(sysread(FILE, $buffer, 1024)) {\n $content\
+ .= $buffer;\n }\n close(FILE);\n }\n return\
+ $content;\n}\n\nsub write_file($$) {\n my ($fi\
+lename, $data) = @_;\n print STDERR 'Creating r\
+esult file: ' . $filename . \"\\n\";\n if($file\
+name eq '-') {\n print STDOUT $data;\n }\n e\
+lse {\n open(FILE, \">$filename\") or die \"Error:\
+ unable to open output file\";\n syswrite(FILE, $d\
+ata);\n close(FILE);\n }\n}\n\nsub usage {\n \
+ print STDERR <<EOF\nWU-BLAST\n========\n\nRapid s\
+equence database search programs utilizing the BLA\
+ST algorithm.\n \n[Required]\n\n --email \
+ : str : user email address \n -p, --program \
+ : str : BLAST program to use: blastn, blastp,\
+ blastx, \n tblastn or\
+ tblastx\n -D, --database : str : database to\
+ search\n seqFile : file : query sequen\
+ce data file (\"-\" for STDIN)\n\n[Optional]\n\n \
+-m, --matrix : str : scoring matrix\n -E, --\
+exp : real : 0<E<= 1000. Statistical significa\
+nce threshold\n for re\
+porting database sequence matches.\n -e, --echofi\
+lter : : display the filtered query sequence\
+ in the output\n -f, --filter : str : activa\
+tes filtering of the query sequence\n -b, --align\
+ments : int : number of alignments to be reporte\
+d\n -s, --scores : int : number of scores to\
+ be reported\n -S, --sensitivity : str :\n -t, \
+--sort : str :\n -T, --stats : str :\\
+n -d, --strand : str : DNA strand to search\
+ with in DNA vs. DNA searches \n -c, --topcombon \
+ : :\n\n[General] \n\n -h, --help : \
+ : prints this help text\n -a, --async : \
+ : forces to make an asynchronous query\n \
+ --status : : poll for the status of a jo\
+b\n --polljob : : poll for the result\
+s of a job\n -j, --jobid : str : jobid that\
+ was returned when an asynchronous job \n \
+ was submitted.\n -O, --outfile\
+ : str : name of the file results should be wr\
+itten to \n (default is\
+ based on the jobid; \"-\" for STDOUT)\n -o, --ou\
+tformat : str : txt or xml output (no file is wr\
+itten)\n --trace : : show SOAP messag\
+es being interchanged \n\nSynchronous job:\n\n Th\
+e results/errors are returned as soon as the job i\
+s finished.\n Usage: $scriptName --email <your\\@\
+email> [options...] seqFile\n Returns: saves the \
+results to disk\n\nAsynchronous job:\n\n Use this\
+ if you want to retrieve the results at a later ti\
+me. The results \n are stored for up to 24 hours.\
+ \n The asynchronous submission mode is recommend\
+ed when users are submitting \n batch jobs or lar\
+ge database searches \n Usage: $scriptName --asyn\
+c --email <your\\@email> [options...] seqFile\n R\
+eturns : jobid\n\n Use the jobid to query for the\
+ status of the job. \n Usage: $scriptName --statu\
+s --jobid <jobId>\n Returns : string indicating t\
he status of the job:\n DONE - job has finished\
\n RUNNING - job is running\n NOT_FOUND - jo\
b cannot be found\n ERROR - the jobs has encoun\
tered an error\n\n When done, use the jobid to re\
trieve the status of the job. \n Usage: $scriptNa\
-me --polljob --jobid <jobId> [--outfile string]\n\\
-n[Help]\n\n For more detailed help information re\
-fer to\n http://www.ebi.ac.uk/DaliLite/\nEOF\n;\n\
-}\n","my $WSDL = 'http://www.ebi.ac.uk/Tools/webse\
-rvices/wsdl/WSWUBlast.wsdl';\n\nuse strict;\nuse S\
-OAP::Lite;\nuse Getopt::Long qw(:config no_ignore_\
-case bundling);\nuse File::Basename;\n\nmy $checkI\
-nterval = 15;\n\nmy $numOpts = scalar(@ARGV);\nmy \
-($outfile, $outformat, $help, $async, $polljob, $s\
-tatus, $ids, $jobid, $trace, $sequence);\nmy %para\
-ms= ( # Defaults\n 'async' => 1, # Force int\
-o async mode\n 'exp' => 10.0, # E-value thre\
-shold\n 'numal' => 50, # Maximum number of a\
-lignments\n 'scores' => 100, # Maximum numbe\
-r of scores\n );\nGetOptions( # Map the\
- options into variables\n \"program|p=s\" =\
-> \\$params{program}, # BLAST program\n \"datab\
-ase|D=s\" => \\$params{database}, # Search data\
-base\n \"matrix|m=s\" => \\$params{matrix}\
-, # Scoring matrix\n \"exp|E=f\" => \\$\
-params{exp}, # E-value threshold\n \"echofilter\
-|e\" => \\$params{echofilter}, # Display filter\
-ed sequence\n \"filter|f=s\" => \\$params{\
-filter}, # Low complexity filter name\n \"align\
-ments|b=i\" => \\$params{numal}, # Number of alig\
-nments\n \"scores|s=i\" => \\$params{score\
-s}, # Number of scores\n \"sensitivity|S=s\" =>\
- \\$params{sensitivity}, # Search sensitivity\n \
- \"sort|t=s\" => \\$params{sort}, # Sort hit\
-s by...\n \"stats|T=s\" => \\$params{stat\
-s}, # Scoring statistic to use\n \"strand|d=s\"\
- => \\$params{strand}, # Strand to use in DNA\
- vs. DNA search\n \"topcombon|c=i\" => \\$par\
-ams{topcombon}, # Consistent sets of HSPs\n \"o\
-utfile=s\" => \\$outfile, # Output file\n \
- \"outformat|o=s\" => \\$outformat, # Output for\
-mat\n \"help|h\" => \\$help, # Usage info\
-\n \"async|a\" => \\$async, # Asynchronou\
-s mode\n \"polljob\" => \\$polljob, # Get\
- results\n \"status\" => \\$status, # Get\
- job status\n \"ids\" => \\$ids, # \
-Get ids from result\n \"jobid|j=s\" => \\\
-$jobid, # JobId\n \"email=s\" => \\$par\
-ams{email}, # E-mail address\n \"trace\" \
- => \\$trace, # SOAP trace\n \"sequence=s\" \
- => \\$sequence, # Query sequence\n );\n\nm\
-y $scriptName = basename($0, ());\nif($help || $nu\
-mOpts == 0) {\n &usage();\n exit(0);\n}\n\ni\
-f($trace){\n print STDERR \"Tracing active\\n\"\
-;\n SOAP::Lite->import(+trace => 'debug');\n}\n\
-\nmy $soap = SOAP::Lite\n ->service($WSDL)\n \
- ->proxy('http://localhost/',\n #proxy => ['htt\
-p' => 'http://your.proxy.server/'], # HTTP proxy\n\
- timeout => 600, # HTTP connection timeout\n \
- )\n ->on_fault(sub { # SOAP fault handler\n \
- my $soap = shift;\n my $res = shift;\n\
- # Throw an exception for all faults\n \
- if(ref($res) eq '') {\n die($res);\n\
- } else {\n die($res->faultstrin\
-g);\n }\n return new SOAP::SOM;\n \
- }\n );\n\nif( !($polljob || $status\
- || $ids) &&\n !( defined($ARGV[0]) || defined(\
-$sequence) )\n ) {\n print STDERR 'Error: ba\
-d option combination', \"\\n\";\n &usage();\n \
- exit(1);\n}\nelsif($polljob && defined($jobid)) \
-{\n print \"Getting results for job $jobid\\n\"\
-;\n getResults($jobid);\n}\nelsif($status && de\
-fined($jobid)) {\n print STDERR \"Getting statu\
-s for job $jobid\\n\";\n my $result = $soap->ch\
-eckStatus($jobid);\n print STDOUT \"$result\\n\\
-";\n if($result eq 'DONE') {\n print STDERR \"T\
-o get results: $scriptName --polljob --jobid $jobi\
-d\\n\";\n }\n} \nelsif($ids && defined($jobid)\
-) {\n print STDERR \"Getting ids from job $jobi\
-d\\n\";\n getIds($jobid);\n}\nelse {\n # Pre\
-pare input data\n my $content;\n my (@conten\
-ts) = ();\n if(-f $ARGV[0] || $ARGV[0] eq '-') \
-{ \n $content={type=>'sequence',content=>read_file\
-($ARGV[0])}; \n }\n if($sequence) { \n if(-f\
- $sequence || $sequence eq '-') { \n $content=\
-{type=>'sequence',content=>read_file($ARGV[0])}; \\
-n } else {\n $content={type=>'sequence',conten\
-t=>$sequence};\n }\n }\n push @contents, $co\
-ntent;\n\n # Submit the job\n my $paramsData\
- = SOAP::Data->name('params')->type(map=>\\%params\
-);\n my $contentData = SOAP::Data->name('conten\
-t')->value(\\@contents);\n # For SOAP::Lite 0.6\
-0 and earlier parameters are passed directly\n \
-if($SOAP::Lite::VERSION eq '0.60' || $SOAP::Lite::\
-VERSION =~ /0\\.[1-5]/) {\n $jobid = $soap-\
->runWUBlast($paramsData, $contentData);\n }\n \
- # For SOAP::Lite 0.69 and later parameter handli\
-ng is different, so pass\n # undef's for templa\
-ted params, and then pass the formatted args.\n \
- else {\n $jobid = $soap->runWUBlast(undef,\
- undef,\n $paramsData, $contentData);\n }\
-\n\n # Asynchronous mode: output jobid and exit\
-.\n if (defined($async)) {\n print STDOUT $jobi\
-d, \"\\n\";\n print STDERR \"To check statu\
-s: $scriptName --status --jobid $jobid\\n\";\n \
-}\n # Synchronous mode: try to get results\n \
- else {\n print STDERR \"JobId: $jobid\\n\"\
-;\n sleep 1;\n getResults($jobid);\n\
- }\n}\n\nsub getIds($) {\n my $jobid = shift\
+me --polljob --jobid <jobId> [--outfile string]\n \
+ Returns: saves the results to disk\n\n[Help]\n\nF\
+or more detailed help information refer to \nhttp:\
+//www.ebi.ac.uk/blast2/WU-Blast2_Help_frame.html\n\
+ \nEOF\n;\n}\n","\nmy $WSDL = 'http://www.ebi.ac.u\
+k/Tools/webservices/wsdl/WSBlastpgp.wsdl';\n\nuse \
+SOAP::Lite;\nuse Getopt::Long qw(:config no_ignore\
+_case bundling);\nuse File::Basename;\n\nmy $check\
+Interval = 15;\n\nmy %params=(\n 'async' => '1\
+', # Use async mode and simulate sync mode in clie\
+nt\n );\nGetOptions(\n \"mode=s\" \
+ => \\$params{mode}, # Search mode: PSI-Blast or P\
+HI-Blast\n \"database|d=s\" => \\$params{da\
+tabase}, # Database to search\n \"matrix|M=s\" \
+ => \\$params{matrix},# Scoring maxtrix\n \
+\"exp|e=f\" => \\$params{exp}, # E-value\\
+n \"expmulti|h=f\" => \\$params{expmulti}, \
+# E-value\n \"filter|F=s\" => \\$params{f\
+ilter}, # Low complexity filter\n \"dropoff|X=i\
+\" => \\$params{dropoff}, # Dropoff score\n \
+ \"finaldropoff|Z=i\" => \\$params{finaldropoff},\
+ # Final dropoff score\n \"scores|v=i\" =\
+> \\$params{scores}, # Max number of scores\n \\
+"align=i\" => \\$params{align}, # Alignme\
+nt view\n \"startregion|S=i\" => \\$params{sta\
+rtregion}, # Start of region in query\n \"endre\
+gion|H=i\" => \\$params{endregion}, # End of re\
+gion in query\n \"maxpasses|j=i\" => \\$para\
+ms{maxpasses}, # Number of PSI iterations\n \"o\
+pengap|G=i\" => \\$params{opengap}, # Gap ope\
+n penalty\n \"extendgap|E=i\" => \\$params{e\
+xtendgap}, # Gap extension penalty\n \"pattern=\
+s\" => \\$params{pattern}, # PHI-BLAST patt\
+ern\n \"usagemode|p=s\" => \\$params{usagemo\
+de}, # PHI-BLAST program\n \"appxml=s\" \
+ => \\$params{appxml}, # Application XML\n \"se\
+quence=s\" => \\$sequence, # Query sequence\\
+n \"help\" => \\$help, # Usage info\n \
+ \"polljob\" => \\$polljob, # Get results\n\
+ \"status\" => \\$status, # Get status\n\
+ \"ids\" => \\$ids, # Get ids from\
+ result\n \"jobid=s\" => \\$jobid, # J\
+obId\n \"outfile=s\" => \\$outfile, # Ou\
+tput filename\n \"outformat|o=s\" => \\$outf\
+ormat, # Output file format\n \"async|a\" \
+ => \\$async, # Async submission\n \"email=s\"\
+ => \\$params{email}, # User e-mail addre\
+ss\n \"trace\" => \\$trace, # Show S\
+OAP messages\n );\n\nmy $scriptName = basename(\
+$0, ());\nif($help) {\n &usage();\n exit(0);\
+\n}\n\nif ($trace){\n print \"Tracing active\\n\
+\";\n SOAP::Lite->import(+trace => 'debug');\n}\
+\n\nmy $soap = SOAP::Lite\n ->service($WSDL)\n \
+ ->on_fault(sub {\n my $soap = shift;\n \
+ my $res = shift;\n # Throw an excepti\
+on for all faults\n if(ref($res) eq '') {\n\
+ die($res);\n } else {\n \
+ die($res->faultstring);\n }\n re\
+turn new SOAP::SOM;\n }\n );\n\ni\
+f( !($polljob || $status || $ids) &&\n !( (defi\
+ned($ARGV[0]) && -f $ARGV[0]) || defined($sequence\
+) )\n ) {\n print STDERR 'Error: bad option \
+combination', \"\\n\";\n &usage();\n exit(1)\
+;\n}\nelsif($polljob && defined($jobid)) {\n pr\
+int \"Getting results for job $jobid\\n\";\n ge\
+tResults($jobid);\n}\nelsif($status && defined($jo\
+bid)) {\n print STDERR \"Getting status for job\
+ $jobid\\n\";\n my $result = $soap->checkStatus\
+($jobid);\n print STDOUT $result, \"\\n\";\n \
+ if($result eq 'DONE') {\n print STDERR \"To get r\
+esults: $scriptName --polljob --jobid $jobid\\n\";\
+\n }\n} \nelsif($ids && defined($jobid)) {\n \
+ print STDERR \"Getting ids from job $jobid\\n\";\
+\n getIds($jobid);\n}\nelse {\n if(-f $ARGV[\
+0]) { \n $content={type=>'sequence', content=>read\
+_file($ARGV[0])}; \n }\n if($sequence) { \n \
+if(-f $sequence) {\n $content={type=>'sequence\
+', content=>read_file($sequence)}; \n } else {\n \
+ $content={type=>'sequence', content=>$sequence}\
+;\n }\n }\n push @content, $content;\n\n \
+my $jobid;\n my $paramsData = SOAP::Data->name(\
+'params')->type(map=>\\%params);\n my $contentD\
+ata = SOAP::Data->name('content')->value(\\@conten\
+t);\n # For SOAP::Lite 0.60 and earlier paramet\
+ers are passed directly\n if($SOAP::Lite::VERSI\
+ON eq '0.60' || $SOAP::Lite::VERSION =~ /0\\.[1-5]\
+/) {\n $jobid = $soap->runBlastpgp($paramsD\
+ata, $contentData);\n }\n # For SOAP::Lite 0\
+.69 and later parameter handling is different, so \
+pass\n # undef's for templated params, and then\
+ pass the formatted args.\n else {\n $jo\
+bid = $soap->runBlastpgp(undef, undef,\n $p\
+aramsData, $contentData);\n }\n\n if (define\
+d($async)) {\n print STDOUT $jobid, \"\\n\";\n \
+ print STDERR \"To check status: $scriptName --\
+status --jobid $jobid\\n\";\n } else { # Synchr\
+onous mode\n print STDERR \"JobId: $jobid\\\
+n\";\n sleep 1;\n getResults($jobid)\
+;\n }\n}\n\nsub getIds($) {\n $jobid = shift\
;\n my $results = $soap->getIds($jobid);\n f\
-or my $result (@$results){\n print \"$result\\n\";\
-\n }\n}\n\nsub clientPoll($) {\n my $jobid =\
- shift;\n my $result = 'PENDING';\n # Check \
-status and wait if not finished\n while($result\
- eq 'RUNNING' || $result eq 'PENDING') {\n \
-$result = $soap->checkStatus($jobid);\n pri\
-nt STDERR \"$result\\n\";\n if($result eq '\
-RUNNING' || $result eq 'PENDING') {\n #\
- Wait before polling again.\n sleep $ch\
-eckInterval;\n }\n }\n}\n\nsub getResult\
-s($) {\n my $jobid = shift;\n my $res;\n \
-# Check status, and wait if not finished\n clie\
-ntPoll($jobid);\n # Use JobId if output file na\
-me is not defined\n unless(defined($outfile)) {\
-\n $outfile=$jobid;\n }\n # Get list \
-of data types\n my $resultTypes = $soap->getRes\
-ults($jobid);\n # Get the data and write it to \
-a file\n if(defined($outformat)) { # Specified \
-data type\n if($outformat eq 'xml') {$outformat = \
-'toolxml';}\n if($outformat eq 'txt') {$outformat \
-= 'tooloutput';}\n my $selResultType;\n \
- foreach my $resultType (@$resultTypes) {\n \
- if($resultType->{type} eq $outformat) {\n \
- $selResultType = $resultType;\n \
- }\n }\n $res=$soap->poll($jo\
-bid, $selResultType->{type});\n if($outfile eq '-'\
-) {\n write_file($outfile, $res);\n } else {\\
-n write_file($outfile.'.'.$selResultType->{ext\
-}, $res);\n }\n } else { # Data types available\
-\n # Write a file for each output type\n \
- for my $resultType (@$resultTypes){\n \
- #print STDERR \"Getting $resultType->{type}\\n\
-\";\n $res=$soap->poll($jobid, $resultT\
-ype->{type});\n if($outfile eq '-') {\n write\
-_file($outfile, $res);\n } else {\n write_fil\
-e($outfile.'.'.$resultType->{ext}, $res);\n }\\
-n }\n }\n}\n\nsub read_file($) {\n my\
- $filename = shift;\n my ($content, $buffer);\n\
- if($filename eq '-') {\n while(sysread(STDIN, \
-$buffer, 1024)) {\n $content .= $buffer;\n }\n\
- }\n else { # File\n open(FILE, $filename) o\
-r die \"Error: unable to open input file\";\n whil\
-e(sysread(FILE, $buffer, 1024)) {\n $content .\
-= $buffer;\n }\n close(FILE);\n }\n return $\
-content;\n}\n\nsub write_file($$) {\n my ($file\
-name, $data) = @_;\n print STDERR 'Creating res\
-ult file: ' . $filename . \"\\n\";\n if($filena\
-me eq '-') {\n print STDOUT $data;\n }\n els\
-e {\n open(FILE, \">$filename\") or die \"Error: u\
-nable to open output file\";\n syswrite(FILE, $dat\
-a);\n close(FILE);\n }\n}\n\nsub usage {\n p\
-rint STDERR <<EOF\nWU-BLAST\n========\n\nRapid seq\
-uence database search programs utilizing the BLAST\
- algorithm.\n \n[Required]\n\n --email \
- : str : user email address \n -p, --program \
- : str : BLAST program to use: blastn, blastp, b\
-lastx, \n tblastn or t\
-blastx\n -D, --database : str : database to s\
-earch\n seqFile : file : query sequence\
- data file (\"-\" for STDIN)\n\n[Optional]\n\n -m\
-, --matrix : str : scoring matrix\n -E, --ex\
-p : real : 0<E<= 1000. Statistical significanc\
-e threshold\n for repo\
-rting database sequence matches.\n -e, --echofilt\
-er : : display the filtered query sequence i\
-n the output\n -f, --filter : str : activate\
-s filtering of the query sequence\n -b, --alignme\
-nts : int : number of alignments to be reported\\
-n -s, --scores : int : number of scores to b\
-e reported\n -S, --sensitivity : str :\n -t, --\
-sort : str :\n -T, --stats : str :\n \
- -d, --strand : str : DNA strand to search w\
-ith in DNA vs. DNA searches \n -c, --topcombon \
-: :\n\n[General] \n\n -h, --help : \
- : prints this help text\n -a, --async : \
- : forces to make an asynchronous query\n -\
--status : : poll for the status of a job\\
-n --polljob : : poll for the results \
-of a job\n -j, --jobid : str : jobid that w\
-as returned when an asynchronous job \n \
- was submitted.\n -O, --outfile \
- : str : name of the file results should be writ\
-ten to \n (default is b\
-ased on the jobid; \"-\" for STDOUT)\n -o, --outf\
-ormat : str : txt or xml output (no file is writ\
-ten)\n --trace : : show SOAP messages\
- being interchanged \n\nSynchronous job:\n\n The \
-results/errors are returned as soon as the job is \
-finished.\n Usage: $scriptName --email <your\\@em\
-ail> [options...] seqFile\n Returns: saves the re\
-sults to disk\n\nAsynchronous job:\n\n Use this i\
-f you want to retrieve the results at a later time\
-. The results \n are stored for up to 24 hours. \\
-n The asynchronous submission mode is recommended\
- when users are submitting \n batch jobs or large\
- database searches \n Usage: $scriptName --async \
---email <your\\@email> [options...] seqFile\n Ret\
-urns : jobid\n\n Use the jobid to query for the s\
-tatus of the job. \n Usage: $scriptName --status \
---jobid <jobId>\n Returns : string indicating the\
- status of the job:\n DONE - job has finished\n\
- RUNNING - job is running\n NOT_FOUND - job \
-cannot be found\n ERROR - the jobs has encounte\
-red an error\n\n When done, use the jobid to retr\
-ieve the status of the job. \n Usage: $scriptName\
- --polljob --jobid <jobId> [--outfile string]\n R\
-eturns: saves the results to disk\n\n[Help]\n\nFor\
- more detailed help information refer to \nhttp://\
-www.ebi.ac.uk/blast2/WU-Blast2_Help_frame.html\n \\
-nEOF\n;\n}\n","\nmy $WSDL = 'http://www.ebi.ac.uk/\
-Tools/webservices/wsdl/WSBlastpgp.wsdl';\n\nuse SO\
-AP::Lite;\nuse Getopt::Long qw(:config no_ignore_c\
-ase bundling);\nuse File::Basename;\n\nmy $checkIn\
-terval = 15;\n\nmy %params=(\n 'async' => '1',\
- # Use async mode and simulate sync mode in client\
-\n );\nGetOptions(\n \"mode=s\" =\
-> \\$params{mode}, # Search mode: PSI-Blast or PHI\
--Blast\n \"database|d=s\" => \\$params{data\
-base}, # Database to search\n \"matrix|M=s\" \
- => \\$params{matrix},# Scoring maxtrix\n \"\
-exp|e=f\" => \\$params{exp}, # E-value\n \
- \"expmulti|h=f\" => \\$params{expmulti}, # \
-E-value\n \"filter|F=s\" => \\$params{fil\
-ter}, # Low complexity filter\n \"dropoff|X=i\"\
- => \\$params{dropoff}, # Dropoff score\n \
-\"finaldropoff|Z=i\" => \\$params{finaldropoff}, #\
- Final dropoff score\n \"scores|v=i\" => \
-\\$params{scores}, # Max number of scores\n \"a\
-lign=i\" => \\$params{align}, # Alignment\
- view\n \"startregion|S=i\" => \\$params{start\
-region}, # Start of region in query\n \"endregi\
-on|H=i\" => \\$params{endregion}, # End of regi\
-on in query\n \"maxpasses|j=i\" => \\$params\
-{maxpasses}, # Number of PSI iterations\n \"ope\
-ngap|G=i\" => \\$params{opengap}, # Gap open \
-penalty\n \"extendgap|E=i\" => \\$params{ext\
-endgap}, # Gap extension penalty\n \"pattern=s\\
-" => \\$params{pattern}, # PHI-BLAST patter\
-n\n \"usagemode|p=s\" => \\$params{usagemode\
-}, # PHI-BLAST program\n \"appxml=s\" =\
-> \\$params{appxml}, # Application XML\n \"sequ\
-ence=s\" => \\$sequence, # Query sequence\n \
- \"help\" => \\$help, # Usage info\n \\
-"polljob\" => \\$polljob, # Get results\n \
- \"status\" => \\$status, # Get status\n \
- \"ids\" => \\$ids, # Get ids from r\
-esult\n \"jobid=s\" => \\$jobid, # Job\
-Id\n \"outfile=s\" => \\$outfile, # Outp\
-ut filename\n \"outformat|o=s\" => \\$outfor\
-mat, # Output file format\n \"async|a\" \
-=> \\$async, # Async submission\n \"email=s\" \
- => \\$params{email}, # User e-mail address\
-\n \"trace\" => \\$trace, # Show SOA\
-P messages\n );\n\nmy $scriptName = basename($0\
-, ());\nif($help) {\n &usage();\n exit(0);\n\
-}\n\nif ($trace){\n print \"Tracing active\\n\"\
-;\n SOAP::Lite->import(+trace => 'debug');\n}\n\
-\nmy $soap = SOAP::Lite\n ->service($WSDL)\n \
- ->on_fault(sub {\n my $soap = shift;\n \
- my $res = shift;\n # Throw an exception\
- for all faults\n if(ref($res) eq '') {\n \
- die($res);\n } else {\n \
- die($res->faultstring);\n }\n retu\
-rn new SOAP::SOM;\n }\n );\n\nif(\
- !($polljob || $status || $ids) &&\n !( (define\
-d($ARGV[0]) && -f $ARGV[0]) || defined($sequence) \
-)\n ) {\n print STDERR 'Error: bad option co\
-mbination', \"\\n\";\n &usage();\n exit(1);\\
-n}\nelsif($polljob && defined($jobid)) {\n prin\
-t \"Getting results for job $jobid\\n\";\n getR\
-esults($jobid);\n}\nelsif($status && defined($jobi\
-d)) {\n print STDERR \"Getting status for job $\
-jobid\\n\";\n my $result = $soap->checkStatus($\
-jobid);\n print STDOUT $result, \"\\n\";\n i\
-f($result eq 'DONE') {\n print STDERR \"To get res\
-ults: $scriptName --polljob --jobid $jobid\\n\";\n\
- }\n} \nelsif($ids && defined($jobid)) {\n \
-print STDERR \"Getting ids from job $jobid\\n\";\n\
- getIds($jobid);\n}\nelse {\n if(-f $ARGV[0]\
-) { \n $content={type=>'sequence', content=>read_f\
-ile($ARGV[0])}; \n }\n if($sequence) { \n if\
-(-f $sequence) {\n $content={type=>'sequence',\
- content=>read_file($sequence)}; \n } else {\n \
- $content={type=>'sequence', content=>$sequence};\\
-n }\n }\n push @content, $content;\n\n my\
- $jobid;\n my $paramsData = SOAP::Data->name('p\
-arams')->type(map=>\\%params);\n my $contentDat\
-a = SOAP::Data->name('content')->value(\\@content)\
-;\n # For SOAP::Lite 0.60 and earlier parameter\
-s are passed directly\n if($SOAP::Lite::VERSION\
- eq '0.60' || $SOAP::Lite::VERSION =~ /0\\.[1-5]/)\
- {\n $jobid = $soap->runBlastpgp($paramsDat\
-a, $contentData);\n }\n # For SOAP::Lite 0.6\
-9 and later parameter handling is different, so pa\
-ss\n # undef's for templated params, and then p\
-ass the formatted args.\n else {\n $jobi\
-d = $soap->runBlastpgp(undef, undef,\n $par\
-amsData, $contentData);\n }\n\n if (defined(\
-$async)) {\n print STDOUT $jobid, \"\\n\";\n \
- print STDERR \"To check status: $scriptName --st\
-atus --jobid $jobid\\n\";\n } else { # Synchron\
-ous mode\n print STDERR \"JobId: $jobid\\n\\
-";\n sleep 1;\n getResults($jobid);\\
-n }\n}\n\nsub getIds($) {\n $jobid = shift;\\
-n my $results = $soap->getIds($jobid);\n for\
- $result (@$results){\n print \"$result\\n\";\n \
- }\n}\n\nsub clientPoll($) {\n my $jobid = shif\
-t;\n my $result = 'PENDING';\n # Check statu\
-s and wait if not finished\n #print STDERR \"Ch\
-ecking status: $jobid\\n\";\n while($result eq \
-'RUNNING' || $result eq 'PENDING') {\n $res\
-ult = $soap->checkStatus($jobid);\n print S\
-TDERR \"$result\\n\";\n if($result eq 'RUNN\
-ING' || $result eq 'PENDING') {\n # Wai\
-t before polling again.\n sleep $checkI\
-nterval;\n }\n }\n}\n\nsub getResults($)\
- {\n $jobid = shift;\n # Check status, and w\
-ait if not finished\n clientPoll($jobid);\n \
-# Use JobId if output file name is not defined\n \
- unless(defined($outfile)) {\n $outfile=$j\
-obid;\n }\n # Get list of data types\n my\
- $resultTypes = $soap->getResults($jobid);\n # \
-Get the data and write it to a file\n if(define\
-d($outformat)) { # Specified data type\n my\
- $selResultType;\n foreach my $resultType (\
-@$resultTypes) {\n if($resultType->{typ\
-e} eq $outformat) {\n $selResultTyp\
-e = $resultType;\n }\n }\n \
- $res=$soap->poll($jobid, $selResultType->{type})\
-;\n write_file($outfile.'.'.$selResultType-\
->{ext}, $res);\n } else { # Data types availabl\
-e\n # Write a file for each output type\n \
- for my $resultType (@$resultTypes){\n \
- #print \"Getting $resultType->{type}\\n\";\n \
- $res=$soap->poll($jobid, $resultType->{\
-type});\n write_file($outfile.'.'.$resu\
-ltType->{ext}, $res);\n }\n }\n}\n\nsub \
-read_file($) {\n my $filename = shift;\n ope\
-n(FILE, $filename);\n my $content;\n my $buf\
-fer;\n while(sysread(FILE, $buffer, 1024)) {\n \
-$content.= $buffer;\n }\n close(FILE); \n \
- return $content;\n}\n\nsub write_file($$) {\n \
- my ($tmp,$entity) = @_;\n print STDERR \"Creat\
-ing result file: \".$tmp.\"\\n\";\n unless(open\
- (FILE, \">$tmp\")) {\n return 0;\n }\n sysw\
-rite(FILE, $entity);\n close (FILE);\n retur\
-n 1;\n}\n\nsub usage {\n print STDERR <<EOF\nBl\
-astpgp\n========\n \nThe blastpgp program implem\
-ents the PSI-BLAST and PHI-BLAST variations\nof NC\
-BI BLAST.\n\nFor more detailed help information re\
-fer to\nhttp://www.ebi.ac.uk/blastpgp/blastpsi_hel\
-p_frame.html\n \nBlastpgp specific options:\n\n[Re\
-quired]\n\n --mode : str : search\
- mode to use: PSI-Blast or PHI-Blast\n -d, --data\
-base : str : protein database to search\n \
- seqFile : file : query sequence\n\n\
-[Optional]\n\n -M, --matrix : str : sco\
-ring matrix\n -e, --exp : real : Expe\
-ctation value\n -h, --expmulti : real : th\
-reshold (multipass model)\n -F, --filter \
- : str : filter query sequence with SEG [T,F]\n \
--m, --align : int : alignment view opti\
-on:\n 0 - pairwise\
-, 1 - M/S identities,\n \
- 2 - M/S non-identities, 3 - Flat identities,\
-\n 4 - Flat non-id\
-entities\n -G, --opengap : int : cost to\
- open a gap\n -E, --extendgap : int : cost\
- to extend a gap\n -g, --gapalign : str :\
- Gapped [T,F]\n -v, --scores : int : nu\
-mber of scores to be reported\n -j, --maxpasses \
- : int : number of iterations\n -X, --dropof\
-f : int : Dropoff score\n -Z, --finaldro\
-poff : int : Dropoff for final alignment\n -S\
-, --startregion : int : Start of required reg\
-ion in query\n -H, --endregion : int : End\
- of required region in query\n -k, --pattern \
- : str : Hit File (PHI-BLAST only)\n -p, --us\
-agemode : str : Program option (PHI-BLAST o\
-nly):\n blastpgp, \
-patseedp, seedp\n\n[General]\n\n --help \
- : : prints this help text\n -a, --asyn\
-c : : forces to make an asynchronou\
-s query\n --status : : poll for\
- the status of a job\n --polljob : \
- : poll for the results of a job\n --jobid \
- : str : jobid of an asynchronous job\n \
- --ids : : get hit identifier\
-s for result \n -O, --outfile : str : na\
-me of the file results should be written to\n \
- (default is based on t\
-he jobid)\n -o, --outformat : str : txt or\
- xml output (no file is written)\n --trace \
- : : show SOAP messages being intercha\
-nged\n\nSynchronous job:\n\n The results/errors a\
-re returned as soon as the job is finished.\n Usa\
-ge: blastpgp.pl --email <your@email> [options...] \
-seqfile\n Returns: saves the results to disk\n\nA\
-synchronous job:\n\n Use this if you want to retr\
-ieve the results at a later time. The results\n a\
-re stored for up to 24 hours.\n The asynchronous \
-submission mode is recommended when users are subm\
-itting\n batch jobs or large database searches\n \
- Usage: blastpgp.pl --email <your@email> --async [\
-options...] seqFile\n Returns: jobid\n\n Use the\
- jobid to query for the status of the job.\n Usag\
-e: blastpgp.pl --status --jobid <jobId>\n Returns\
-: string indicating the status of the job\n DON\
-E - job has finished\n RUNNING - job is running\
-\n NOT_FOUND - job cannot be found\n ERROR -\
- the jobs has encountered an error\n\n When done,\
- use the jobid to retrieve the results of the job.\
-\n Usage: blastpgp.pl --polljob --jobid <jobId> [\
---outfile <fileName>]\n Returns: saves the result\
-s to disk\nEOF\n;\n}\n","\n=head1 NAME\n\nncbiblas\
-t_lwp.pl\n\n=head1 DESCRIPTION\n\nNCBI BLAST REST \
-web service Perl client using L<LWP>.\n\nTested wi\
-th:\n\n=over\n\n=item *\nL<LWP> 5.79, L<XML::Simpl\
-e> 2.12 and Perl 5.8.3\n\n=item *\nL<LWP> 5.805, L\
-<XML::Simple> 2.14 and Perl 5.8.7\n\n=item *\nL<LW\
-P> 5.820, L<XML::Simple> 2.18 and Perl 5.10.0 (Ubu\
-ntu 9.04)\n\n=back\n\nFor further information see:\
-\n\n=over\n\n=item *\nL<http://www.ebi.ac.uk/Tools\
-/webservices/services/sss/ncbi_blast_rest>\n\n=ite\
-m *\nL<http://www.ebi.ac.uk/Tools/webservices/tuto\
-rials/perl>\n\n=back\n\n=head1 VERSION\n\n$Id: ncb\
-iblast_lwp.pl 1317 2009-09-03 15:44:11Z hpm $\n\n=\
-cut\n\nuse strict;\nuse warnings;\n\nuse English;\\
-nuse LWP;\nuse XML::Simple;\nuse Getopt::Long qw(:\
-config no_ignore_case bundling);\nuse File::Basena\
-me;\nuse Data::Dumper;\n\nmy $baseUrl = 'http://ww\
-w.ebi.ac.uk/Tools/services/rest/ncbiblast';\n\nmy \
-$checkInterval = 3;\n\nmy $outputLevel = 1;\n\nmy \
-$numOpts = scalar(@ARGV);\nmy %params = ( 'debugLe\
-vel' => 0 );\n\nmy %tool_params = ();\nGetOptions(\
-\n\n # Tool specific options\n 'program|p=s' => \\
-\$tool_params{'program'}, # blastp, blastn, blas\
-tx, etc.\n 'database|D=s' => \\$params{'database'}\
-, # Database(s) to search\n 'matrix|m=s' =\
-> \\$tool_params{'matrix'}, # Scoring martix to\
- use\n 'exp|E=f' => \\$tool_params{'exp'}, \
- # E-value threshold\n 'filter|f=s' => \\$too\
-l_params{'filter'}, # Low complexity filter\n '\
-align|A=i' => \\$tool_params{'align'}, # Pa\
-irwise alignment format\n 'scores|s=i' => \\$too\
-l_params{'scores'}, # Number of scores\n 'align\
-ments|n=i' => \\$tool_params{'alignments'}, # Nu\
-mber of alignments\n 'dropoff|d=i' => \\$tool_p\
-arams{'dropoff'}, # Dropoff score\n 'match_sc\
-ores=s' => \\$tool_params{'match_scores'}, # Match\
-/missmatch scores\n 'match|u=i' => \\$params{\
-'match'}, # Match score\n 'mismatch|v=\
-i' => \\$params{'mismatch'}, # Mismatch\
- score\n 'gapopen|o=i' => \\$tool_params{'gapop\
-en'}, # Open gap penalty\n 'gapext|x=i' =\
-> \\$tool_params{'gapext'}, # Gap extension \
-penality\n 'gapalign|g' => \\$tool_params{'gap\
-align'}, # Optimise gap alignments\n 'stype=s'\
- => \\$tool_params{'stype'}, # Sequence type\n \
-'seqrange=s' => \\$tool_params{'seqrange'}, # Q\
-uery subsequence\n 'sequence=s' => \\$params{'sequ\
-ence'}, # Query sequence\n 'multifasta' =>\
- \\$params{'multifasta'}, # Multiple fasta i\
-nput\n\n # Compatability options, old command-line\
-\n 'numal|n=i' => \\$params{'numal'}, #\
- Number of alignments\n 'opengap|o=i' => \\$para\
-ms{'opengap'}, # Open gap penalty\n 'extendga\
-p|x=i' => \\$params{'extendgap'}, # Gap extensi\
-on penality\n \n # Generic options\n 'email=s' \
- => \\$params{'email'}, # User e-mail a\
-ddress\n 'title=s' => \\$params{'title'}, \
- # Job title\n 'outfile=s' => \\$params{\
-'outfile'}, # Output file name\n 'outformat\
-=s' => \\$params{'outformat'}, # Output fil\
-e type\n 'jobid=s' => \\$params{'jobid'}, \
- # JobId\n 'help|h' => \\$params{'hel\
-p'}, # Usage help\n 'async' => \\
-\$params{'async'}, # Asynchronous submiss\
-ion\n 'polljob' => \\$params{'polljob'}, \
- # Get results\n 'resultTypes' => \\$params{'\
-resultTypes'}, # Get result types\n 'status' \
- => \\$params{'status'}, # Get status\\
-n 'params' => \\$params{'params'}, \
-# List input parameters\n 'paramDetail=s' => \\$pa\
-rams{'paramDetail'}, # Get details for paramete\
-r\n 'quiet' => \\$params{'quiet'}, \
- # Decrease output level\n 'verbose' => \\$\
-params{'verbose'}, # Increase output level\\
-n 'debugLevel=i' => \\$params{'debugLevel'}, \
-# Debug output level\n 'baseUrl=s' => \\$baseU\
-rl, # Base URL for service.\n);\n\
-if ( $params{'verbose'} ) { $outputLevel++ }\nif (\
- $params{'$quiet'} ) { $outputLevel-- }\n\n&print\
-_debug_message( 'MAIN', 'LWP::VERSION: ' . $LWP::V\
-ERSION,\n 1 );\n\n&print_debug_message( 'MAIN', \"\
-params:\\n\" . Dumper( \\%params ), 11 )\
-;\n&print_debug_message( 'MAIN', \"tool_params:\\n\
-\" . Dumper( \\%tool_params ), 11 );\n\nmy $script\
-Name = basename( $0, () );\n\nif ( $params{'help'}\
- || $numOpts == 0 ) {\n &usage();\n exit(0);\n}\n\\
-n&print_debug_message( 'MAIN', 'baseUrl: ' . $base\
-Url, 1 );\n\nif (\n !(\n $params{'polljob'}\n \
- || $params{'resultTypes'}\n || $params{'status'}\
-\n || $params{'params'}\n || $params{'paramDetai\
-l'}\n )\n && !( defined( $ARGV[0] ) || defined( $p\
-arams{'sequence'} ) )\n )\n{\n\n # Bad argument c\
-ombination, so print error message and usage\n pri\
-nt STDERR 'Error: bad option combination', \"\\n\"\
-;\n &usage();\n exit(1);\n}\n\nelsif ( $params{'pa\
-rams'} ) {\n &print_tool_params();\n}\n\nelsif ( $\
-params{'paramDetail'} ) {\n &print_param_details( \
-$params{'paramDetail'} );\n}\n\nelsif ( $params{'s\
-tatus'} && defined( $params{'jobid'} ) ) {\n &prin\
-t_job_status( $params{'jobid'} );\n}\n\nelsif ( $p\
-arams{'resultTypes'} && defined( $params{'jobid'} \
-) ) {\n &print_result_types( $params{'jobid'} );\n\
-}\n\nelsif ( $params{'polljob'} && defined( $param\
-s{'jobid'} ) ) {\n &get_results( $params{'jobid'} \
-);\n}\n\nelse {\n\n # Multiple input sequence mode\
-, assume fasta format.\n if ( $params{'multifasta'\
-} ) {\n &multi_submit_job();\n }\n\n # Entry iden\
-tifier list file.\n elsif (( defined( $params{'seq\
-uence'} ) && $params{'sequence'} =~ m/^\\@/ )\n |\
-| ( defined( $ARGV[0] ) && $ARGV[0] =~ m/^\\@/ ) )\
-\n {\n my $list_filename = $params{'sequence'} ||\
- $ARGV[0];\n $list_filename =~ s/^\\@//;\n &list\
-_file_submit_job($list_filename);\n }\n\n # Defaul\
-t: single sequence/identifier.\n else {\n\n # Loa\
-d the sequence data and submit.\n &submit_job( &l\
-oad_data() );\n }\n}\n\n=head1 FUNCTIONS\n\n=cut\n\
-\n\n=head2 rest_request()\n\nPerform a REST reques\
-t.\n\n my $response_str = &rest_request($url);\n\\
-n=cut\n\nsub rest_request {\n print_debug_message(\
- 'rest_request', 'Begin', 11 );\n my $requestUrl =\
- shift;\n print_debug_message( 'rest_request', 'UR\
-L: ' . $requestUrl, 11 );\n\n # Create a user agen\
-t\n my $ua = LWP::UserAgent->new();\n '$Revision: \
-1317 $' =~ m/(\\d+)/;\n $ua->agent(\"EBI-Sample-Cl\
-ient/$1 ($scriptName; $OSNAME) \" . $ua->agent());\
-\n $ua->env_proxy;\n\n # Perform the request\n my \
-$response = $ua->get($requestUrl);\n print_debug_m\
-essage( 'rest_request', 'HTTP status: ' . $respons\
-e->code,\n 11 );\n\n # Check for HTTP error codes\
-\n if ( $response->is_error ) {\n $response->cont\
-ent() =~ m/<h1>([^<]+)<\\/h1>/;\n die 'http statu\
-s: ' . $response->code . ' ' . $response->message \
-. ' ' . $1;\n }\n print_debug_message( 'rest_requ\
-est', 'End', 11 );\n\n # Return the response data\\
-n return $response->content();\n}\n\n=head2 rest_g\
-et_parameters()\n\nGet list of tool parameter name\
-s.\n\n my (@param_list) = &rest_get_parameters();\
-\n\n=cut\n\nsub rest_get_parameters {\n print_debu\
-g_message( 'rest_get_parameters', 'Begin', 1 );\n \
-my $url = $baseUrl . '/parameters/'\
-;\n my $param_list_xml_str = rest_request($url);\n\
- my $param_list_xml = XMLin($param_list_xml_st\
-r);\n my (@param_list) = @{ $param_list_xml-\
->{'id'} };\n print_debug_message( 'rest_get_parame\
-ters', 'End', 1 );\n return (@param_list);\n}\n\n=\
-head2 rest_get_parameter_details()\n\nGet details \
-of a tool parameter.\n\n my $paramDetail = &rest_\
-get_parameter_details($param_name);\n\n=cut\n\nsub\
- rest_get_parameter_details {\n print_debug_messag\
-e( 'rest_get_parameter_details', 'Begin', 1 );\n m\
-y $parameterId = shift;\n print_debug_message( 're\
-st_get_parameter_details',\n 'parameterId: ' . $p\
-arameterId, 1 );\n my $url = $bas\
-eUrl . '/parameterdetails/' . $parameterId;\n my $\
-param_detail_xml_str = rest_request($url);\n my $p\
-aram_detail_xml = XMLin($param_detail_xml_str)\
-;\n print_debug_message( 'rest_get_parameter_detai\
-ls', 'End', 1 );\n return ($param_detail_xml);\n}\\
-n\n=head2 rest_run()\n\nSubmit a job.\n\n my $job\
-_id = &rest_run($email, $title, \\%params );\n\n=c\
-ut\n\nsub rest_run {\n print_debug_message( 'rest_\
-run', 'Begin', 1 );\n my $email = shift;\n my $ti\
-tle = shift;\n my $params = shift;\n print_debug_\
-message( 'rest_run', 'email: ' . $email, 1 );\n if\
- ( defined($title) ) {\n print_debug_message( 're\
-st_run', 'title: ' . $title, 1 );\n }\n print_debu\
-g_message( 'rest_run', 'params: ' . Dumper($params\
-), 1 );\n\n # User agent to perform http requests\\
-n my $ua = LWP::UserAgent->new();\n $ua->env_proxy\
-;\n\n # Clean up parameters\n my (%tmp_params) = %\
-{$params};\n $tmp_params{'email'} = $email;\n $tmp\
-_params{'title'} = $title;\n foreach my $param_nam\
-e ( keys(%tmp_params) ) {\n if ( !defined( $tmp_p\
-arams{$param_name} ) ) {\n delete $tmp_params{$p\
-aram_name};\n }\n }\n\n # Submit the job as a POS\
-T\n my $url = $baseUrl . '/run';\n my $response = \
-$ua->post( $url, \\%tmp_params );\n print_debug_me\
-ssage( 'rest_run', 'HTTP status: ' . $response->co\
-de, 11 );\n print_debug_message( 'rest_run',\n 'r\
-equest: ' . $response->request()->content(), 11 );\
-\n\n # Check for HTTP error codes\n if ( $response\
-->is_error ) {\n $response->content() =~ m/<h1>([\
-^<]+)<\\/h1>/;\n die 'http status: ' . $response-\
->code . ' ' . $response->message . ' ' . $1;\n }\\
-n\n # The job id is returned\n my $job_id = $respo\
-nse->content();\n print_debug_message( 'rest_run',\
- 'End', 1 );\n return $job_id;\n}\n\n=head2 rest_g\
-et_status()\n\nCheck the status of a job.\n\n my \
-$status = &rest_get_status($job_id);\n\n=cut\n\nsu\
-b rest_get_status {\n print_debug_message( 'rest_g\
-et_status', 'Begin', 1 );\n my $job_id = shift;\n \
-print_debug_message( 'rest_get_status', 'jobid: ' \
-. $job_id, 2 );\n my $status_str = 'UNKNOWN';\n my\
- $url = $baseUrl . '/status/' . $job_id;\n \
-$status_str = &rest_request($url);\n print_debug_m\
-essage( 'rest_get_status', 'status_str: ' . $statu\
-s_str, 2 );\n print_debug_message( 'rest_get_statu\
-s', 'End', 1 );\n return $status_str;\n}\n\n=head2\
- rest_get_result_types()\n\nGet list of result typ\
-es for finished job.\n\n my (@result_types) = &re\
-st_get_result_types($job_id);\n\n=cut\n\nsub rest_\
-get_result_types {\n print_debug_message( 'rest_ge\
-t_result_types', 'Begin', 1 );\n my $job_id = shif\
-t;\n print_debug_message( 'rest_get_result_types',\
- 'jobid: ' . $job_id, 2 );\n my (@resultTypes);\n \
-my $url = $baseUrl . '/result\
-types/' . $job_id;\n my $result_type_list_xml_str \
-= &rest_request($url);\n my $result_type_list_xml \
- = XMLin($result_type_list_xml_str);\n (@result\
-Types) = @{ $result_type_list_xml->{'type'} };\n p\
-rint_debug_message( 'rest_get_result_types',\n sc\
-alar(@resultTypes) . ' result types', 2 );\n print\
-_debug_message( 'rest_get_result_types', 'End', 1 \
-);\n return (@resultTypes);\n}\n\n=head2 rest_get_\
-result()\n\nGet result data of a specified type fo\
-r a finished job.\n\n my $result = rest_get_resul\
-t($job_id, $result_type);\n\n=cut\n\nsub rest_get_\
-result {\n print_debug_message( 'rest_get_result',\
- 'Begin', 1 );\n my $job_id = shift;\n my $type \
-= shift;\n print_debug_message( 'rest_get_result',\
- 'jobid: ' . $job_id, 1 );\n print_debug_message( \
-'rest_get_result', 'type: ' . $type, 1 );\n my \
-$url = $baseUrl . '/result/' . $job_id . '/' . \
-$type;\n my $result = &rest_request($url);\n print\
-_debug_message( 'rest_get_result', length($result)\
- . ' characters',\n 1 );\n print_debug_message( '\
-rest_get_result', 'End', 1 );\n return $result;\n}\
-\n\n\n=head2 print_debug_message()\n\nPrint debug \
-message at specified debug level.\n\n &print_debu\
-g_message($method_name, $message, $level);\n\n=cut\
-\n\nsub print_debug_message {\n my $function_name \
-= shift;\n my $message = shift;\n my $level \
- = shift;\n if ( $level <= $params{'debugLe\
-vel'} ) {\n print STDERR '[', $function_name, '()\
-] ', $message, \"\\n\";\n }\n}\n\n=head2 print_too\
-l_params()\n\nPrint list of tool parameters.\n\n \
-&print_tool_params();\n\n=cut\n\nsub print_tool_pa\
-rams {\n print_debug_message( 'print_tool_params',\
- 'Begin', 1 );\n my (@param_list) = &rest_get_para\
-meters();\n foreach my $param ( sort(@param_list) \
-) {\n print $param, \"\\n\";\n }\n print_debug_me\
-ssage( 'print_tool_params', 'End', 1 );\n}\n\n=hea\
-d2 print_param_details()\n\nPrint details of a too\
-l parameter.\n\n &print_param_details($param_name\
-);\n\n=cut\n\nsub print_param_details {\n print_de\
-bug_message( 'print_param_details', 'Begin', 1 );\\
-n my $paramName = shift;\n print_debug_message( 'p\
-rint_param_details', 'paramName: ' . $paramName, 2\
- );\n my $paramDetail = &rest_get_parameter_detail\
-s($paramName);\n print $paramDetail->{'name'}, \"\\
-\t\", $paramDetail->{'type'}, \"\\n\";\n print $pa\
-ramDetail->{'description'}, \"\\n\";\n foreach my \
-$value ( @{ $paramDetail->{'values'}->{'value'} } \
-) {\n print $value->{'value'};\n if ( $value->{'\
-defaultValue'} eq 'true' ) {\n print \"\\t\", 'd\
-efault';\n }\n print \"\\n\";\n print \"\\t\", \
-$value->{'label'}, \"\\n\";\n }\n print_debug_mess\
-age( 'print_param_details', 'End', 1 );\n}\n\n=hea\
-d2 print_job_status()\n\nPrint status of a job.\n\\
-n &print_job_status($job_id);\n\n=cut\n\nsub prin\
-t_job_status {\n print_debug_message( 'print_job_s\
-tatus', 'Begin', 1 );\n my $jobid = shift;\n print\
-_debug_message( 'print_job_status', 'jobid: ' . $j\
-obid, 1 );\n if ( $outputLevel > 0 ) {\n print ST\
-DERR 'Getting status for job ', $jobid, \"\\n\";\n\
- }\n my $result = &rest_get_status($jobid);\n prin\
-t \"$result\\n\";\n if ( $result eq 'FINISHED' && \
-$outputLevel > 0 ) {\n print STDERR \"To get resu\
-lts: $scriptName --polljob --jobid \" . $jobid\n \
- . \"\\n\";\n }\n print_debug_message( 'print_job\
-_status', 'End', 1 );\n}\n\n=head2 print_result_ty\
-pes()\n\nPrint available result types for a job.\n\
-\n &print_result_types($job_id);\n\n=cut\n\nsub p\
-rint_result_types {\n print_debug_message( 'result\
-_types', 'Begin', 1 );\n my $jobid = shift;\n prin\
-t_debug_message( 'result_types', 'jobid: ' . $jobi\
-d, 1 );\n if ( $outputLevel > 0 ) {\n print STDER\
-R 'Getting result types for job ', $jobid, \"\\n\"\
-;\n }\n my $status = &rest_get_status($jobid);\n i\
-f ( $status eq 'PENDING' || $status eq 'RUNNING' )\
- {\n print STDERR 'Error: Job status is ', $statu\
-s,\n '. To get result types the job must be fin\
-ished.', \"\\n\";\n }\n else {\n my (@resultTypes\
-) = &rest_get_result_types($jobid);\n if ( $outpu\
-tLevel > 0 ) {\n print STDOUT 'Available result \
-types:', \"\\n\";\n }\n foreach my $resultType (\
-@resultTypes) {\n print STDOUT $resultType->{'id\
-entifier'}, \"\\n\";\n if ( defined( $resultType\
-->{'label'} ) ) {\n print STDOUT \"\\t\", $resu\
-ltType->{'label'}, \"\\n\";\n }\n if ( defined\
-( $resultType->{'description'} ) ) {\n print ST\
-DOUT \"\\t\", $resultType->{'description'}, \"\\n\\
-";\n }\n if ( defined( $resultType->{'mediaTyp\
-e'} ) ) {\n print STDOUT \"\\t\", $resultType->\
-{'mediaType'}, \"\\n\";\n }\n if ( defined( $r\
-esultType->{'fileSuffix'} ) ) {\n print STDOUT \
-\"\\t\", $resultType->{'fileSuffix'}, \"\\n\";\n \
- }\n }\n if ( $status eq 'FINISHED' && $outputLe\
-vel > 0 ) {\n print STDERR \"\\n\", 'To get resu\
-lts:', \"\\n\",\n \" $scriptName --polljob --\
-jobid \" . $params{'jobid'} . \"\\n\",\n \" $\
-scriptName --polljob --outformat <type> --jobid \"\
-\n . $params{'jobid'} . \"\\n\";\n }\n }\n pr\
-int_debug_message( 'result_types', 'End', 1 );\n}\\
-n\n=head2 submit_job()\n\nSubmit a job to the serv\
-ice.\n\n &submit_job($seq);\n\n=cut\n\nsub submit\
-_job {\n print_debug_message( 'submit_job', 'Begin\
-', 1 );\n\n # Set input sequence\n $tool_params{'s\
-equence'} = shift;\n\n # Load parameters\n &load_p\
-arams();\n\n # Submit the job\n my $jobid = &rest_\
-run( $params{'email'}, $params{'title'}, \\%tool_p\
-arams );\n\n # Simulate sync/async mode\n if ( def\
-ined( $params{'async'} ) ) {\n print STDOUT $jobi\
-d, \"\\n\";\n if ( $outputLevel > 0 ) {\n print\
- STDERR\n \"To check status: $scriptName --sta\
-tus --jobid $jobid\\n\";\n }\n }\n else {\n if (\
- $outputLevel > 0 ) {\n print STDERR \"JobId: $j\
-obid\\n\";\n }\n sleep 1;\n &get_results($jobid\
-);\n }\n print_debug_message( 'submit_job', 'End',\
- 1 );\n}\n\n=head2 multi_submit_job()\n\nSubmit mu\
-ltiple jobs assuming input is a collection of fast\
-a formatted sequences.\n\n &multi_submit_job();\n\
-\n=cut\n\nsub multi_submit_job {\n print_debug_mes\
-sage( 'multi_submit_job', 'Begin', 1 );\n my $jobI\
-dForFilename = 1;\n $jobIdForFilename = 0 if ( def\
-ined( $params{'outfile'} ) );\n my (@filename_list\
-) = ();\n\n # Query sequence\n if ( defined( $ARGV\
-[0] ) ) { # Bare option\n if ( -f $ARGV[0] || \
-$ARGV[0] eq '-' ) { # File\n push( @filename_\
-list, $ARGV[0] );\n }\n }\n if ( $params{'sequenc\
-e'} ) { # Via --sequence\n if (\
- -f $params{'sequence'} || $params{'sequence'} eq \
-'-' ) { # File\n push( @filename_list, $param\
-s{'sequence'} );\n }\n }\n\n $/ = '>';\n foreach \
-my $filename (@filename_list) {\n open( my $INFIL\
-E, '<', $filename )\n or die \"Error: unable to\
- open file $filename ($!)\";\n while (<$INFILE>) \
-{\n my $seq = $_;\n $seq =~ s/>$//;\n if ( $\
-seq =~ m/(\\S+)/ ) {\n print STDERR \"Submittin\
-g job for: $1\\n\"\n if ( $outputLevel > 0 );\
-\n $seq = '>' . $seq;\n &print_debug_message\
-( 'multi_submit_job', $seq, 11 );\n &submit_job\
-($seq);\n $params{'outfile'} = undef if ( $jobI\
-dForFilename == 1 );\n }\n }\n close $INFILE;\\
-n }\n print_debug_message( 'multi_submit_job', 'En\
-d', 1 );\n}\n\n=head2 list_file_submit_job()\n\nSu\
-bmit multiple jobs using a file containing a list \
-of entry identifiers as \ninput.\n\n &list_file_s\
-ubmit_job($list_filename)\n\n=cut\n\nsub list_file\
-_submit_job {\n my $filename = shift;\n my\
- $jobIdForFilename = 1;\n $jobIdForFilename = 0 if\
- ( defined( $params{'outfile'} ) );\n\n # Iterate \
-over identifiers, submitting each job\n open( my $\
-LISTFILE, '<', $filename )\n or die 'Error: unab\
+or $result (@$results){\n print \"$result\\n\";\n \
+ }\n}\n\nsub clientPoll($) {\n my $jobid = sh\
+ift;\n my $result = 'PENDING';\n # Check sta\
+tus and wait if not finished\n #print STDERR \"\
+Checking status: $jobid\\n\";\n while($result e\
+q 'RUNNING' || $result eq 'PENDING') {\n $r\
+esult = $soap->checkStatus($jobid);\n print\
+ STDERR \"$result\\n\";\n if($result eq 'RU\
+NNING' || $result eq 'PENDING') {\n # W\
+ait before polling again.\n sleep $chec\
+kInterval;\n }\n }\n}\n\nsub getResults(\
+$) {\n $jobid = shift;\n # Check status, and\
+ wait if not finished\n clientPoll($jobid);\n \
+ # Use JobId if output file name is not defined\n\
+ unless(defined($outfile)) {\n $outfile=\
+$jobid;\n }\n # Get list of data types\n \
+my $resultTypes = $soap->getResults($jobid);\n \
+# Get the data and write it to a file\n if(defi\
+ned($outformat)) { # Specified data type\n \
+my $selResultType;\n foreach my $resultType\
+ (@$resultTypes) {\n if($resultType->{t\
+ype} eq $outformat) {\n $selResultT\
+ype = $resultType;\n }\n }\n \
+ $res=$soap->poll($jobid, $selResultType->{type\
+});\n write_file($outfile.'.'.$selResultTyp\
+e->{ext}, $res);\n } else { # Data types availa\
+ble\n # Write a file for each output type\n\
+ for my $resultType (@$resultTypes){\n \
+ #print \"Getting $resultType->{type}\\n\";\\
+n $res=$soap->poll($jobid, $resultType-\
+>{type});\n write_file($outfile.'.'.$re\
+sultType->{ext}, $res);\n }\n }\n}\n\nsu\
+b read_file($) {\n my $filename = shift;\n o\
+pen(FILE, $filename);\n my $content;\n my $b\
+uffer;\n while(sysread(FILE, $buffer, 1024)) {\\
+n $content.= $buffer;\n }\n close(FILE); \n\
+ return $content;\n}\n\nsub write_file($$) {\n \
+ my ($tmp,$entity) = @_;\n print STDERR \"Cre\
+ating result file: \".$tmp.\"\\n\";\n unless(op\
+en (FILE, \">$tmp\")) {\n return 0;\n }\n sy\
+swrite(FILE, $entity);\n close (FILE);\n ret\
+urn 1;\n}\n\nsub usage {\n print STDERR <<EOF\n\
+Blastpgp\n========\n \nThe blastpgp program impl\
+ements the PSI-BLAST and PHI-BLAST variations\nof \
+NCBI BLAST.\n\nFor more detailed help information \
+refer to\nhttp://www.ebi.ac.uk/blastpgp/blastpsi_h\
+elp_frame.html\n \nBlastpgp specific options:\n\n[\
+Required]\n\n --mode : str : sear\
+ch mode to use: PSI-Blast or PHI-Blast\n -d, --da\
+tabase : str : protein database to search\\
+n seqFile : file : query sequence\n\
+\n[Optional]\n\n -M, --matrix : str : s\
+coring matrix\n -e, --exp : real : Ex\
+pectation value\n -h, --expmulti : real : \
+threshold (multipass model)\n -F, --filter \
+ : str : filter query sequence with SEG [T,F]\n\
+ -m, --align : int : alignment view op\
+tion:\n 0 - pairwi\
+se, 1 - M/S identities,\n \
+ 2 - M/S non-identities, 3 - Flat identitie\
+s,\n 4 - Flat non-\
+identities\n -G, --opengap : int : cost \
+to open a gap\n -E, --extendgap : int : co\
+st to extend a gap\n -g, --gapalign : str \
+ : Gapped [T,F]\n -v, --scores : int : \
+number of scores to be reported\n -j, --maxpasses\
+ : int : number of iterations\n -X, --drop\
+off : int : Dropoff score\n -Z, --finald\
+ropoff : int : Dropoff for final alignment\n \
+-S, --startregion : int : Start of required r\
+egion in query\n -H, --endregion : int : E\
+nd of required region in query\n -k, --pattern \
+ : str : Hit File (PHI-BLAST only)\n -p, --\
+usagemode : str : Program option (PHI-BLAST\
+ only):\n blastpgp\
+, patseedp, seedp\n\n[General]\n\n --help \
+ : : prints this help text\n -a, --as\
+ync : : forces to make an asynchron\
+ous query\n --status : : poll f\
+or the status of a job\n --polljob : \
+ : poll for the results of a job\n --jobi\
+d : str : jobid of an asynchronous job\\
+n --ids : : get hit identifi\
+ers for result \n -O, --outfile : str : \
+name of the file results should be written to\n \
+ (default is based on\
+ the jobid)\n -o, --outformat : str : txt \
+or xml output (no file is written)\n --trace \
+ : : show SOAP messages being interc\
+hanged\n\nSynchronous job:\n\n The results/errors\
+ are returned as soon as the job is finished.\n U\
+sage: blastpgp.pl --email <your@email> [options...\
+] seqfile\n Returns: saves the results to disk\n\\
+nAsynchronous job:\n\n Use this if you want to re\
+trieve the results at a later time. The results\n \
+ are stored for up to 24 hours.\n The asynchronou\
+s submission mode is recommended when users are su\
+bmitting\n batch jobs or large database searches\\
+n Usage: blastpgp.pl --email <your@email> --async\
+ [options...] seqFile\n Returns: jobid\n\n Use t\
+he jobid to query for the status of the job.\n Us\
+age: blastpgp.pl --status --jobid <jobId>\n Retur\
+ns: string indicating the status of the job\n D\
+ONE - job has finished\n RUNNING - job is runni\
+ng\n NOT_FOUND - job cannot be found\n ERROR\
+ - the jobs has encountered an error\n\n When don\
+e, use the jobid to retrieve the results of the jo\
+b.\n Usage: blastpgp.pl --polljob --jobid <jobId>\
+ [--outfile <fileName>]\n Returns: saves the resu\
+lts to disk\nEOF\n;\n}\n","\n=head1 NAME\n\nncbibl\
+ast_lwp.pl\n\n=head1 DESCRIPTION\n\nNCBI BLAST (RE\
+ST) web service Perl client using L<LWP>.\n\nTeste\
+d with:\n\n=over\n\n=item *\nL<LWP> 5.79, L<XML::S\
+imple> 2.12 and Perl 5.8.3\n\n=item *\nL<LWP> 5.80\
+8, L<XML::Simple> 2.18 and Perl 5.8.8 (Ubuntu 8.04\
+ LTS)\n\n=item *\nL<LWP> 5.834, L<XML::Simple> 2.1\
+8 and Perl 5.10.1 (Ubuntu 10.04 LTS)\n\n=item *\nL\
+<LWP> 6.03, L<XML::Simple> 2.18 and Perl 5.14.2 (U\
+buntu 12.04 LTS)\n\n=back\n\nFor further informati\
+on see:\n\n=over\n\n=item *\nL<http://www.ebi.ac.u\
+k/Tools/webservices/services/sss/ncbi_blast_rest>\\
+n\n=item *\nL<http://www.ebi.ac.uk/Tools/webservic\
+es/tutorials/perl>\n\n=back\n\n=head1 LICENSE\n\nC\
+opyright 2012-2013 EMBL - European Bioinformatics \
+Institute\n\nLicensed under the Apache License, Ve\
+rsion 2.0 (the \"License\");\nyou may not use this\
+ file except in compliance with the License.\nYou \
+may obtain a copy of the License at\n\n http://\
+www.apache.org/licenses/LICENSE-2.0\n\nUnless requ\
+ired by applicable law or agreed to in writing, so\
+ftware\ndistributed under the License is distribut\
+ed on an \"AS IS\" BASIS,\nWITHOUT WARRANTIES OR C\
+ONDITIONS OF ANY KIND, either express or implied.\\
+nSee the License for the specific language governi\
+ng permissions and\nlimitations under the License.\
+\n\n=head1 VERSION\n\n$Id: ncbiblast_lwp.pl 2560 2\
+013-03-20 12:56:31Z hpm $\n\n=cut\n\nuse strict;\n\
+use warnings;\n\nuse English;\nuse LWP;\nuse XML::\
+Simple;\nuse Getopt::Long qw(:config no_ignore_cas\
+e bundling);\nuse File::Basename;\nuse Data::Dumpe\
+r;\n\nmy $baseUrl = 'http://www.ebi.ac.uk/Tools/se\
+rvices/rest/ncbiblast';\n\nmy $checkInterval = 3;\\
+n\nmy $outputLevel = 1;\n\nmy $numOpts = scalar(@A\
+RGV);\nmy %params = ( 'debugLevel' => 0 );\n\nmy %\
+tool_params = ();\nGetOptions(\n\n # Tool specific\
+ options\n 'program|p=s' => \\$tool_params{'progr\
+am'}, # blastp, blastn, blastx, etc.\n 'database\
+|D=s' => \\$params{'database'}, # Database(s\
+) to search\n 'matrix|m=s' => \\$tool_params{'ma\
+trix'}, # Scoring martix to use\n 'exp|E=f' \
+ => \\$tool_params{'exp'}, # E-value thresh\
+old\n 'filter|f=s' => \\$tool_params{'filter'}, \
+ # Low complexity filter\n 'align|A=i' => \\$\
+tool_params{'align'}, # Pairwise alignment for\
+mat\n 'scores|s=i' => \\$tool_params{'scores'}, \
+ # Number of scores\n 'alignments|n=i' => \\$too\
+l_params{'alignments'}, # Number of alignments\n\
+ 'dropoff|d=i' => \\$tool_params{'dropoff'}, \
+ # Dropoff score\n 'match_scores=s' => \\$tool_p\
+arams{'match_scores'}, # Match/missmatch scores\n \
+'match|u=i' => \\$params{'match'}, \
+ # Match score\n 'mismatch|v=i' => \\$params{'m\
+ismatch'}, # Mismatch score\n 'gapopen|o=\
+i' => \\$tool_params{'gapopen'}, # Open ga\
+p penalty\n 'gapext|x=i' => \\$tool_params{'ga\
+pext'}, # Gap extension penality\n 'gapalign\
+|g' => \\$tool_params{'gapalign'}, # Optim\
+ise gap alignments\n 'stype=s' => \\$tool_params{'\
+stype'}, # Sequence type\n 'seqrange=s' => \\$t\
+ool_params{'seqrange'}, # Query subsequence\n '\
+sequence=s' => \\$params{'sequence'}, # Qu\
+ery sequence\n 'multifasta' => \\$params{'multifas\
+ta'}, # Multiple fasta input\n\n # Compatabi\
+lity options, old command-line\n 'numal|n=i' =\
+> \\$params{'numal'}, # Number of alignment\
+s\n 'opengap|o=i' => \\$params{'opengap'}, \
+# Open gap penalty\n 'extendgap|x=i' => \\$params{\
+'extendgap'}, # Gap extension penality\n \n # G\
+eneric options\n 'email=s' => \\$params{'ema\
+il'}, # User e-mail address\n 'title=s' \
+ => \\$params{'title'}, # Job title\n\
+ 'outfile=s' => \\$params{'outfile'}, #\
+ Output file name\n 'outformat=s' => \\$params{'\
+outformat'}, # Output file type\n 'jobid=s' \
+ => \\$params{'jobid'}, # JobId\n 'he\
+lp|h' => \\$params{'help'}, # Usa\
+ge help\n 'async' => \\$params{'async'}, \
+ # Asynchronous submission\n 'polljob' \
+ => \\$params{'polljob'}, # Get results\n \
+'resultTypes' => \\$params{'resultTypes'}, # \
+Get result types\n 'status' => \\$params{'s\
+tatus'}, # Get status\n 'params' =>\
+ \\$params{'params'}, # List input paramet\
+ers\n 'paramDetail=s' => \\$params{'paramDetail'},\
+ # Get details for parameter\n 'quiet' \
+=> \\$params{'quiet'}, # Decrease output \
+level\n 'verbose' => \\$params{'verbose'}, \
+ # Increase output level\n 'debugLevel=i' =>\
+ \\$params{'debugLevel'}, # Debug output level\
+\n 'baseUrl=s' => \\$baseUrl, \
+ # Base URL for service.\n);\nif ( $params{'verbos\
+e'} ) { $outputLevel++ }\nif ( $params{'quiet'} ) \
+ { $outputLevel-- }\n\n&print_debug_message( 'MAIN\
+', 'LWP::VERSION: ' . $LWP::VERSION,\n 1 );\n\n&pr\
+int_debug_message( 'MAIN', \"params:\\n\" . Dumper\
+( \\%params ), 11 );\n&print_debug_messa\
+ge( 'MAIN', \"tool_params:\\n\" . Dumper( \\%tool_\
+params ), 11 );\n\nmy $ua;\n\nmy $scriptName = bas\
+ename( $0, () );\n\nif ( $params{'help'} || $numOp\
+ts == 0 ) {\n &usage();\n exit(0);\n}\n\n&print_de\
+bug_message( 'MAIN', 'baseUrl: ' . $baseUrl, 1 );\\
+n\nif (\n !(\n $params{'polljob'}\n || $param\
+s{'resultTypes'}\n || $params{'status'}\n || $pa\
+rams{'params'}\n || $params{'paramDetail'}\n )\n \
+&& !( defined( $ARGV[0] ) || defined( $params{'seq\
+uence'} ) )\n )\n{\n\n # Bad argument combination\
+, so print error message and usage\n print STDERR \
+'Error: bad option combination', \"\\n\";\n &usage\
+();\n exit(1);\n}\n\nelsif ( $params{'params'} ) {\
+\n &print_tool_params();\n}\n\nelsif ( $params{'pa\
+ramDetail'} ) {\n &print_param_details( $params{'p\
+aramDetail'} );\n}\n\nelsif ( $params{'status'} &&\
+ defined( $params{'jobid'} ) ) {\n &print_job_stat\
+us( $params{'jobid'} );\n}\n\nelsif ( $params{'res\
+ultTypes'} && defined( $params{'jobid'} ) ) {\n &p\
+rint_result_types( $params{'jobid'} );\n}\n\nelsif\
+ ( $params{'polljob'} && defined( $params{'jobid'}\
+ ) ) {\n &get_results( $params{'jobid'} );\n}\n\ne\
+lse {\n\n # Multiple input sequence mode, assume f\
+asta format.\n if ( $params{'multifasta'} ) {\n &\
+multi_submit_job();\n }\n\n # Entry identifier lis\
+t file.\n elsif (( defined( $params{'sequence'} ) \
+&& $params{'sequence'} =~ m/^\\@/ )\n || ( define\
+d( $ARGV[0] ) && $ARGV[0] =~ m/^\\@/ ) )\n {\n my\
+ $list_filename = $params{'sequence'} || $ARGV[0];\
+\n $list_filename =~ s/^\\@//;\n &list_file_subm\
+it_job($list_filename);\n }\n\n # Default: single \
+sequence/identifier.\n else {\n\n # Load the sequ\
+ence data and submit.\n &submit_job( &load_data()\
+ );\n }\n}\n\n=head1 FUNCTIONS\n\n=cut\n\n\n=head2\
+ rest_user_agent()\n\nGet a LWP UserAgent to use t\
+o perform REST requests.\n\n my $ua = &rest_user_\
+agent();\n\n=cut\n\nsub rest_user_agent() {\n prin\
+t_debug_message( 'rest_user_agent', 'Begin', 21 );\
+\n # Create an LWP UserAgent for making HTTP calls\
+.\n my $ua = LWP::UserAgent->new();\n # Set 'User-\
+Agent' HTTP header to identifiy the client.\n '$Re\
+vision: 2560 $' =~ m/(\\d+)/;\n $ua->agent(\"EBI-S\
+ample-Client/$1 ($scriptName; $OSNAME) \" . $ua->a\
+gent());\n # Configure HTTP proxy support from env\
+ironment.\n $ua->env_proxy;\n print_debug_message(\
+ 'rest_user_agent', 'End', 21 );\n return $ua;\n}\\
+n\n=head2 rest_error()\n\nCheck a REST response fo\
+r an error condition. An error is mapped to a die.\
+\n\n &rest_error($response, $content_data);\n\n=c\
+ut\n\nsub rest_error() {\n print_debug_message( 'r\
+est_error', 'Begin', 21 );\n my $response = shift;\
+\n my $contentdata;\n if(scalar(@_) > 0) {\n $con\
+tentdata = shift;\n }\n if(!defined($contentdata) \
+|| $contentdata eq '') {\n $contentdata = $respon\
+se->content();\n }\n # Check for HTTP error codes\\
+n if ( $response->is_error ) {\n my $error_messag\
+e = '';\n # HTML response.\n if( $contentdata =~\
+ m/<h1>([^<]+)<\\/h1>/ ) {\n $error_message = $1\
+;\n }\n # XML response.\n elsif($contentdata =\
+~ m/<description>([^<]+)<\\/description>/) {\n $\
+error_message = $1;\n }\n die 'http status: ' . \
+$response->code . ' ' . $response->message . ' ' \
+. $error_message;\n }\n print_debug_message( 'rest\
+_error', 'End', 21 );\n}\n\n=head2 rest_request()\\
+n\nPerform a REST request (HTTP GET).\n\n my $res\
+ponse_str = &rest_request($url);\n\n=cut\n\nsub re\
+st_request {\n print_debug_message( 'rest_request'\
+, 'Begin', 11 );\n my $requestUrl = shift;\n print\
+_debug_message( 'rest_request', 'URL: ' . $request\
+Url, 11 );\n\n # Get an LWP UserAgent.\n $ua = &re\
+st_user_agent() unless defined($ua);\n # Available\
+ HTTP compression methods.\n my $can_accept;\n eva\
+l {\n $can_accept = HTTP::Message::decodable()\
+;\n };\n $can_accept = '' unless defined($can_acce\
+pt);\n # Perform the request\n my $response = $ua-\
+>get($requestUrl,\n 'Accept-Encoding' => $can_acc\
+ept, # HTTP compression.\n );\n print_debug_messag\
+e( 'rest_request', 'HTTP status: ' . $response->co\
+de,\n 11 );\n print_debug_message( 'rest_request'\
+,\n 'response length: ' . length($response->conte\
+nt()), 11 );\n print_debug_message( 'rest_request'\
+,\n 'request:' .\"\\n\" . $response->request()->a\
+s_string(), 32 );\n print_debug_message( 'rest_req\
+uest',\n 'response: ' . \"\\n\" . $response->as_s\
+tring(), 32 );\n # Unpack possibly compressed resp\
+onse.\n my $retVal;\n if ( defined($can_accept) &&\
+ $can_accept ne '') {\n $retVal = $response->d\
+ecoded_content();\n }\n # If unable to decode use \
+orginal content.\n $retVal = $response->content() \
+unless defined($retVal);\n # Check for an error.\n\
+ &rest_error($response, $retVal);\n print_debug_me\
+ssage( 'rest_request', 'retVal: ' . $retVal, 12 );\
+\n print_debug_message( 'rest_request', 'End', 11 \
+);\n\n # Return the response data\n return $retVal\
+;\n}\n\n=head2 rest_get_parameters()\n\nGet list o\
+f tool parameter names.\n\n my (@param_list) = &r\
+est_get_parameters();\n\n=cut\n\nsub rest_get_para\
+meters {\n print_debug_message( 'rest_get_paramete\
+rs', 'Begin', 1 );\n my $url = $bas\
+eUrl . '/parameters/';\n my $param_list_xml_str = \
+rest_request($url);\n my $param_list_xml = XML\
+in($param_list_xml_str);\n my (@param_list) \
+= @{ $param_list_xml->{'id'} };\n print_debug_mess\
+age( 'rest_get_parameters', 'End', 1 );\n return (\
+@param_list);\n}\n\n=head2 rest_get_parameter_deta\
+ils()\n\nGet details of a tool parameter.\n\n my \
+$paramDetail = &rest_get_parameter_details($param_\
+name);\n\n=cut\n\nsub rest_get_parameter_details {\
+\n print_debug_message( 'rest_get_parameter_detail\
+s', 'Begin', 1 );\n my $parameterId = shift;\n pri\
+nt_debug_message( 'rest_get_parameter_details',\n \
+ 'parameterId: ' . $parameterId, 1 );\n my $url \
+ = $baseUrl . '/parameterdetails/' .\
+ $parameterId;\n my $param_detail_xml_str = rest_r\
+equest($url);\n my $param_detail_xml = XMLin($\
+param_detail_xml_str);\n print_debug_message( 'res\
+t_get_parameter_details', 'End', 1 );\n return ($p\
+aram_detail_xml);\n}\n\n=head2 rest_run()\n\nSubmi\
+t a job.\n\n my $job_id = &rest_run($email, $titl\
+e, \\%params );\n\n=cut\n\nsub rest_run {\n print_\
+debug_message( 'rest_run', 'Begin', 1 );\n my $ema\
+il = shift;\n my $title = shift;\n my $params = \
+shift;\n print_debug_message( 'rest_run', 'email: \
+' . $email, 1 );\n if ( defined($title) ) {\n pri\
+nt_debug_message( 'rest_run', 'title: ' . $title, \
+1 );\n }\n print_debug_message( 'rest_run', 'param\
+s: ' . Dumper($params), 1 );\n\n # Get an LWP User\
+Agent.\n $ua = &rest_user_agent() unless defined($\
+ua);\n\n # Clean up parameters\n my (%tmp_params) \
+= %{$params};\n $tmp_params{'email'} = $email;\n $\
+tmp_params{'title'} = $title;\n foreach my $param_\
+name ( keys(%tmp_params) ) {\n if ( !defined( $tm\
+p_params{$param_name} ) ) {\n delete $tmp_params\
+{$param_name};\n }\n }\n\n # Submit the job as a \
+POST\n my $url = $baseUrl . '/run';\n my $response\
+ = $ua->post( $url, \\%tmp_params );\n print_debug\
+_message( 'rest_run', 'HTTP status: ' . $response-\
+>code, 11 );\n print_debug_message( 'rest_run',\n \
+ 'request:' .\"\\n\" . $response->request()->as_st\
+ring(), 11 );\n print_debug_message( 'rest_run',\n\
+ 'response: ' . length($response->as_string()) . \
+\"\\n\" . $response->as_string(), 11 );\n\n # Chec\
+k for an error.\n &rest_error($response);\n\n # Th\
+e job id is returned\n my $job_id = $response->con\
+tent();\n print_debug_message( 'rest_run', 'End', \
+1 );\n return $job_id;\n}\n\n=head2 rest_get_statu\
+s()\n\nCheck the status of a job.\n\n my $status \
+= &rest_get_status($job_id);\n\n=cut\n\nsub rest_g\
+et_status {\n print_debug_message( 'rest_get_statu\
+s', 'Begin', 1 );\n my $job_id = shift;\n print_de\
+bug_message( 'rest_get_status', 'jobid: ' . $job_i\
+d, 2 );\n my $status_str = 'UNKNOWN';\n my $url \
+ = $baseUrl . '/status/' . $job_id;\n $status_\
+str = &rest_request($url);\n print_debug_message( \
+'rest_get_status', 'status_str: ' . $status_str, 2\
+ );\n print_debug_message( 'rest_get_status', 'End\
+', 1 );\n return $status_str;\n}\n\n=head2 rest_ge\
+t_result_types()\n\nGet list of result types for f\
+inished job.\n\n my (@result_types) = &rest_get_r\
+esult_types($job_id);\n\n=cut\n\nsub rest_get_resu\
+lt_types {\n print_debug_message( 'rest_get_result\
+_types', 'Begin', 1 );\n my $job_id = shift;\n pri\
+nt_debug_message( 'rest_get_result_types', 'jobid:\
+ ' . $job_id, 2 );\n my (@resultTypes);\n my $url \
+ = $baseUrl . '/resulttypes/' \
+. $job_id;\n my $result_type_list_xml_str = &rest_\
+request($url);\n my $result_type_list_xml = XM\
+Lin($result_type_list_xml_str);\n (@resultTypes) =\
+ @{ $result_type_list_xml->{'type'} };\n print_deb\
+ug_message( 'rest_get_result_types',\n scalar(@re\
+sultTypes) . ' result types', 2 );\n print_debug_m\
+essage( 'rest_get_result_types', 'End', 1 );\n ret\
+urn (@resultTypes);\n}\n\n=head2 rest_get_result()\
+\n\nGet result data of a specified type for a fini\
+shed job.\n\n my $result = rest_get_result($job_i\
+d, $result_type);\n\n=cut\n\nsub rest_get_result {\
+\n print_debug_message( 'rest_get_result', 'Begin'\
+, 1 );\n my $job_id = shift;\n my $type = shift;\
+\n print_debug_message( 'rest_get_result', 'jobid:\
+ ' . $job_id, 1 );\n print_debug_message( 'rest_ge\
+t_result', 'type: ' . $type, 1 );\n my $url \
+= $baseUrl . '/result/' . $job_id . '/' . $type;\n\
+ my $result = &rest_request($url);\n print_debug_m\
+essage( 'rest_get_result', length($result) . ' cha\
+racters',\n 1 );\n print_debug_message( 'rest_get\
+_result', 'End', 1 );\n return $result;\n}\n\n\n=h\
+ead2 print_debug_message()\n\nPrint debug message \
+at specified debug level.\n\n &print_debug_messag\
+e($method_name, $message, $level);\n\n=cut\n\nsub \
+print_debug_message {\n my $function_name = shift;\
+\n my $message = shift;\n my $level \
+= shift;\n if ( $level <= $params{'debugLevel'} ) \
+{\n print STDERR '[', $function_name, '()] ', $me\
+ssage, \"\\n\";\n }\n}\n\n=head2 print_tool_params\
+()\n\nPrint list of tool parameters.\n\n &print_t\
+ool_params();\n\n=cut\n\nsub print_tool_params {\n\
+ print_debug_message( 'print_tool_params', 'Begin'\
+, 1 );\n my (@param_list) = &rest_get_parameters()\
+;\n foreach my $param ( sort(@param_list) ) {\n p\
+rint $param, \"\\n\";\n }\n print_debug_message( '\
+print_tool_params', 'End', 1 );\n}\n\n=head2 print\
+_param_details()\n\nPrint details of a tool parame\
+ter.\n\n &print_param_details($param_name);\n\n=c\
+ut\n\nsub print_param_details {\n print_debug_mess\
+age( 'print_param_details', 'Begin', 1 );\n my $pa\
+ramName = shift;\n print_debug_message( 'print_par\
+am_details', 'paramName: ' . $paramName, 2 );\n my\
+ $paramDetail = &rest_get_parameter_details($param\
+Name);\n print $paramDetail->{'name'}, \"\\t\", $p\
+aramDetail->{'type'}, \"\\n\";\n print $paramDetai\
+l->{'description'}, \"\\n\";\n if(defined($paramDe\
+tail->{'values'}->{'value'})) {\n if(ref($paramDe\
+tail->{'values'}->{'value'}) eq 'ARRAY') {\n for\
+each my $value ( @{ $paramDetail->{'values'}->{'va\
+lue'} } ) {\n &print_param_value($value);\n }\
+\n }\n else {\n &print_param_value($paramDeta\
+il->{'values'}->{'value'});\n }\n }\n print_debug\
+_message( 'print_param_details', 'End', 1 );\n}\n\\
+n=head2 print_param_value()\n\nPrint details of a \
+tool parameter value.\n\n &print_param_details($p\
+aram_value);\n\nUsed by print_param_details() to h\
+andle both singluar and array values.\n\n=cut\n\ns\
+ub print_param_value {\n my $value = shift;\n prin\
+t $value->{'value'};\n if ( $value->{'defaultValue\
+'} eq 'true' ) {\n print \"\\t\", 'default';\n }\\
+n print \"\\n\";\n print \"\\t\", $value->{'label'\
+}, \"\\n\";\n if ( defined( $value->{'properties'}\
+ ) ) {\n foreach\n my $key ( sort( keys( %{ $v\
+alue->{'properties'}{'property'} } ) ) )\n {\n \
+if ( ref( $value->{'properties'}{'property'}{$key}\
+ ) eq 'HASH'\n && defined( $value->{'properties\
+'}{'property'}{$key}{'value'} )\n )\n {\n \
+ print \"\\t\", $key, \"\\t\",\n $value->{'pr\
+operties'}{'property'}{$key}{'value'}, \"\\n\";\n \
+ }\n else {\n print \"\\t\", $value->{'prope\
+rties'}{'property'}{'key'},\n \"\\t\", $value\
+->{'properties'}{'property'}{'value'}, \"\\n\";\n \
+ last;\n }\n }\n }\n}\n\n=head2 print_job_sta\
+tus()\n\nPrint status of a job.\n\n &print_job_st\
+atus($job_id);\n\n=cut\n\nsub print_job_status {\n\
+ print_debug_message( 'print_job_status', 'Begin',\
+ 1 );\n my $jobid = shift;\n print_debug_message( \
+'print_job_status', 'jobid: ' . $jobid, 1 );\n if \
+( $outputLevel > 0 ) {\n print STDERR 'Getting st\
+atus for job ', $jobid, \"\\n\";\n }\n my $result \
+= &rest_get_status($jobid);\n print \"$result\\n\"\
+;\n if ( $result eq 'FINISHED' && $outputLevel > 0\
+ ) {\n print STDERR \"To get results: $scriptName\
+ --polljob --jobid \" . $jobid\n . \"\\n\";\n }\
+\n print_debug_message( 'print_job_status', 'End',\
+ 1 );\n}\n\n=head2 print_result_types()\n\nPrint a\
+vailable result types for a job.\n\n &print_resul\
+t_types($job_id);\n\n=cut\n\nsub print_result_type\
+s {\n print_debug_message( 'result_types', 'Begin'\
+, 1 );\n my $jobid = shift;\n print_debug_message(\
+ 'result_types', 'jobid: ' . $jobid, 1 );\n if ( $\
+outputLevel > 0 ) {\n print STDERR 'Getting resul\
+t types for job ', $jobid, \"\\n\";\n }\n my $stat\
+us = &rest_get_status($jobid);\n if ( $status eq '\
+PENDING' || $status eq 'RUNNING' ) {\n print STDE\
+RR 'Error: Job status is ', $status,\n '. To ge\
+t result types the job must be finished.', \"\\n\"\
+;\n }\n else {\n my (@resultTypes) = &rest_get_re\
+sult_types($jobid);\n if ( $outputLevel > 0 ) {\n\
+ print STDOUT 'Available result types:', \"\\n\"\
+;\n }\n foreach my $resultType (@resultTypes) {\\
+n print STDOUT $resultType->{'identifier'}, \"\\\
+n\";\n if ( defined( $resultType->{'label'} ) ) \
+{\n print STDOUT \"\\t\", $resultType->{'label'\
+}, \"\\n\";\n }\n if ( defined( $resultType->{\
+'description'} ) ) {\n print STDOUT \"\\t\", $r\
+esultType->{'description'}, \"\\n\";\n }\n if \
+( defined( $resultType->{'mediaType'} ) ) {\n p\
+rint STDOUT \"\\t\", $resultType->{'mediaType'}, \\
+"\\n\";\n }\n if ( defined( $resultType->{'fil\
+eSuffix'} ) ) {\n print STDOUT \"\\t\", $result\
+Type->{'fileSuffix'}, \"\\n\";\n }\n }\n if ( \
+$status eq 'FINISHED' && $outputLevel > 0 ) {\n \
+print STDERR \"\\n\", 'To get results:', \"\\n\",\\
+n \" $scriptName --polljob --jobid \" . $para\
+ms{'jobid'} . \"\\n\",\n \" $scriptName --pol\
+ljob --outformat <type> --jobid \"\n . $params\
+{'jobid'} . \"\\n\";\n }\n }\n print_debug_messag\
+e( 'result_types', 'End', 1 );\n}\n\n=head2 submit\
+_job()\n\nSubmit a job to the service.\n\n &submi\
+t_job($seq);\n\n=cut\n\nsub submit_job {\n print_d\
+ebug_message( 'submit_job', 'Begin', 1 );\n\n # Se\
+t input sequence\n $tool_params{'sequence'} = shif\
+t;\n\n # Load parameters\n &load_params();\n\n # S\
+ubmit the job\n my $jobid = &rest_run( $params{'em\
+ail'}, $params{'title'}, \\%tool_params );\n\n # S\
+imulate sync/async mode\n if ( defined( $params{'a\
+sync'} ) ) {\n print STDOUT $jobid, \"\\n\";\n i\
+f ( $outputLevel > 0 ) {\n print STDERR\n \"\
+To check status: $scriptName --status --jobid $job\
+id\\n\";\n }\n }\n else {\n if ( $outputLevel > \
+0 ) {\n print STDERR \"JobId: $jobid\\n\";\n }\\
+n sleep 1;\n &get_results($jobid);\n }\n print_d\
+ebug_message( 'submit_job', 'End', 1 );\n}\n\n=hea\
+d2 multi_submit_job()\n\nSubmit multiple jobs assu\
+ming input is a collection of fasta formatted sequ\
+ences.\n\n &multi_submit_job();\n\n=cut\n\nsub mu\
+lti_submit_job {\n print_debug_message( 'multi_sub\
+mit_job', 'Begin', 1 );\n my $jobIdForFilename = 1\
+;\n $jobIdForFilename = 0 if ( defined( $params{'o\
+utfile'} ) );\n my (@filename_list) = ();\n\n # Qu\
+ery sequence\n if ( defined( $ARGV[0] ) ) { # B\
+are option\n if ( -f $ARGV[0] || $ARGV[0] eq '-' \
+) { # File\n push( @filename_list, $ARGV[0] )\
+;\n }\n else {\n warn 'Warning: Input file \"'\
+ . $ARGV[0] . '\" does not exist'\n }\n }\n if ( \
+$params{'sequence'} ) { # Via --\
+sequence\n if ( -f $params{'sequence'} || $params\
+{'sequence'} eq '-' ) { # File\n push( @filen\
+ame_list, $params{'sequence'} );\n }\n else {\n \
+ warn 'Warning: Input file \"' . $params{'sequenc\
+e'} . '\" does not exist'\n }\n }\n\n $/ = '>';\n\
+ foreach my $filename (@filename_list) {\n my $IN\
+FILE;\n if($filename eq '-') { # STDIN.\n open(\
+ $INFILE, '<-' )\n or die 'Error: unable to ST\
+DIN (' . $! . ')';\n } else { # File.\n open( $\
+INFILE, '<', $filename )\n or die 'Error: unab\
le to open file ' . $filename . ' (' . $! . ')';\n\
- while (<$LISTFILE>) {\n my $line = $_;\n chomp(\
-$line);\n if ( $line ne '' ) {\n &print_debug_m\
-essage( 'list_file_submit_job', 'line: ' . $line, \
-2 );\n if ( $line =~ m/\\w:\\w/ ) { # Check t\
-his is an identifier\n print STDERR \"Submittin\
-g job for: $line\\n\"\n if ( $outputLevel > 0\
- );\n &submit_job($line);\n }\n else {\n \
- print STDERR\n\"Warning: line \\\"$line\\\" is no\
-t recognised as an identifier\\n\";\n }\n }\n \
-$params{'outfile'} = undef if ( $jobIdForFilename \
-== 1 );\n }\n close $LISTFILE;\n}\n\n=head2 load_d\
-ata()\n\nLoad sequence data from file or option sp\
-ecified on the command-line.\n\n &load_data();\n\\
-n=cut\n\nsub load_data {\n print_debug_message( 'l\
-oad_data', 'Begin', 1 );\n my $retSeq;\n\n # Query\
- sequence\n if ( defined( $ARGV[0] ) ) { # Bare\
- option\n if ( -f $ARGV[0] || $ARGV[0] eq '-' ) {\
- # File\n $retSeq = &read_file( $ARGV[0] );\n\
- }\n else { \
-# DB:ID or sequence\n $retSeq = $ARGV[0];\n }\n\
- }\n if ( $params{'sequence'} ) { \
- # Via --sequence\n if ( -f $params{'sequence'} \
-|| $params{'sequence'} eq '-' ) { # File\n $r\
-etSeq = &read_file( $params{'sequence'} );\n }\n \
- else { # DB:ID or sequence\n $retSeq = $para\
-ms{'sequence'};\n }\n }\n print_debug_message( 'l\
-oad_data', 'End', 1 );\n return $retSeq;\n}\n\n=he\
-ad2 load_params()\n\nLoad job parameters from comm\
-and-line options.\n\n &load_params();\n\n=cut\n\n\
-sub load_params {\n print_debug_message( 'load_par\
-ams', 'Begin', 1 );\n\n # Database(s) to search\n \
-my (@dbList) = split /[ ,]/, $params{'database'};\\
-n $tool_params{'database'} = \\@dbList;\n\n # Matc\
-h/missmatch\n if ( $params{'match'} && $params{'mi\
-ssmatch'} ) {\n $tool_params{'match_scores'} =\n \
- $params{'match'} . ',' . $params{'missmatch'};\\
-n }\n \n # Compatability options, old command-line\
-\n if(!$tool_params{'alignments'} && $params{'numa\
-l'}) {\n $tool_params{'alignments'} = $params{'nu\
-mal'};\n }\n if(!$tool_params{'gapopen'} && $param\
-s{'opengap'}) {\n $tool_params{'gapopen'} = $para\
-ms{'opengap'};\n }\n if(!$tool_params{'gapext'} &&\
- $params{'extendgap'}) {\n $tool_params{'gapext'}\
- = $params{'extendgap'};\n }\n\n print_debug_messa\
-ge( 'load_params', 'End', 1 );\n}\n\n=head2 client\
-_poll()\n\nClient-side job polling.\n\n &client_p\
-oll($job_id);\n\n=cut\n\nsub client_poll {\n print\
-_debug_message( 'client_poll', 'Begin', 1 );\n my \
-$jobid = shift;\n my $status = 'PENDING';\n\n my \
-$errorCount = 0;\n while ($status eq 'RUNNING'\n \
-|| $status eq 'PENDING'\n || ( $status eq 'ERROR'\
- && $errorCount < 2 ) )\n {\n $status = rest_get_\
-status($jobid);\n print STDERR \"$status\\n\" if \
-( $outputLevel > 0 );\n if ( $status eq 'ERROR' )\
- {\n $errorCount++;\n }\n elsif ( $errorCount \
-> 0 ) {\n $errorCount--;\n }\n if ( $status \
-eq 'RUNNING'\n || $status eq 'PENDING'\n || $s\
-tatus eq 'ERROR' )\n {\n\n # Wait before pollin\
-g again.\n sleep $checkInterval;\n }\n }\n prin\
-t_debug_message( 'client_poll', 'End', 1 );\n retu\
-rn $status;\n}\n\n=head2 get_results()\n\nGet the \
-results for a job identifier.\n\n &get_results($j\
-ob_id);\n\n=cut\n\nsub get_results {\n print_debug\
-_message( 'get_results', 'Begin', 1 );\n my $jobid\
- = shift;\n print_debug_message( 'get_results', 'j\
-obid: ' . $jobid, 1 );\n\n # Verbose\n if ( $outpu\
-tLevel > 1 ) {\n print 'Getting results for job '\
-, $jobid, \"\\n\";\n }\n\n # Check status, and wai\
-t if not finished\n client_poll($jobid);\n\n # Use\
- JobId if output file name is not defined\n unless\
- ( defined( $params{'outfile'} ) ) {\n $params{'o\
-utfile'} = $jobid;\n }\n\n # Get list of data type\
-s\n my (@resultTypes) = rest_get_result_types($job\
-id);\n\n # Get the data and write it to a file\n i\
-f ( defined( $params{'outformat'} ) ) { # Speci\
-fied data type\n my $selResultType;\n foreach my\
- $resultType (@resultTypes) {\n if ( $resultType\
-->{'identifier'} eq $params{'outformat'} ) {\n \
-$selResultType = $resultType;\n }\n }\n if ( d\
-efined($selResultType) ) {\n my $result =\n \
-rest_get_result( $jobid, $selResultType->{'identif\
-ier'} );\n if ( $params{'outfile'} eq '-' ) {\n \
- write_file( $params{'outfile'}, $result );\n \
-}\n else {\n write_file(\n $params{'outfi\
-le'} . '.'\n . $selResultType->{'identifier'\
-} . '.'\n . $selResultType->{'fileSuffix'},\\
-n $result\n );\n }\n }\n else {\n die\
- 'Error: unknown result format \"' . $params{'outf\
-ormat'} . '\"';\n }\n }\n else { # Data types \
-available\n # Write a file for each output \
-type\n for my $resultType (@resultTypes) {\n if\
- ( $outputLevel > 1 ) {\n print STDERR 'Getting\
- ', $resultType->{'identifier'}, \"\\n\";\n }\n \
- my $result = rest_get_result( $jobid, $resultTyp\
-e->{'identifier'} );\n if ( $params{'outfile'} e\
-q '-' ) {\n write_file( $params{'outfile'}, $re\
-sult );\n }\n else {\n write_file(\n $p\
-arams{'outfile'} . '.'\n . $resultType->{'id\
-entifier'} . '.'\n . $resultType->{'fileSuff\
-ix'},\n $result\n );\n }\n }\n }\n print\
-_debug_message( 'get_results', 'End', 1 );\n}\n\n=\
-head2 read_file()\n\nRead a file into a scalar. Th\
-e special filename '-' can be used to read from \n\
-standard input (STDIN).\n\n my $data = &read_file\
-($filename);\n\n=cut\n\nsub read_file {\n print_de\
-bug_message( 'read_file', 'Begin', 1 );\n my $file\
-name = shift;\n print_debug_message( 'read_file', \
-'filename: ' . $filename, 2 );\n my ( $content, $b\
-uffer );\n if ( $filename eq '-' ) {\n while ( sy\
-sread( STDIN, $buffer, 1024 ) ) {\n $content .= \
-$buffer;\n }\n }\n else { # File\n open( my $\
-FILE, '<', $filename )\n or die \"Error: unable\
- to open input file $filename ($!)\";\n while ( s\
-ysread( $FILE, $buffer, 1024 ) ) {\n $content .=\
- $buffer;\n }\n close($FILE);\n }\n print_debug_\
-message( 'read_file', 'End', 1 );\n return $conten\
-t;\n}\n\n=head2 write_file()\n\nWrite data to a fi\
-le. The special filename '-' can be used to write \
-to \nstandard output (STDOUT).\n\n &write_file($f\
-ilename, $data);\n\n=cut\n\nsub write_file {\n pri\
-nt_debug_message( 'write_file', 'Begin', 1 );\n my\
- ( $filename, $data ) = @_;\n print_debug_message(\
- 'write_file', 'filename: ' . $filename, 2 );\n if\
- ( $outputLevel > 0 ) {\n print STDERR 'Creating \
-result file: ' . $filename . \"\\n\";\n }\n if ( $\
-filename eq '-' ) {\n print STDOUT $data;\n }\n e\
-lse {\n open( my $FILE, '>', $filename )\n or \
-die \"Error: unable to open output file $filename \
-($!)\";\n syswrite( $FILE, $data );\n close($FIL\
-E);\n }\n print_debug_message( 'write_file', 'End'\
-, 1 );\n}\n\n=head2 usage()\n\nPrint program usage\
- message.\n\n &usage();\n\n=cut\n\nsub usage {\n \
-print STDERR <<EOF\nNCBI BLAST\n==========\n \nR\
-apid sequence database search programs utilizing t\
-he BLAST algorithm\n \n[Required]\n\n -p, --pr\
-ogram : str : BLAST program to use, see --pa\
-ramDetail program\n -D, --database : str : d\
-atabase(s) to search, space separated. See\n \
- --paramDetail database\n \
- --stype : str : query sequence type, s\
-ee --paramDetail stype\n seqFile : fil\
-e : query sequence (\"-\" for STDIN, \\@filename f\
-or\n identifier list \
-file)\n\n[Optional]\n\n -m, --matrix : str \
- : scoring matrix, see --paramDetail matrix\n -e,\
- --exp : real : 0<E<= 1000. Statistical s\
-ignificance threshold \n \
- for reporting database sequence matches.\n -f\
-, --filter : : filter the query sequenc\
-e for low complexity \n \
- regions, see --paramDetail filter\n -A, --alig\
-n : int : pairwise alignment format, see -\
--paramDetail align\n -s, --scores : int : \
-number of scores to be reported\n -n, --alignment\
-s : int : number of alignments to report\n -u,\
- --match : int : Match score (BLASTN only)\
-\n -v, --mismatch : int : Mismatch score (BL\
-ASTN only)\n -o, --gapopen : int : Gap open\
- penalty\n -x, --gapext : int : Gap extens\
-ion penalty\n -d, --dropoff : int : Drop-of\
-f\n -g, --gapalign : : Optimise gapped a\
-lignments\n --seqrange : str : region wi\
-thin input to use as query\n --multifasta :\
- : treat input as a set of fasta formatted se\
-quences\n\n[General]\n\n -h, --help : \
- : prints this help text\n --async : \
- : forces to make an asynchronous query\n -\
--email : str : e-mail address\n --titl\
-e : str : title for job\n --status \
- : : get job status\n --resultTypes : \
- : get available result types for job\n --\
-polljob : : poll for the status of a job\\
-n --jobid : str : jobid that was retur\
-ned when an asynchronous job \n \
- was submitted.\n --outfile : st\
-r : file name for results (default is jobid;\n \
- \"-\" for STDOUT)\n \
- --outformat : str : result format to retrieve\\
-n --params : : list input parameter\
-s\n --paramDetail : str : display details fo\
-r input parameter\n --quiet : : de\
-crease output\n --verbose : : increa\
-se output\n --trace : : show SOAP \
-messages being interchanged \n \nSynchronous job\
-:\n\n The results/errors are returned as soon as \
-the job is finished.\n Usage: $scriptName --email\
- <your\\@email> [options...] seqFile\n Returns: r\
-esults as an attachment\n\nAsynchronous job:\n\n \
-Use this if you want to retrieve the results at a \
-later time. The results \n are stored for up to 2\
-4 hours. \n Usage: $scriptName --async --email <\
-your\\@email> [options...] seqFile\n Returns: job\
-id\n\n Use the jobid to query for the status of t\
-he job. If the job is finished, \n it also return\
-s the results/errors.\n Usage: $scriptName --poll\
-job --jobid <jobId> [--outfile string]\n Returns:\
- string indicating the status of the job and if ap\
-plicable, results \n as an attachment.\n\nFurther\
- information:\n\n http://www.ebi.ac.uk/Tools/webs\
-ervices/services/sss/ncbi_blast_rest\n http://www\
-.ebi.ac.uk/Tools/webservices/tutorials/perl\n\nSup\
-port/Feedback:\n\n http://www.ebi.ac.uk/support/\\
-nEOF\n}\n\n=head1 FEEDBACK/SUPPORT\n\nPlease conta\
-ct us at L<http://www.ebi.ac.uk/support/> if you h\
-ave any \nfeedback, suggestions or issues with the\
- service or this client.\n\n=cut\n","\n=head1 NAME\
-\n\nwublast_lwp.pl\n\n=head1 DESCRIPTION\n\nWU-BLA\
-ST REST web service Perl client using L<LWP>.\n\nT\
-ested with:\n\n=over\n\n=item *\nL<LWP> 5.79, L<XM\
-L::Simple> 2.12 and Perl 5.8.3\n\n=item *\nL<LWP> \
-5.805, L<XML::Simple> 2.14 and Perl 5.8.7\n\n=item\
- *\nL<LWP> 5.820, L<XML::Simple> 2.18 and Perl 5.1\
-0.0 (Ubuntu 9.04)\n\n=back\n\nFor further informat\
-ion see:\n\n=over\n\n=item *\nL<http://www.ebi.ac.\
-uk/Tools/webservices/services/sss/wu_blast_rest>\n\
-\n=item *\nL<http://www.ebi.ac.uk/Tools/webservice\
-s/tutorials/perl>\n\n=back\n\n=head1 VERSION\n\n$I\
-d: wublast_lwp.pl 1317 2009-09-03 15:44:11Z hpm $\\
+ }\n while (<$INFILE>) {\n my $seq = $_;\n $\
+seq =~ s/>$//;\n if ( $seq =~ m/(\\S+)/ ) {\n \
+ print STDERR \"Submitting job for: $1\\n\"\n \
+ if ( $outputLevel > 0 );\n $seq = '>' . $seq;\\
+n &print_debug_message( 'multi_submit_job', $se\
+q, 11 );\n &submit_job($seq);\n $params{'out\
+file'} = undef if ( $jobIdForFilename == 1 );\n \
+}\n }\n close $INFILE;\n }\n print_debug_message\
+( 'multi_submit_job', 'End', 1 );\n}\n\n=head2 lis\
+t_file_submit_job()\n\nSubmit multiple jobs using \
+a file containing a list of entry identifiers as \\
+ninput.\n\n &list_file_submit_job($list_filename)\
+\n\n=cut\n\nsub list_file_submit_job {\n my $filen\
+ame = shift;\n my $jobIdForFilename = 1;\n\
+ $jobIdForFilename = 0 if ( defined( $params{'outf\
+ile'} ) );\n\n # Iterate over identifiers, submitt\
+ing each job\n my $LISTFILE;\n if($filename eq '-'\
+) { # STDIN.\n open( $LISTFILE, '<-' )\n or di\
+e 'Error: unable to STDIN (' . $! . ')';\n } else \
+{ # File.\n open( $LISTFILE, '<', $filename )\n \
+ or die 'Error: unable to open file ' . $filename\
+ . ' (' . $! . ')';\n }\n while (<$LISTFILE>) {\n \
+ my $line = $_;\n chomp($line);\n if ( $line ne \
+'' ) {\n &print_debug_message( 'list_file_submit\
+_job', 'line: ' . $line, 2 );\n if ( $line =~ m/\
+\\w:\\w/ ) { # Check this is an identifier\n \
+ print STDERR \"Submitting job for: $line\\n\"\n \
+ if ( $outputLevel > 0 );\n &submit_job($lin\
+e);\n }\n else {\n print STDERR\n\"Warning:\
+ line \\\"$line\\\" is not recognised as an identi\
+fier\\n\";\n }\n }\n $params{'outfile'} = unde\
+f if ( $jobIdForFilename == 1 );\n }\n close $LIST\
+FILE;\n}\n\n=head2 load_data()\n\nLoad sequence da\
+ta from file or option specified on the command-li\
+ne.\n\n &load_data();\n\n=cut\n\nsub load_data {\\
+n print_debug_message( 'load_data', 'Begin', 1 );\\
+n my $retSeq;\n\n # Query sequence\n if ( defined(\
+ $ARGV[0] ) ) { # Bare option\n if ( -f $ARGV[\
+0] || $ARGV[0] eq '-' ) { # File\n $retSeq = \
+&read_file( $ARGV[0] );\n }\n else { \
+ # DB:ID or sequence\n $\
+retSeq = $ARGV[0];\n }\n }\n if ( $params{'sequen\
+ce'} ) { # Via --sequence\n if \
+( -f $params{'sequence'} || $params{'sequence'} eq\
+ '-' ) { # File\n $retSeq = &read_file( $para\
+ms{'sequence'} );\n }\n else { # DB:ID or seq\
+uence\n $retSeq = $params{'sequence'};\n }\n }\\
+n print_debug_message( 'load_data', 'End', 1 );\n \
+return $retSeq;\n}\n\n=head2 load_params()\n\nLoad\
+ job parameters from command-line options.\n\n &l\
+oad_params();\n\n=cut\n\nsub load_params {\n print\
+_debug_message( 'load_params', 'Begin', 1 );\n\n #\
+ Database(s) to search\n my (@dbList) = split /[ ,\
+]/, $params{'database'};\n $tool_params{'database'\
+} = \\@dbList;\n\n # Match/missmatch\n if ( $param\
+s{'match'} && $params{'missmatch'} ) {\n $tool_pa\
+rams{'match_scores'} =\n $params{'match'} . ','\
+ . $params{'missmatch'};\n }\n \n # Compatability \
+options, old command-line\n if(!$tool_params{'alig\
+nments'} && $params{'numal'}) {\n $tool_params{'a\
+lignments'} = $params{'numal'};\n }\n if(!$tool_pa\
+rams{'gapopen'} && $params{'opengap'}) {\n $tool_\
+params{'gapopen'} = $params{'opengap'};\n }\n if(!\
+$tool_params{'gapext'} && $params{'extendgap'}) {\\
+n $tool_params{'gapext'} = $params{'extendgap'};\\
+n }\n\n print_debug_message( 'load_params', 'End',\
+ 1 );\n}\n\n=head2 client_poll()\n\nClient-side jo\
+b polling.\n\n &client_poll($job_id);\n\n=cut\n\n\
+sub client_poll {\n print_debug_message( 'client_p\
+oll', 'Begin', 1 );\n my $jobid = shift;\n my $st\
+atus = 'PENDING';\n\n my $errorCount = 0;\n while \
+($status eq 'RUNNING'\n || $status eq 'PENDING'\n\
+ || ( $status eq 'ERROR' && $errorCount < 2 ) )\n\
+ {\n $status = rest_get_status($jobid);\n print \
+STDERR \"$status\\n\" if ( $outputLevel > 0 );\n \
+if ( $status eq 'ERROR' ) {\n $errorCount++;\n \
+}\n elsif ( $errorCount > 0 ) {\n $errorCount--\
+;\n }\n if ( $status eq 'RUNNING'\n || $stat\
+us eq 'PENDING'\n || $status eq 'ERROR' )\n {\n\
+\n # Wait before polling again.\n sleep $check\
+Interval;\n }\n }\n print_debug_message( 'client_\
+poll', 'End', 1 );\n return $status;\n}\n\n=head2 \
+get_results()\n\nGet the results for a job identif\
+ier.\n\n &get_results($job_id);\n\n=cut\n\nsub ge\
+t_results {\n print_debug_message( 'get_results', \
+'Begin', 1 );\n my $jobid = shift;\n print_debug_m\
+essage( 'get_results', 'jobid: ' . $jobid, 1 );\n\\
+n # Verbose\n if ( $outputLevel > 1 ) {\n print '\
+Getting results for job ', $jobid, \"\\n\";\n }\n\\
+n # Check status, and wait if not finished\n clien\
+t_poll($jobid);\n\n # Use JobId if output file nam\
+e is not defined\n unless ( defined( $params{'outf\
+ile'} ) ) {\n $params{'outfile'} = $jobid;\n }\n\\
+n # Get list of data types\n my (@resultTypes) = r\
+est_get_result_types($jobid);\n\n # Get the data a\
+nd write it to a file\n if ( defined( $params{'out\
+format'} ) ) { # Specified data type\n my $sel\
+ResultType;\n foreach my $resultType (@resultType\
+s) {\n if ( $resultType->{'identifier'} eq $para\
+ms{'outformat'} ) {\n $selResultType = $resultT\
+ype;\n }\n }\n if ( defined($selResultType) ) \
+{\n my $result =\n rest_get_result( $jobid, \
+$selResultType->{'identifier'} );\n if ( $params\
+{'outfile'} eq '-' ) {\n write_file( $params{'o\
+utfile'}, $result );\n }\n else {\n write_f\
+ile(\n $params{'outfile'} . '.'\n . $sel\
+ResultType->{'identifier'} . '.'\n . $selRes\
+ultType->{'fileSuffix'},\n $result\n );\n \
+ }\n }\n else {\n die 'Error: unknown result f\
+ormat \"' . $params{'outformat'} . '\"';\n }\n }\\
+n else { # Data types available\n # Writ\
+e a file for each output type\n for my $resultTyp\
+e (@resultTypes) {\n if ( $outputLevel > 1 ) {\n\
+ print STDERR 'Getting ', $resultType->{'identi\
+fier'}, \"\\n\";\n }\n my $result = rest_get_r\
+esult( $jobid, $resultType->{'identifier'} );\n \
+if ( $params{'outfile'} eq '-' ) {\n write_file\
+( $params{'outfile'}, $result );\n }\n else {\\
+n write_file(\n $params{'outfile'} . '.'\n \
+ . $resultType->{'identifier'} . '.'\n \
+. $resultType->{'fileSuffix'},\n $result\n \
+);\n }\n }\n }\n print_debug_message( 'get_resu\
+lts', 'End', 1 );\n}\n\n=head2 read_file()\n\nRead\
+ a file into a scalar. The special filename '-' ca\
+n be used to read from \nstandard input (STDIN).\n\
+\n my $data = &read_file($filename);\n\n=cut\n\ns\
+ub read_file {\n print_debug_message( 'read_file',\
+ 'Begin', 1 );\n my $filename = shift;\n print_deb\
+ug_message( 'read_file', 'filename: ' . $filename,\
+ 2 );\n my ( $content, $buffer );\n if ( $filename\
+ eq '-' ) {\n while ( sysread( STDIN, $buffer, 10\
+24 ) ) {\n $content .= $buffer;\n }\n }\n else \
+{ # File\n open( my $FILE, '<', $filename )\n \
+ or die \"Error: unable to open input file $file\
+name ($!)\";\n while ( sysread( $FILE, $buffer, 1\
+024 ) ) {\n $content .= $buffer;\n }\n close($\
+FILE);\n }\n print_debug_message( 'read_file', 'En\
+d', 1 );\n return $content;\n}\n\n=head2 write_fil\
+e()\n\nWrite data to a file. The special filename \
+'-' can be used to write to \nstandard output (STD\
+OUT).\n\n &write_file($filename, $data);\n\n=cut\\
+n\nsub write_file {\n print_debug_message( 'write_\
+file', 'Begin', 1 );\n my ( $filename, $data ) = @\
+_;\n print_debug_message( 'write_file', 'filename:\
+ ' . $filename, 2 );\n if ( $outputLevel > 0 ) {\n\
+ print STDERR 'Creating result file: ' . $filenam\
+e . \"\\n\";\n }\n if ( $filename eq '-' ) {\n pr\
+int STDOUT $data;\n }\n else {\n open( my $FILE, \
+'>', $filename )\n or die \"Error: unable to op\
+en output file $filename ($!)\";\n syswrite( $FIL\
+E, $data );\n close($FILE);\n }\n print_debug_mes\
+sage( 'write_file', 'End', 1 );\n}\n\n=head2 usage\
+()\n\nPrint program usage message.\n\n &usage();\\
+n\n=cut\n\nsub usage {\n print STDERR <<EOF\nNCBI \
+BLAST\n==========\n \nRapid sequence database se\
+arch programs utilizing the BLAST algorithm\n \\
+n[Required]\n\n -p, --program : str : BLAST\
+ program to use, see --paramDetail program\n -D, \
+--database : str : database(s) to search, spa\
+ce separated. See\n -\
+-paramDetail database\n --stype : str \
+ : query sequence type, see --paramDetail stype\n \
+ seqFile : file : query sequence (\"-\"\
+ for STDIN, \\@filename for\n \
+ identifier list file)\n\n[Optional]\n\n \
+-m, --matrix : str : scoring matrix, see --\
+paramDetail matrix\n -e, --exp : real : \
+0<E<= 1000. Statistical significance threshold \n \
+ for reporting databas\
+e sequence matches.\n -f, --filter : :\
+ filter the query sequence for low complexity \n \
+ regions, see --paramDe\
+tail filter\n -A, --align : int : pairwis\
+e alignment format, see --paramDetail align\n -s,\
+ --scores : int : number of scores to be re\
+ported\n -n, --alignments : int : number of al\
+ignments to report\n -u, --match : int : \
+Match score (BLASTN only)\n -v, --mismatch : \
+int : Mismatch score (BLASTN only)\n -o, --gapop\
+en : int : Gap open penalty\n -x, --gapext \
+ : int : Gap extension penalty\n -d, --drop\
+off : int : Drop-off\n -g, --gapalign :\
+ : Optimise gapped alignments\n --seqran\
+ge : str : region within input to use as quer\
+y\n --multifasta : : treat input as a \
+set of fasta formatted sequences\n\n[General]\n\n \
+ -h, --help : : prints this help text\
+\n --async : : forces to make an \
+asynchronous query\n --email : str : \
+e-mail address\n --title : str : titl\
+e for job\n --status : : get job s\
+tatus\n --resultTypes : : get available\
+ result types for job\n --polljob : \
+ : poll for the status of a job\n --jobid \
+ : str : jobid that was returned when an async\
+hronous job \n was su\
+bmitted.\n --outfile : str : file name \
+for results (default is jobid;\n \
+ \"-\" for STDOUT)\n --outformat \
+ : str : result format to retrieve\n --para\
+ms : : list input parameters\n --p\
+aramDetail : str : display details for input par\
+ameter\n --quiet : : decrease out\
+put\n --verbose : : increase output\
+\n \nSynchronous job:\n\n The results/errors ar\
+e returned as soon as the job is finished.\n Usag\
+e: $scriptName --email <your\\@email> [options...]\
+ seqFile\n Returns: results as an attachment\n\nA\
+synchronous job:\n\n Use this if you want to retr\
+ieve the results at a later time. The results \n \
+are stored for up to 24 hours. \n Usage: $script\
+Name --async --email <your\\@email> [options...] s\
+eqFile\n Returns: jobid\n\n Use the jobid to que\
+ry for the status of the job. If the job is finish\
+ed, \n it also returns the results/errors.\n Usa\
+ge: $scriptName --polljob --jobid <jobId> [--outfi\
+le string]\n Returns: string indicating the statu\
+s of the job and if applicable, results \n as an \
+attachment.\n\nFurther information:\n\n http://ww\
+w.ebi.ac.uk/Tools/webservices/services/sss/ncbi_bl\
+ast_rest\n http://www.ebi.ac.uk/Tools/webservices\
+/tutorials/perl\n\nSupport/Feedback:\n\n http://w\
+ww.ebi.ac.uk/support/\nEOF\n}\n\n=head1 FEEDBACK/S\
+UPPORT\n\nPlease contact us at L<http://www.ebi.ac\
+.uk/support/> if you have any \nfeedback, suggesti\
+ons or issues with the service or this client.\n\n\
+=cut\n","\n=head1 NAME\n\nwublast_lwp.pl\n\n=head1\
+ DESCRIPTION\n\nWU-BLAST (REST) web service Perl c\
+lient using L<LWP>.\n\nTested with:\n\n=over\n\n=i\
+tem *\nL<LWP> 5.79, L<XML::Simple> 2.12 and Perl 5\
+.8.3\n\n=item *\nL<LWP> 5.808, L<XML::Simple> 2.18\
+ and Perl 5.8.8 (Ubuntu 8.04 LTS)\n\n=item *\nL<LW\
+P> 5.834, L<XML::Simple> 2.18 and Perl 5.10.1 (Ubu\
+ntu 10.04 LTS)\n\n=item *\nL<LWP> 6.03, L<XML::Sim\
+ple> 2.18 and Perl 5.14.2 (Ubuntu 12.04 LTS)\n\n=b\
+ack\n\nFor further information see:\n\n=over\n\n=i\
+tem *\nL<http://www.ebi.ac.uk/Tools/webservices/se\
+rvices/sss/wu_blast_rest>\n\n=item *\nL<http://www\
+.ebi.ac.uk/Tools/webservices/tutorials/perl>\n\n=b\
+ack\n\n=head1 LICENSE\n\nCopyright 2012-2013 EMBL \
+- European Bioinformatics Institute\n\nLicensed un\
+der the Apache License, Version 2.0 (the \"License\
+\");\nyou may not use this file except in complian\
+ce with the License.\nYou may obtain a copy of the\
+ License at\n\n http://www.apache.org/licenses/\
+LICENSE-2.0\n\nUnless required by applicable law o\
+r agreed to in writing, software\ndistributed unde\
+r the License is distributed on an \"AS IS\" BASIS\
+,\nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, e\
+ither express or implied.\nSee the License for the\
+ specific language governing permissions and\nlimi\
+tations under the License.\n\n=head1 VERSION\n\n$I\
+d: wublast_lwp.pl 2560 2013-03-20 12:56:31Z hpm $\\
n\n=cut\n\nuse strict;\nuse warnings;\n\nuse Engli\
sh;\nuse LWP;\nuse XML::Simple;\nuse Getopt::Long \
qw(:config no_ignore_case bundling);\nuse File::Ba\
'debugLevel'}, # Debug output level\n 'baseUrl\
=s' => \\$baseUrl, # Base URL\
for service.\n);\nif ( $params{'verbose'} ) { $ou\
-tputLevel++ }\nif ( $params{'$quiet'} ) { $output\
-Level-- }\n\n&print_debug_message( 'MAIN', 'LWP::V\
-ERSION: ' . $LWP::VERSION,\n 1 );\n\n&print_debug_\
-message( 'MAIN', \"params:\\n\" . Dumper( \\%param\
-s ), 11 );\n&print_debug_message( 'MAIN'\
-, \"tool_params:\\n\" . Dumper( \\%tool_params ), \
-11 );\n\nmy $scriptName = basename( $0, () );\n\ni\
-f ( $params{'help'} || $numOpts == 0 ) {\n &usage(\
-);\n exit(0);\n}\n\n&print_debug_message( 'MAIN', \
-'baseUrl: ' . $baseUrl, 1 );\n\nif (\n !(\n $p\
-arams{'polljob'}\n || $params{'resultTypes'}\n |\
-| $params{'status'}\n || $params{'params'}\n || \
-$params{'paramDetail'}\n )\n && !( defined( $ARGV[\
-0] ) || defined( $params{'sequence'} ) )\n )\n{\n\
-\n # Bad argument combination, so print error mess\
-age and usage\n print STDERR 'Error: bad option co\
-mbination', \"\\n\";\n &usage();\n exit(1);\n}\n\n\
-elsif ( $params{'params'} ) {\n &print_tool_params\
-();\n}\n\nelsif ( $params{'paramDetail'} ) {\n &pr\
-int_param_details( $params{'paramDetail'} );\n}\n\\
-nelsif ( $params{'status'} && defined( $params{'jo\
-bid'} ) ) {\n &print_job_status( $params{'jobid'} \
-);\n}\n\nelsif ( $params{'resultTypes'} && defined\
-( $params{'jobid'} ) ) {\n &print_result_types( $p\
-arams{'jobid'} );\n}\n\nelsif ( $params{'polljob'}\
- && defined( $params{'jobid'} ) ) {\n &get_results\
-( $params{'jobid'} );\n}\n\nelse {\n\n # Multiple \
-input sequence mode, assume fasta format.\n if ( $\
-params{'multifasta'} ) {\n &multi_submit_job();\n\
- }\n\n # Entry identifier list file.\n elsif (( de\
-fined( $params{'sequence'} ) && $params{'sequence'\
-} =~ m/^\\@/ )\n || ( defined( $ARGV[0] ) && $ARG\
-V[0] =~ m/^\\@/ ) )\n {\n my $list_filename = $pa\
-rams{'sequence'} || $ARGV[0];\n $list_filename =~\
- s/^\\@//;\n &list_file_submit_job($list_filename\
-);\n }\n\n # Default: single sequence/identifier.\\
-n else {\n\n # Load the sequence data and submit.\
-\n &submit_job( &load_data() );\n }\n}\n\n=head1 \
-FUNCTIONS\n\n=cut\n\n\n=head2 rest_request()\n\nPe\
-rform a REST request.\n\n my $response_str = &res\
-t_request($url);\n\n=cut\n\nsub rest_request {\n p\
-rint_debug_message( 'rest_request', 'Begin', 11 );\
-\n my $requestUrl = shift;\n print_debug_message( \
-'rest_request', 'URL: ' . $requestUrl, 11 );\n\n #\
- Create a user agent\n my $ua = LWP::UserAgent->ne\
-w();\n '$Revision: 1317 $' =~ m/(\\d+)/;\n $ua->ag\
-ent(\"EBI-Sample-Client/$1 ($scriptName; $OSNAME) \
-\" . $ua->agent());\n $ua->env_proxy;\n\n # Perfor\
-m the request\n my $response = $ua->get($requestUr\
-l);\n print_debug_message( 'rest_request', 'HTTP s\
-tatus: ' . $response->code,\n 11 );\n\n # Check f\
-or HTTP error codes\n if ( $response->is_error ) {\
-\n $response->content() =~ m/<h1>([^<]+)<\\/h1>/;\
-\n die 'http status: ' . $response->code . ' ' . \
-$response->message . ' ' . $1;\n }\n print_debug_\
-message( 'rest_request', 'End', 11 );\n\n # Return\
- the response data\n return $response->content();\\
-n}\n\n=head2 rest_get_parameters()\n\nGet list of \
-tool parameter names.\n\n my (@param_list) = &res\
-t_get_parameters();\n\n=cut\n\nsub rest_get_parame\
-ters {\n print_debug_message( 'rest_get_parameters\
-', 'Begin', 1 );\n my $url = $baseU\
-rl . '/parameters/';\n my $param_list_xml_str = re\
-st_request($url);\n my $param_list_xml = XMLin\
-($param_list_xml_str);\n my (@param_list) = \
-@{ $param_list_xml->{'id'} };\n print_debug_messag\
-e( 'rest_get_parameters', 'End', 1 );\n return (@p\
-aram_list);\n}\n\n=head2 rest_get_parameter_detail\
-s()\n\nGet details of a tool parameter.\n\n my $p\
-aramDetail = &rest_get_parameter_details($param_na\
-me);\n\n=cut\n\nsub rest_get_parameter_details {\n\
- print_debug_message( 'rest_get_parameter_details'\
-, 'Begin', 1 );\n my $parameterId = shift;\n print\
-_debug_message( 'rest_get_parameter_details',\n '\
-parameterId: ' . $parameterId, 1 );\n my $url \
- = $baseUrl . '/parameterdetails/' . $\
-parameterId;\n my $param_detail_xml_str = rest_req\
-uest($url);\n my $param_detail_xml = XMLin($pa\
-ram_detail_xml_str);\n print_debug_message( 'rest_\
-get_parameter_details', 'End', 1 );\n return ($par\
-am_detail_xml);\n}\n\n=head2 rest_run()\n\nSubmit \
-a job.\n\n my $job_id = &rest_run($email, $title,\
- \\%params );\n\n=cut\n\nsub rest_run {\n print_de\
-bug_message( 'rest_run', 'Begin', 1 );\n my $email\
- = shift;\n my $title = shift;\n my $params = sh\
-ift;\n print_debug_message( 'rest_run', 'email: ' \
-. $email, 1 );\n if ( defined($title) ) {\n print\
-_debug_message( 'rest_run', 'title: ' . $title, 1 \
-);\n }\n print_debug_message( 'rest_run', 'params:\
- ' . Dumper($params), 1 );\n\n # User agent to per\
-form http requests\n my $ua = LWP::UserAgent->new(\
-);\n $ua->env_proxy;\n\n # Clean up parameters\n m\
-y (%tmp_params) = %{$params};\n $tmp_params{'email\
-'} = $email;\n $tmp_params{'title'} = $title;\n fo\
-reach my $param_name ( keys(%tmp_params) ) {\n if\
- ( !defined( $tmp_params{$param_name} ) ) {\n de\
-lete $tmp_params{$param_name};\n }\n }\n\n # Subm\
-it the job as a POST\n my $url = $baseUrl . '/run'\
-;\n my $response = $ua->post( $url, \\%tmp_params \
-);\n print_debug_message( 'rest_run', 'HTTP status\
-: ' . $response->code, 11 );\n print_debug_message\
-( 'rest_run',\n 'request: ' . $response->request(\
-)->content(), 11 );\n\n # Check for HTTP error cod\
-es\n if ( $response->is_error ) {\n $response->co\
-ntent() =~ m/<h1>([^<]+)<\\/h1>/;\n die 'http sta\
-tus: ' . $response->code . ' ' . $response->messag\
-e . ' ' . $1;\n }\n\n # The job id is returned\n \
-my $job_id = $response->content();\n print_debug_m\
-essage( 'rest_run', 'End', 1 );\n return $job_id;\\
-n}\n\n=head2 rest_get_status()\n\nCheck the status\
- of a job.\n\n my $status = &rest_get_status($job\
-_id);\n\n=cut\n\nsub rest_get_status {\n print_deb\
-ug_message( 'rest_get_status', 'Begin', 1 );\n my \
-$job_id = shift;\n print_debug_message( 'rest_get_\
-status', 'jobid: ' . $job_id, 2 );\n my $status_st\
-r = 'UNKNOWN';\n my $url = $baseUrl . '/sta\
-tus/' . $job_id;\n $status_str = &rest_request($ur\
-l);\n print_debug_message( 'rest_get_status', 'sta\
-tus_str: ' . $status_str, 2 );\n print_debug_messa\
-ge( 'rest_get_status', 'End', 1 );\n return $statu\
-s_str;\n}\n\n=head2 rest_get_result_types()\n\nGet\
- list of result types for finished job.\n\n my (@\
-result_types) = &rest_get_result_types($job_id);\n\
-\n=cut\n\nsub rest_get_result_types {\n print_debu\
-g_message( 'rest_get_result_types', 'Begin', 1 );\\
-n my $job_id = shift;\n print_debug_message( 'rest\
-_get_result_types', 'jobid: ' . $job_id, 2 );\n my\
- (@resultTypes);\n my $url = \
-$baseUrl . '/resulttypes/' . $job_id;\n my $result\
-_type_list_xml_str = &rest_request($url);\n my $re\
-sult_type_list_xml = XMLin($result_type_list_x\
-ml_str);\n (@resultTypes) = @{ $result_type_list_x\
-ml->{'type'} };\n print_debug_message( 'rest_get_r\
-esult_types',\n scalar(@resultTypes) . ' result t\
-ypes', 2 );\n print_debug_message( 'rest_get_resul\
-t_types', 'End', 1 );\n return (@resultTypes);\n}\\
-n\n=head2 rest_get_result()\n\nGet result data of \
-a specified type for a finished job.\n\n my $resu\
-lt = rest_get_result($job_id, $result_type);\n\n=c\
-ut\n\nsub rest_get_result {\n print_debug_message(\
- 'rest_get_result', 'Begin', 1 );\n my $job_id = s\
-hift;\n my $type = shift;\n print_debug_message(\
- 'rest_get_result', 'jobid: ' . $job_id, 1 );\n pr\
-int_debug_message( 'rest_get_result', 'type: ' . $\
-type, 1 );\n my $url = $baseUrl . '/result/'\
- . $job_id . '/' . $type;\n my $result = &rest_req\
-uest($url);\n print_debug_message( 'rest_get_resul\
-t', length($result) . ' characters',\n 1 );\n pri\
-nt_debug_message( 'rest_get_result', 'End', 1 );\n\
- return $result;\n}\n\n\n=head2 print_debug_messag\
-e()\n\nPrint debug message at specified debug leve\
-l.\n\n &print_debug_message($method_name, $messag\
-e, $level);\n\n=cut\n\nsub print_debug_message {\n\
- my $function_name = shift;\n my $message = \
-shift;\n my $level = shift;\n if ( $level \
-<= $params{'debugLevel'} ) {\n print STDERR '[', \
-$function_name, '()] ', $message, \"\\n\";\n }\n}\\
-n\n=head2 print_tool_params()\n\nPrint list of too\
-l parameters.\n\n &print_tool_params();\n\n=cut\n\
-\nsub print_tool_params {\n print_debug_message( '\
-print_tool_params', 'Begin', 1 );\n my (@param_lis\
-t) = &rest_get_parameters();\n foreach my $param (\
- sort(@param_list) ) {\n print $param, \"\\n\";\n\
- }\n print_debug_message( 'print_tool_params', 'En\
-d', 1 );\n}\n\n=head2 print_param_details()\n\nPri\
-nt details of a tool parameter.\n\n &print_param_\
-details($param_name);\n\n=cut\n\nsub print_param_d\
-etails {\n print_debug_message( 'print_param_detai\
-ls', 'Begin', 1 );\n my $paramName = shift;\n prin\
-t_debug_message( 'print_param_details', 'paramName\
-: ' . $paramName, 2 );\n my $paramDetail = &rest_g\
-et_parameter_details($paramName);\n print $paramDe\
-tail->{'name'}, \"\\t\", $paramDetail->{'type'}, \\
-"\\n\";\n print $paramDetail->{'description'}, \"\\
-\n\";\n foreach my $value ( @{ $paramDetail->{'val\
-ues'}->{'value'} } ) {\n print $value->{'value'};\
-\n if ( $value->{'defaultValue'} eq 'true' ) {\n \
- print \"\\t\", 'default';\n }\n print \"\\n\";\
-\n print \"\\t\", $value->{'label'}, \"\\n\";\n }\
-\n print_debug_message( 'print_param_details', 'En\
-d', 1 );\n}\n\n=head2 print_job_status()\n\nPrint \
-status of a job.\n\n &print_job_status($job_id);\\
-n\n=cut\n\nsub print_job_status {\n print_debug_me\
-ssage( 'print_job_status', 'Begin', 1 );\n my $job\
-id = shift;\n print_debug_message( 'print_job_stat\
-us', 'jobid: ' . $jobid, 1 );\n if ( $outputLevel \
-> 0 ) {\n print STDERR 'Getting status for job ',\
- $jobid, \"\\n\";\n }\n my $result = &rest_get_sta\
-tus($jobid);\n print \"$result\\n\";\n if ( $resul\
-t eq 'FINISHED' && $outputLevel > 0 ) {\n print S\
-TDERR \"To get results: $scriptName --polljob --jo\
-bid \" . $jobid\n . \"\\n\";\n }\n print_debug_\
-message( 'print_job_status', 'End', 1 );\n}\n\n=he\
-ad2 print_result_types()\n\nPrint available result\
- types for a job.\n\n &print_result_types($job_id\
-);\n\n=cut\n\nsub print_result_types {\n print_deb\
-ug_message( 'result_types', 'Begin', 1 );\n my $jo\
-bid = shift;\n print_debug_message( 'result_types'\
-, 'jobid: ' . $jobid, 1 );\n if ( $outputLevel > 0\
- ) {\n print STDERR 'Getting result types for job\
- ', $jobid, \"\\n\";\n }\n my $status = &rest_get_\
-status($jobid);\n if ( $status eq 'PENDING' || $st\
-atus eq 'RUNNING' ) {\n print STDERR 'Error: Job \
-status is ', $status,\n '. To get result types \
-the job must be finished.', \"\\n\";\n }\n else {\\
-n my (@resultTypes) = &rest_get_result_types($job\
-id);\n if ( $outputLevel > 0 ) {\n print STDOUT\
- 'Available result types:', \"\\n\";\n }\n forea\
-ch my $resultType (@resultTypes) {\n print STDOU\
-T $resultType->{'identifier'}, \"\\n\";\n if ( d\
-efined( $resultType->{'label'} ) ) {\n print ST\
-DOUT \"\\t\", $resultType->{'label'}, \"\\n\";\n \
- }\n if ( defined( $resultType->{'description'} \
-) ) {\n print STDOUT \"\\t\", $resultType->{'de\
-scription'}, \"\\n\";\n }\n if ( defined( $res\
-ultType->{'mediaType'} ) ) {\n print STDOUT \"\\
-\t\", $resultType->{'mediaType'}, \"\\n\";\n }\n\
- if ( defined( $resultType->{'fileSuffix'} ) ) {\
-\n print STDOUT \"\\t\", $resultType->{'fileSuf\
-fix'}, \"\\n\";\n }\n }\n if ( $status eq 'FIN\
-ISHED' && $outputLevel > 0 ) {\n print STDERR \"\
-\\n\", 'To get results:', \"\\n\",\n \" $scri\
-ptName --polljob --jobid \" . $params{'jobid'} . \\
-"\\n\",\n \" $scriptName --polljob --outforma\
-t <type> --jobid \"\n . $params{'jobid'} . \"\\
-\n\";\n }\n }\n print_debug_message( 'result_type\
-s', 'End', 1 );\n}\n\n=head2 submit_job()\n\nSubmi\
-t a job to the service.\n\n &submit_job($seq);\n\\
-n=cut\n\nsub submit_job {\n print_debug_message( '\
-submit_job', 'Begin', 1 );\n\n # Set input sequenc\
-e\n $tool_params{'sequence'} = shift;\n\n # Load p\
-arameters\n &load_params();\n\n # Submit the job\n\
- my $jobid = &rest_run( $params{'email'}, $params{\
-'title'}, \\%tool_params );\n\n # Simulate sync/as\
-ync mode\n if ( defined( $params{'async'} ) ) {\n \
- print STDOUT $jobid, \"\\n\";\n if ( $outputLeve\
-l > 0 ) {\n print STDERR\n \"To check status\
-: $scriptName --status --jobid $jobid\\n\";\n }\n\
- }\n else {\n if ( $outputLevel > 0 ) {\n print\
- STDERR \"JobId: $jobid\\n\";\n }\n sleep 1;\n \
-&get_results($jobid);\n }\n print_debug_message( '\
-submit_job', 'End', 1 );\n}\n\n=head2 multi_submit\
-_job()\n\nSubmit multiple jobs assuming input is a\
- collection of fasta formatted sequences.\n\n &mu\
-lti_submit_job();\n\n=cut\n\nsub multi_submit_job \
-{\n print_debug_message( 'multi_submit_job', 'Begi\
-n', 1 );\n my $jobIdForFilename = 1;\n $jobIdForFi\
-lename = 0 if ( defined( $params{'outfile'} ) );\n\
- my (@filename_list) = ();\n\n # Query sequence\n \
-if ( defined( $ARGV[0] ) ) { # Bare option\n i\
-f ( -f $ARGV[0] || $ARGV[0] eq '-' ) { # File\n\
- push( @filename_list, $ARGV[0] );\n }\n }\n if\
- ( $params{'sequence'} ) { # Via\
- --sequence\n if ( -f $params{'sequence'} || $par\
-ams{'sequence'} eq '-' ) { # File\n push( @fi\
-lename_list, $params{'sequence'} );\n }\n }\n\n $\
-/ = '>';\n foreach my $filename (@filename_list) {\
-\n open( my $INFILE, '<', $filename )\n or die\
- \"Error: unable to open file $filename ($!)\";\n \
- while (<$INFILE>) {\n my $seq = $_;\n $seq =~\
- s/>$//;\n if ( $seq =~ m/(\\S+)/ ) {\n print\
- STDERR \"Submitting job for: $1\\n\"\n if ( \
-$outputLevel > 0 );\n $seq = '>' . $seq;\n &\
-print_debug_message( 'multi_submit_job', $seq, 11 \
-);\n &submit_job($seq);\n $params{'outfile'}\
- = undef if ( $jobIdForFilename == 1 );\n }\n }\
-\n close $INFILE;\n }\n print_debug_message( 'mul\
-ti_submit_job', 'End', 1 );\n}\n\n=head2 list_file\
-_submit_job()\n\nSubmit multiple jobs using a file\
- containing a list of entry identifiers as \ninput\
-.\n\n &list_file_submit_job($list_filename)\n\n=c\
-ut\n\nsub list_file_submit_job {\n my $filename \
- = shift;\n my $jobIdForFilename = 1;\n $jobI\
-dForFilename = 0 if ( defined( $params{'outfile'} \
-) );\n\n # Iterate over identifiers, submitting ea\
-ch job\n open( my $LISTFILE, '<', $filename )\n \
-or die 'Error: unable to open file ' . $filename .\
- ' (' . $! . ')';\n while (<$LISTFILE>) {\n my $l\
-ine = $_;\n chomp($line);\n if ( $line ne '' ) {\
-\n &print_debug_message( 'list_file_submit_job',\
- 'line: ' . $line, 2 );\n if ( $line =~ m/\\w:\\\
-w/ ) { # Check this is an identifier\n print\
- STDERR \"Submitting job for: $line\\n\"\n if\
- ( $outputLevel > 0 );\n &submit_job($line);\n \
- }\n else {\n print STDERR\n\"Warning: line \
-\\\"$line\\\" is not recognised as an identifier\\\
-n\";\n }\n }\n $params{'outfile'} = undef if (\
- $jobIdForFilename == 1 );\n }\n close $LISTFILE;\\
-n}\n\n=head2 load_data()\n\nLoad sequence data fro\
-m file or option specified on the command-line.\n\\
-n &load_data();\n\n=cut\n\nsub load_data {\n prin\
-t_debug_message( 'load_data', 'Begin', 1 );\n my $\
-retSeq;\n\n # Query sequence\n if ( defined( $ARGV\
-[0] ) ) { # Bare option\n if ( -f $ARGV[0] || \
-$ARGV[0] eq '-' ) { # File\n $retSeq = &read_\
-file( $ARGV[0] );\n }\n else { \
- # DB:ID or sequence\n $retSeq\
- = $ARGV[0];\n }\n }\n if ( $params{'sequence'} )\
- { # Via --sequence\n if ( -f $\
-params{'sequence'} || $params{'sequence'} eq '-' )\
- { # File\n $retSeq = &read_file( $params{'se\
-quence'} );\n }\n else { # DB:ID or sequence\\
-n $retSeq = $params{'sequence'};\n }\n }\n prin\
-t_debug_message( 'load_data', 'End', 1 );\n return\
- $retSeq;\n}\n\n=head2 load_params()\n\nLoad job p\
-arameters from command-line options.\n\n &load_pa\
-rams();\n\n=cut\n\nsub load_params {\n print_debug\
-_message( 'load_params', 'Begin', 1 );\n\n # Datab\
-ase(s) to search\n my (@dbList) = split /[ ,]/, $p\
-arams{'database'};\n $tool_params{'database'} = \\\
-@dbList;\n\n # Compatability options, old command-\
-line.\n if(!$tool_params{'viewfilter'} && $params{\
-'echofilter'}) {\n $tool_params{'viewfilter'} = '\
-true';\n }\n if(!$tool_params{'alignments'} && $pa\
-rams{'numal'}) {\n $tool_params{'alignments'} = $\
-params{'numal'};\n }\n # TODO: set alignment forma\
-t option to get NCBI BLAST XML.\n if($params{'appx\
-ml'}) {\n $tool_params{'align'} = '';\n }\n\n pri\
-nt_debug_message( 'load_params', 'End', 1 );\n}\n\\
-n=head2 client_poll()\n\nClient-side job polling.\\
-n\n &client_poll($job_id);\n\n=cut\n\nsub client_\
-poll {\n print_debug_message( 'client_poll', 'Begi\
-n', 1 );\n my $jobid = shift;\n my $status = 'PEN\
-DING';\n\n my $errorCount = 0;\n while ($status eq\
- 'RUNNING'\n || $status eq 'PENDING'\n || ( $sta\
-tus eq 'ERROR' && $errorCount < 2 ) )\n {\n $stat\
-us = rest_get_status($jobid);\n print STDERR \"$s\
-tatus\\n\" if ( $outputLevel > 0 );\n if ( $statu\
-s eq 'ERROR' ) {\n $errorCount++;\n }\n elsif \
-( $errorCount > 0 ) {\n $errorCount--;\n }\n i\
-f ( $status eq 'RUNNING'\n || $status eq 'PEND\
-ING'\n || $status eq 'ERROR' )\n {\n\n # Wait\
- before polling again.\n sleep $checkInterval;\n\
- }\n }\n print_debug_message( 'client_poll', 'End\
-', 1 );\n return $status;\n}\n\n=head2 get_results\
-()\n\nGet the results for a job identifier.\n\n &\
-get_results($job_id);\n\n=cut\n\nsub get_results {\
-\n print_debug_message( 'get_results', 'Begin', 1 \
-);\n my $jobid = shift;\n print_debug_message( 'ge\
-t_results', 'jobid: ' . $jobid, 1 );\n\n # Verbose\
-\n if ( $outputLevel > 1 ) {\n print 'Getting res\
-ults for job ', $jobid, \"\\n\";\n }\n\n # Check s\
-tatus, and wait if not finished\n client_poll($job\
-id);\n\n # Use JobId if output file name is not de\
-fined\n unless ( defined( $params{'outfile'} ) ) {\
-\n $params{'outfile'} = $jobid;\n }\n\n # Get lis\
-t of data types\n my (@resultTypes) = rest_get_res\
-ult_types($jobid);\n\n # Get the data and write it\
- to a file\n if ( defined( $params{'outformat'} ) \
-) { # Specified data type\n my $selResultType;\
-\n foreach my $resultType (@resultTypes) {\n if\
- ( $resultType->{'identifier'} eq $params{'outform\
-at'} ) {\n $selResultType = $resultType;\n }\\
-n }\n if ( defined($selResultType) ) {\n my $r\
-esult =\n rest_get_result( $jobid, $selResultT\
-ype->{'identifier'} );\n if ( $params{'outfile'}\
- eq '-' ) {\n write_file( $params{'outfile'}, $\
-result );\n }\n else {\n write_file(\n \
-$params{'outfile'} . '.'\n . $selResultType-\
->{'identifier'} . '.'\n . $selResultType->{'\
-fileSuffix'},\n $result\n );\n }\n }\n \
-else {\n die 'Error: unknown result format \"' .\
- $params{'outformat'} . '\"';\n }\n }\n else { \
- # Data types available\n # Write a file fo\
-r each output type\n for my $resultType (@resultT\
-ypes) {\n if ( $outputLevel > 1 ) {\n print S\
-TDERR 'Getting ', $resultType->{'identifier'}, \"\\
-\n\";\n }\n my $result = rest_get_result( $job\
-id, $resultType->{'identifier'} );\n if ( $param\
-s{'outfile'} eq '-' ) {\n write_file( $params{'\
-outfile'}, $result );\n }\n else {\n write_\
-file(\n $params{'outfile'} . '.'\n . $re\
-sultType->{'identifier'} . '.'\n . $resultTy\
-pe->{'fileSuffix'},\n $result\n );\n }\n \
- }\n }\n print_debug_message( 'get_results', 'End'\
-, 1 );\n}\n\n=head2 read_file()\n\nRead a file int\
-o a scalar. The special filename '-' can be used t\
-o read from \nstandard input (STDIN).\n\n my $dat\
-a = &read_file($filename);\n\n=cut\n\nsub read_fil\
-e {\n print_debug_message( 'read_file', 'Begin', 1\
- );\n my $filename = shift;\n print_debug_message(\
- 'read_file', 'filename: ' . $filename, 2 );\n my \
-( $content, $buffer );\n if ( $filename eq '-' ) {\
-\n while ( sysread( STDIN, $buffer, 1024 ) ) {\n \
- $content .= $buffer;\n }\n }\n else { # File\
-\n open( my $FILE, '<', $filename )\n or die \\
-"Error: unable to open input file $filename ($!)\"\
-;\n while ( sysread( $FILE, $buffer, 1024 ) ) {\n\
- $content .= $buffer;\n }\n close($FILE);\n }\\
-n print_debug_message( 'read_file', 'End', 1 );\n \
-return $content;\n}\n\n=head2 write_file()\n\nWrit\
-e data to a file. The special filename '-' can be \
-used to write to \nstandard output (STDOUT).\n\n \
-&write_file($filename, $data);\n\n=cut\n\nsub writ\
-e_file {\n print_debug_message( 'write_file', 'Beg\
-in', 1 );\n my ( $filename, $data ) = @_;\n print_\
-debug_message( 'write_file', 'filename: ' . $filen\
-ame, 2 );\n if ( $outputLevel > 0 ) {\n print STD\
-ERR 'Creating result file: ' . $filename . \"\\n\"\
-;\n }\n if ( $filename eq '-' ) {\n print STDOUT \
-$data;\n }\n else {\n open( my $FILE, '>', $filen\
-ame )\n or die \"Error: unable to open output f\
-ile $filename ($!)\";\n syswrite( $FILE, $data );\
-\n close($FILE);\n }\n print_debug_message( 'writ\
-e_file', 'End', 1 );\n}\n\n=head2 usage()\n\nPrint\
- program usage message.\n\n &usage();\n\n=cut\n\n\
-sub usage {\n print STDERR <<EOF\nWU-BLAST\n======\
-==\n \nRapid sequence database search programs u\
-tilizing the BLAST algorithm\n \n[Required]\n\n\
- -p, --program : str : BLAST program to use\
-, see --paramDetail program\n -D, --database \
-: str : database(s) to search, space separated. S\
-ee\n --paramDetail da\
-tabase\n --stype : str : query sequen\
-ce type, see --paramDetail stype\n seqFile \
- : file : query sequence (\"-\" for STDIN, \\@\
-filename for\n identi\
-fier list file)\n\n[Optional]\n\n -m, --matrix \
- : str : scoring matrix, see --paramDetail mat\
-rix\n -e, --exp : real : 0<E<= 1000. Sta\
-tistical significance threshold \n \
- for reporting database sequence matc\
-hes.\n -e, --viewfilter : : display the fi\
-ltered query sequence\n -f, --filter : str \
- : filter the query sequence for low complexity \n\
- regions, see --param\
-Detail filter\n -A, --align : int : pairw\
-ise alignment format, see --paramDetail align\n -\
-s, --scores : int : number of scores to be \
-reported\n -b, --alignments : int : number of \
-alignments to report\n -S, --sensitivity : str \
-: sensitivity of the search, \n \
- see --paramDetail sensitivity\n -t, --\
-sort : str : sort order for hits, see --para\
-mDetail sort\n -T, --stats : str : statis\
-tical model, see --paramDetail stats\n -d, --stra\
-nd : str : DNA strand to search with,\n \
- see --paramDetail strand\
-\n -c, --topcombon : str : consistent sets of\
- HSPs\n --multifasta : : treat input a\
-s a set of fasta formatted sequences\n\n[General]\\
-n\n -h, --help : : prints this help t\
-ext\n --async : : forces to make a\
-n asynchronous query\n --email : str :\
- e-mail address\n --title : str : titl\
-e for job\n --status : : get job st\
-atus\n --resultTypes : : get available r\
-esult types for job\n --polljob : : \
-poll for the status of a job\n --jobid \
-: str : jobid that was returned when an asynchron\
-ous job \n was submitt\
-ed.\n --outfile : str : file name for re\
-sults (default is jobid;\n \
- \"-\" for STDOUT)\n --outformat : str \
- : result format to retrieve\n --params \
-: : list input parameters\n --paramDetai\
-l : str : display details for input parameter\n \
- --quiet : : decrease output\n \
---verbose : : increase output\n --tr\
-ace : : show SOAP messages being interc\
-hanged \n \nSynchronous job:\n\n The results/er\
-rors are returned as soon as the job is finished.\\
-n Usage: $scriptName --email <your\\@email> [opti\
-ons...] seqFile\n Returns: results as an attachme\
-nt\n\nAsynchronous job:\n\n Use this if you want \
-to retrieve the results at a later time. The resul\
-ts \n are stored for up to 24 hours. \n Usage: \
-$scriptName --async --email <your\\@email> [option\
-s...] seqFile\n Returns: jobid\n\n Use the jobid\
- to query for the status of the job. If the job is\
- finished, \n it also returns the results/errors.\
-\n Usage: $scriptName --polljob --jobid <jobId> [\
---outfile string]\n Returns: string indicating th\
-e status of the job and if applicable, results \n \
- as an attachment.\n\nFurther information:\n\n ht\
-tp://www.ebi.ac.uk/Tools/webservices/services/sss/\
-wu_blast_rest\n http://www.ebi.ac.uk/Tools/webser\
-vices/tutorials/perl\n\nSupport/Feedback:\n\n htt\
-p://www.ebi.ac.uk/support/\nEOF\n}\n\n=head1 FEEDB\
-ACK/SUPPORT\n\nPlease contact us at L<http://www.e\
-bi.ac.uk/support/> if you have any \nfeedback, sug\
-gestions or issues with the service or this client\
-.\n\n=cut\n","\n\n\nmy $PROBTRESH = 0.3;# base pai\
-rs below this prob threshold will be ignored\nmy $\
-WEIGHT = 100.0; # float!!\nmy $NUCALPH = \"ACGTUNR\
-YMKSWHBVD\";\nuse vars qw($NUCALPH $WEIGHT);\n\nmy\
- $myname = basename($0);\n\nuse strict;\nuse warni\
-ngs;\n\nuse File::Basename;\nuse Getopt::Long;\nus\
-e File::Glob ':glob';\nuse File::Spec;\nuse File::\
-Temp qw/ tempfile tempdir /;\n\n\n\n\nsub tcoffeel\
-ib_header($;$)\n{\n my ($nseq, $fd) = @_;\n \
-if (! defined($fd)) {\n $fd = *STDOUT;\n \
- }\n printf $fd \"! TC_LIB_FORMAT_01\\n\";\n \
- printf $fd \"%d\\n\", $nseq;\n}\n\n\nsub tcoffeel\
-ib_header_addseq($$;$)\n{\n my ($id, $seq, $fd)\
- = @_;\n if (! defined($fd)) {\n $fd = *\
-STDOUT;\n }\n printf $fd \"%s %d %s\\n\", $i\
-d, length($seq), $seq;\n}\n\n\nsub tcoffeelib_comm\
-ent($;$)\n{\n my ($comment, $fd) = @_;\n if \
-(! defined($fd)) {\n $fd = *STDOUT;\n }\\
-n printf $fd \"!\" . $comment . \"\\n\";\n}\n\n\
-\nsub tcoffeelib_struct($$$;$)\n{\n my ($nseq, \
-$len, $bpm, $fd) = @_;\n\n if (! defined($fd)) \
-{\n $fd = *STDOUT;\n }\n\n # output b\
-asepair indices with fixed weight\n printf $fd \
-\"#%d %d\\n\", $nseq, $nseq;\n # output basepai\
-rs (only once) and with unit-offset\n for (my $\
-i=0; $i<$len; $i++) {\n for (my $j=$i+1; $j\
-<$len; $j++) {\n if (! defined($bpm->[$\
-i][$j])) {\n print STDERR \"ERROR: \
-\\$bpm->[$i][$j] undefined\\n\";\n }\n \
- if ($bpm->[$i][$j]>0) {\n \
- print $fd $i+1;\n print $fd \" \"\
-;\n print $fd $j+1;\n \
- print $fd \" \" . $bpm->[$i][$j] . \"\\n\";\n \
- }\n }\n }\n}\n\n\nsub tcoffeeli\
-b_footer(;$)\n{\n my ($fd) = @_;\n if (! def\
-ined($fd)) {\n $fd = *STDOUT;\n }\n p\
-rint $fd \"! SEQ_1_TO_N\\n\";\n}\n\n\n \nsub pl\
-fold($$$)\n{ \n my ($id, $seq, $probtresh) =\
- @_;\n my (@struct);# return\n my ($templ, $\
-fhtmp, $fnametmp, $cmd, $ctr, $window_size);\n \
-our $ntemp++;\n \n $templ = $myname . \".pid\
--\" . $$ .$ntemp .\".XXXXXX\";\n ($fhtmp, $fnam\
-etmp) = tempfile($templ, UNLINK => 1); \n print\
- $fhtmp \">$id\\n$seq\\n\";\n\n # --- init base\
-pair array\n #\n for (my $i=0; $i<length($se\
-q); $i++) {\n for (my $j=$i+1; $j<length($s\
-eq); $j++) {\n $struct[$i][$j]=0;\n \
- }\n }\n\n\n # --- call rnaplfold and dro\
-p a readme\n #\n $window_size=(length($seq)<\
-70)?length($seq):70;\n $cmd = \"RNAplfold -W $w\
-indow_size < $fnametmp >/dev/null\";\n system($\
-cmd);\n \n if ($? != 0) {\n printf ST\
-DERR \"ERROR: RNAplfold ($cmd) exited with error s\
-tatus %d\\n\", $? >> 8;\n return;\n }\n \
- #unlink($fnametmp);\n my $fps = sprintf(\"%s\
-_dp.ps\", $id); # check long name\n \n if (!\
- -s $fps) {\n {\n\n $fps = sprintf(\"%s_dp.ps\
-\", substr($id,0,12)); # check short name\n if (!\
- -s $fps)\n {\n die(\"couldn't find expected\
- file $fps\\n\");\n return;\n }\n }\n \
- }\n\n \n # --- read base pairs from create\
-d postscript\n #\n open(FH, $fps);\n whil\
-e (my $line = <FH>) {\n my ($nti, $ntj, $pr\
-ob);\n chomp($line); \n # lin\
-e: bp bp sqrt-prob ubox\n my @match = ($lin\
-e =~ m/^([0-9]+) +([0-9]+) +([0-9\\.]+) +ubox$/);\\
-n if (scalar(@match)) {\n $nti=$\
-1;\n $ntj=$2;\n $prob=$3*$3;\
-# prob stored as square root\n\n if ($p\
-rob>$probtresh) {\n #printf STDERR \
-\"\\$struct[$nti][$ntj] sqrtprob=$3 prob=$prob > $\
-probtresh\\n\";\n $struct[$nti-1][$\
-ntj-1] = $WEIGHT\n }\n # sto\
-re with zero-offset\n }\n }\n close(F\
-H);\n\n # remove or gzi postscript\n #\n \
-unlink($fps);\n #\n # or gzip\n #$cmd = \\
-"gzip -qf $fps\";\n #system($cmd);\n #if ($?\
- != 0) {\n # printf STDERR \"ERROR: gzip ($c\
-md) exited with error status %d\\n\", $? >> 8;\n \
- #}\n\n return \\@struct;\n}\n\n\n\n\n\nsub rn\
-aseqfmt($)\n{\n my ($seq) = @_;\n # remove g\
-aps\n $seq =~ s/-//g;\n # uppercase RNA\n \
- $seq = uc($seq);\n # T -> U\n $seq =~ s/T/U\
-/g;\n # check for invalid charaters\n $_ = $\
-seq;\n s/[^$NUCALPH]//g;\n return $_;\n}\n\n\
-\n\n\nsub usage(;$)\n{ \n my ($errmsg) = @_;\
-\n if ($errmsg) {\n print STDERR \"ERROR\
-: $errmsg\\n\";\n }\n print STDERR << \"EOF\\
-";\n$myname:\n Creates a T-Coffee RNA structure li\
-brary from RNAplfold prediction.\n See FIXME:citat\
-ion\nUsage:\n $myname -in seq_file -out tcoffee_li\
-b\nEOF\n exit(1);\n}\n\nsub read_fasta_seq \n \
-{\n my $f=$_[0];\n my %hseq;\n my (@seq, \
-@com, @name);\n my ($a, $s,$nseq);\n\n open \
-(F, $f);\n while (<F>)\n {\n $s.=$_;\n \
- }\n close (F);\n\n \n @name=($s=~/>(\\S\
-*).*\\n[^>]*/g);\n \n @seq =($s=~/>.*.*\\n([\
-^>]*)/g);\n @com =($s=~/>(\\S*)(.*)\\n([^>]*)/g\
-);\n\n\n $nseq=$#name+1;\n \n for ($a=0; $a\
-<$nseq; $a++)\n {\n my $n=$name[$a];\n my $s;\
-\n $hseq{$n}{name}=$n;\n $s=$seq[$a];$s=~s/\\s//g;\
-\n \n $hseq{$n}{seq}=$s;\n $hseq{$n}{com}=$com[$a]\
-;\n }\n return %hseq;\n }\n\n\n\n\n\n\n\n\
-my $fmsq = \"\";\nmy $flib = \"\";\nmy %OPTS;\nmy \
-%seq;\nmy ($id, $nseq, $i);\nmy @nl;\n\nGetOptions\
-(\"in=s\" => \\$fmsq, \"out=s\" => \\$flib);\n\nif\
- (! -s $fmsq) {\n usage(\"empty or non-existant\
- file \\\"$fmsq\\\"\")\n}\nif (length($flib)==0) {\
-\n usage(\"empty out-filename\")\n}\n\n\n\n\n\n\
-\n%seq=read_fasta_seq($fmsq);\n\n\n@nl=keys(%seq);\
-\n\n$nseq=$#nl+1;\nopen FD_LIB, \">$flib\" or die \
-\"can't open $flib!\";\ntcoffeelib_header($nseq, *\
-FD_LIB);\nforeach $id (keys (%seq))\n {\n my (\
-$seq, $fmtseq);\n \n $seq = $seq{$id}{seq};\\
-n \n $fmtseq = rnaseqfmt($seq);# check here,\
- formatting for folding important later\n if (l\
-ength($seq)!=length($fmtseq)) {\n print STD\
-ERR \"ERROR: invalid sequence $id is not an RNA se\
-quence. read seq is: $seq\\n\";\n exit\n \
- }\n \n tcoffeelib_header_addseq($id, uc($s\
-eq), *FD_LIB);\n }\ntcoffeelib_comment(\"generate\
-d by $myname on \" . localtime(), *FD_LIB);\n\n\n\\
-n$i=0;\nforeach $id (keys (%seq))\n {\n my ($c\
-leanid, $seq, $bpm);\n $seq=$seq{$id}{seq};\n \
- $cleanid = $id;\n $cleanid =~ s,[/ ],_,g;# ne\
-eded for rnaplfold\n $seq = rnaseqfmt($seq);\n \
- \n $bpm = plfold($cleanid, rnaseqfmt($seq), \
-$PROBTRESH); \n \n tcoffeelib_struct($\
-i+1, length($seq), $bpm, *FD_LIB);\n $i++;\n}\n\
-\n\ntcoffeelib_footer(*FD_LIB);\nclose FD_LIB;\nex\
-it (0);\n\n","\n\n\n\n\n$cmd=join ' ', @ARGV;\nif \
-($cmd=~/-infile=(\\S+)/){ $seqfile=$1;}\nif ($cmd=\
-~/-outfile=(\\S+)/){ $libfile=$1;}\n\n\n\n%s=read_\
-fasta_seq ($seqfile);\n\nopen (F, \">$libfile\");\\
-nforeach $name (keys (%s))\n {\n my $tclib=\"$\
-name.RNAplfold_tclib\";\n print (F \">$name _F_\
- $tclib\\n\");\n seq2RNAplfold2tclib ($name, $s\
-{$name}{seq}, $tclib);\n }\nclose (F);\nexit (EXI\
-T_SUCCESS);\n\nsub seq2RNAplfold2tclib\n {\n m\
-y ($name, $seq, $tclib)=@_;\n my ($tmp);\n $\
-n++;\n $tmp=\"tmp4seq2RNAplfold_tclib.$$.$n.pep\
-\";\n open (RF, \">$tmp\");\n print (RF \">$\
-name\\n$seq\\n\");\n close (RF);\n \n sys\
-tem \"t_coffee -other_pg RNAplfold2tclib.pl -in=$t\
-mp -out=$tclib\";\n \n unlink ($tmp);\n r\
-eturn $tclib;\n }\n \n \nsub read_fasta_seq\
- \n {\n my $f=@_[0];\n my %hseq;\n my (@\
-seq, @com, @name);\n my ($a, $s,$nseq);\n\n \
+tputLevel++ }\nif ( $params{'quiet'} ) { $outputL\
+evel-- }\n\n&print_debug_message( 'MAIN', 'LWP::VE\
+RSION: ' . $LWP::VERSION,\n 1 );\n\n&print_debug_m\
+essage( 'MAIN', \"params:\\n\" . Dumper( \\%params\
+ ), 11 );\n&print_debug_message( 'MAIN',\
+ \"tool_params:\\n\" . Dumper( \\%tool_params ), 1\
+1 );\n\nmy $ua;\n\nmy $scriptName = basename( $0, \
+() );\n\nif ( $params{'help'} || $numOpts == 0 ) {\
+\n &usage();\n exit(0);\n}\n\n&print_debug_message\
+( 'MAIN', 'baseUrl: ' . $baseUrl, 1 );\n\nif (\n !\
+(\n $params{'polljob'}\n || $params{'resultTy\
+pes'}\n || $params{'status'}\n || $params{'param\
+s'}\n || $params{'paramDetail'}\n )\n && !( defin\
+ed( $ARGV[0] ) || defined( $params{'sequence'} ) )\
+\n )\n{\n\n # Bad argument combination, so print \
+error message and usage\n print STDERR 'Error: bad\
+ option combination', \"\\n\";\n &usage();\n exit(\
+1);\n}\n\nelsif ( $params{'params'} ) {\n &print_t\
+ool_params();\n}\n\nelsif ( $params{'paramDetail'}\
+ ) {\n &print_param_details( $params{'paramDetail'\
+} );\n}\n\nelsif ( $params{'status'} && defined( $\
+params{'jobid'} ) ) {\n &print_job_status( $params\
+{'jobid'} );\n}\n\nelsif ( $params{'resultTypes'} \
+&& defined( $params{'jobid'} ) ) {\n &print_result\
+_types( $params{'jobid'} );\n}\n\nelsif ( $params{\
+'polljob'} && defined( $params{'jobid'} ) ) {\n &g\
+et_results( $params{'jobid'} );\n}\n\nelse {\n\n #\
+ Multiple input sequence mode, assume fasta format\
+.\n if ( $params{'multifasta'} ) {\n &multi_submi\
+t_job();\n }\n\n # Entry identifier list file.\n e\
+lsif (( defined( $params{'sequence'} ) && $params{\
+'sequence'} =~ m/^\\@/ )\n || ( defined( $ARGV[0]\
+ ) && $ARGV[0] =~ m/^\\@/ ) )\n {\n my $list_file\
+name = $params{'sequence'} || $ARGV[0];\n $list_f\
+ilename =~ s/^\\@//;\n &list_file_submit_job($lis\
+t_filename);\n }\n\n # Default: single sequence/id\
+entifier.\n else {\n\n # Load the sequence data a\
+nd submit.\n &submit_job( &load_data() );\n }\n}\\
+n\n=head1 FUNCTIONS\n\n=cut\n\n\n=head2 rest_user_\
+agent()\n\nGet a LWP UserAgent to use to perform R\
+EST requests.\n\n my $ua = &rest_user_agent();\n\\
+n=cut\n\nsub rest_user_agent() {\n print_debug_mes\
+sage( 'rest_user_agent', 'Begin', 21 );\n # Create\
+ an LWP UserAgent for making HTTP calls.\n my $ua \
+= LWP::UserAgent->new();\n # Set 'User-Agent' HTTP\
+ header to identifiy the client.\n '$Revision: 256\
+0 $' =~ m/(\\d+)/;\n $ua->agent(\"EBI-Sample-Clien\
+t/$1 ($scriptName; $OSNAME) \" . $ua->agent());\n \
+# Configure HTTP proxy support from environment.\n\
+ $ua->env_proxy;\n print_debug_message( 'rest_user\
+_agent', 'End', 21 );\n return $ua;\n}\n\n=head2 r\
+est_error()\n\nCheck a REST response for an error \
+condition. An error is mapped to a die.\n\n &rest\
+_error($response, $content_data);\n\n=cut\n\nsub r\
+est_error() {\n print_debug_message( 'rest_error',\
+ 'Begin', 21 );\n my $response = shift;\n my $cont\
+entdata;\n if(scalar(@_) > 0) {\n $contentdata = \
+shift;\n }\n if(!defined($contentdata) || $content\
+data eq '') {\n $contentdata = $response->content\
+();\n }\n # Check for HTTP error codes\n if ( $res\
+ponse->is_error ) {\n my $error_message = '';\n \
+# HTML response.\n if( $contentdata =~ m/<h1>([^<\
+]+)<\\/h1>/ ) {\n $error_message = $1;\n }\n #\
+ XML response.\n elsif($contentdata =~ m/<descri\
+ption>([^<]+)<\\/description>/) {\n $error_messa\
+ge = $1;\n }\n die 'http status: ' . $response->\
+code . ' ' . $response->message . ' ' . $error_me\
+ssage;\n }\n print_debug_message( 'rest_error', 'E\
+nd', 21 );\n}\n\n=head2 rest_request()\n\nPerform \
+a REST request (HTTP GET).\n\n my $response_str =\
+ &rest_request($url);\n\n=cut\n\nsub rest_request \
+{\n print_debug_message( 'rest_request', 'Begin', \
+11 );\n my $requestUrl = shift;\n print_debug_mess\
+age( 'rest_request', 'URL: ' . $requestUrl, 11 );\\
+n\n # Get an LWP UserAgent.\n $ua = &rest_user_age\
+nt() unless defined($ua);\n # Available HTTP compr\
+ession methods.\n my $can_accept;\n eval {\n $\
+can_accept = HTTP::Message::decodable();\n };\n $c\
+an_accept = '' unless defined($can_accept);\n # Pe\
+rform the request\n my $response = $ua->get($reque\
+stUrl,\n 'Accept-Encoding' => $can_accept, # HTTP\
+ compression.\n );\n print_debug_message( 'rest_re\
+quest', 'HTTP status: ' . $response->code,\n 11 )\
+;\n print_debug_message( 'rest_request',\n 'respo\
+nse length: ' . length($response->content()), 11 )\
+;\n print_debug_message( 'rest_request',\n 'reque\
+st:' .\"\\n\" . $response->request()->as_string(),\
+ 32 );\n print_debug_message( 'rest_request',\n '\
+response: ' . \"\\n\" . $response->as_string(), 32\
+ );\n # Unpack possibly compressed response.\n my \
+$retVal;\n if ( defined($can_accept) && $can_accep\
+t ne '') {\n $retVal = $response->decoded_cont\
+ent();\n }\n # If unable to decode use orginal con\
+tent.\n $retVal = $response->content() unless defi\
+ned($retVal);\n # Check for an error.\n &rest_erro\
+r($response, $retVal);\n print_debug_message( 'res\
+t_request', 'retVal: ' . $retVal, 12 );\n print_de\
+bug_message( 'rest_request', 'End', 11 );\n\n # Re\
+turn the response data\n return $retVal;\n}\n\n=he\
+ad2 rest_get_parameters()\n\nGet list of tool para\
+meter names.\n\n my (@param_list) = &rest_get_par\
+ameters();\n\n=cut\n\nsub rest_get_parameters {\n \
+print_debug_message( 'rest_get_parameters', 'Begin\
+', 1 );\n my $url = $baseUrl . '/pa\
+rameters/';\n my $param_list_xml_str = rest_reques\
+t($url);\n my $param_list_xml = XMLin($param_l\
+ist_xml_str);\n my (@param_list) = @{ $param\
+_list_xml->{'id'} };\n print_debug_message( 'rest_\
+get_parameters', 'End', 1 );\n return (@param_list\
+);\n}\n\n=head2 rest_get_parameter_details()\n\nGe\
+t details of a tool parameter.\n\n my $paramDetai\
+l = &rest_get_parameter_details($param_name);\n\n=\
+cut\n\nsub rest_get_parameter_details {\n print_de\
+bug_message( 'rest_get_parameter_details', 'Begin'\
+, 1 );\n my $parameterId = shift;\n print_debug_me\
+ssage( 'rest_get_parameter_details',\n 'parameter\
+Id: ' . $parameterId, 1 );\n my $url \
+ = $baseUrl . '/parameterdetails/' . $parameter\
+Id;\n my $param_detail_xml_str = rest_request($url\
+);\n my $param_detail_xml = XMLin($param_detai\
+l_xml_str);\n print_debug_message( 'rest_get_param\
+eter_details', 'End', 1 );\n return ($param_detail\
+_xml);\n}\n\n=head2 rest_run()\n\nSubmit a job.\n\\
+n my $job_id = &rest_run($email, $title, \\%param\
+s );\n\n=cut\n\nsub rest_run {\n print_debug_messa\
+ge( 'rest_run', 'Begin', 1 );\n my $email = shift\
+;\n my $title = shift;\n my $params = shift;\n pr\
+int_debug_message( 'rest_run', 'email: ' . $email,\
+ 1 );\n if ( defined($title) ) {\n print_debug_me\
+ssage( 'rest_run', 'title: ' . $title, 1 );\n }\n \
+print_debug_message( 'rest_run', 'params: ' . Dump\
+er($params), 1 );\n\n # Get an LWP UserAgent.\n $u\
+a = &rest_user_agent() unless defined($ua);\n\n # \
+Clean up parameters\n my (%tmp_params) = %{$params\
+};\n $tmp_params{'email'} = $email;\n $tmp_params{\
+'title'} = $title;\n foreach my $param_name ( keys\
+(%tmp_params) ) {\n if ( !defined( $tmp_params{$p\
+aram_name} ) ) {\n delete $tmp_params{$param_nam\
+e};\n }\n }\n\n # Submit the job as a POST\n my $\
+url = $baseUrl . '/run';\n my $response = $ua->pos\
+t( $url, \\%tmp_params );\n print_debug_message( '\
+rest_run', 'HTTP status: ' . $response->code, 11 )\
+;\n print_debug_message( 'rest_run',\n 'request:'\
+ .\"\\n\" . $response->request()->as_string(), 11 \
+);\n print_debug_message( 'rest_run',\n 'response\
+: ' . length($response->as_string()) . \"\\n\" . $\
+response->as_string(), 11 );\n\n # Check for an er\
+ror.\n &rest_error($response);\n\n # The job id is\
+ returned\n my $job_id = $response->content();\n p\
+rint_debug_message( 'rest_run', 'End', 1 );\n retu\
+rn $job_id;\n}\n\n=head2 rest_get_status()\n\nChec\
+k the status of a job.\n\n my $status = &rest_get\
+_status($job_id);\n\n=cut\n\nsub rest_get_status {\
+\n print_debug_message( 'rest_get_status', 'Begin'\
+, 1 );\n my $job_id = shift;\n print_debug_message\
+( 'rest_get_status', 'jobid: ' . $job_id, 2 );\n m\
+y $status_str = 'UNKNOWN';\n my $url = $bas\
+eUrl . '/status/' . $job_id;\n $status_str = &rest\
+_request($url);\n print_debug_message( 'rest_get_s\
+tatus', 'status_str: ' . $status_str, 2 );\n print\
+_debug_message( 'rest_get_status', 'End', 1 );\n r\
+eturn $status_str;\n}\n\n=head2 rest_get_result_ty\
+pes()\n\nGet list of result types for finished job\
+.\n\n my (@result_types) = &rest_get_result_types\
+($job_id);\n\n=cut\n\nsub rest_get_result_types {\\
+n print_debug_message( 'rest_get_result_types', 'B\
+egin', 1 );\n my $job_id = shift;\n print_debug_me\
+ssage( 'rest_get_result_types', 'jobid: ' . $job_i\
+d, 2 );\n my (@resultTypes);\n my $url \
+ = $baseUrl . '/resulttypes/' . $job_id;\\
+n my $result_type_list_xml_str = &rest_request($ur\
+l);\n my $result_type_list_xml = XMLin($result\
+_type_list_xml_str);\n (@resultTypes) = @{ $result\
+_type_list_xml->{'type'} };\n print_debug_message(\
+ 'rest_get_result_types',\n scalar(@resultTypes) \
+. ' result types', 2 );\n print_debug_message( 're\
+st_get_result_types', 'End', 1 );\n return (@resul\
+tTypes);\n}\n\n=head2 rest_get_result()\n\nGet res\
+ult data of a specified type for a finished job.\n\
+\n my $result = rest_get_result($job_id, $result_\
+type);\n\n=cut\n\nsub rest_get_result {\n print_de\
+bug_message( 'rest_get_result', 'Begin', 1 );\n my\
+ $job_id = shift;\n my $type = shift;\n print_de\
+bug_message( 'rest_get_result', 'jobid: ' . $job_i\
+d, 1 );\n print_debug_message( 'rest_get_result', \
+'type: ' . $type, 1 );\n my $url = $baseUrl \
+. '/result/' . $job_id . '/' . $type;\n my $result\
+ = &rest_request($url);\n print_debug_message( 're\
+st_get_result', length($result) . ' characters',\n\
+ 1 );\n print_debug_message( 'rest_get_result', '\
+End', 1 );\n return $result;\n}\n\n\n=head2 print_\
+debug_message()\n\nPrint debug message at specifie\
+d debug level.\n\n &print_debug_message($method_n\
+ame, $message, $level);\n\n=cut\n\nsub print_debug\
+_message {\n my $function_name = shift;\n my $mess\
+age = shift;\n my $level = shift;\n \
+if ( $level <= $params{'debugLevel'} ) {\n print \
+STDERR '[', $function_name, '()] ', $message, \"\\\
+n\";\n }\n}\n\n=head2 print_tool_params()\n\nPrint\
+ list of tool parameters.\n\n &print_tool_params(\
+);\n\n=cut\n\nsub print_tool_params {\n print_debu\
+g_message( 'print_tool_params', 'Begin', 1 );\n my\
+ (@param_list) = &rest_get_parameters();\n foreach\
+ my $param ( sort(@param_list) ) {\n print $param\
+, \"\\n\";\n }\n print_debug_message( 'print_tool_\
+params', 'End', 1 );\n}\n\n=head2 print_param_deta\
+ils()\n\nPrint details of a tool parameter.\n\n &\
+print_param_details($param_name);\n\n=cut\n\nsub p\
+rint_param_details {\n print_debug_message( 'print\
+_param_details', 'Begin', 1 );\n my $paramName = s\
+hift;\n print_debug_message( 'print_param_details'\
+, 'paramName: ' . $paramName, 2 );\n my $paramDeta\
+il = &rest_get_parameter_details($paramName);\n pr\
+int $paramDetail->{'name'}, \"\\t\", $paramDetail-\
+>{'type'}, \"\\n\";\n print $paramDetail->{'descri\
+ption'}, \"\\n\";\n if(defined($paramDetail->{'val\
+ues'}->{'value'})) {\n if(ref($paramDetail->{'val\
+ues'}->{'value'}) eq 'ARRAY') {\n foreach my $va\
+lue ( @{ $paramDetail->{'values'}->{'value'} } ) {\
+\n &print_param_value($value);\n }\n }\n el\
+se {\n &print_param_value($paramDetail->{'value\
+s'}->{'value'});\n }\n }\n print_debug_message( '\
+print_param_details', 'End', 1 );\n}\n\n=head2 pri\
+nt_param_value()\n\nPrint details of a tool parame\
+ter value.\n\n &print_param_details($param_value)\
+;\n\nUsed by print_param_details() to handle both \
+singluar and array values.\n\n=cut\n\nsub print_pa\
+ram_value {\n my $value = shift;\n print $value->{\
+'value'};\n if ( $value->{'defaultValue'} eq 'true\
+' ) {\n print \"\\t\", 'default';\n }\n print \"\\
+\n\";\n print \"\\t\", $value->{'label'}, \"\\n\";\
+\n if ( defined( $value->{'properties'} ) ) {\n f\
+oreach\n my $key ( sort( keys( %{ $value->{'pro\
+perties'}{'property'} } ) ) )\n {\n if ( ref( $\
+value->{'properties'}{'property'}{$key} ) eq 'HASH\
+'\n && defined( $value->{'properties'}{'propert\
+y'}{$key}{'value'} )\n )\n {\n print \"\\\
+t\", $key, \"\\t\",\n $value->{'properties'}{\
+'property'}{$key}{'value'}, \"\\n\";\n }\n els\
+e {\n print \"\\t\", $value->{'properties'}{'pr\
+operty'}{'key'},\n \"\\t\", $value->{'propert\
+ies'}{'property'}{'value'}, \"\\n\";\n last;\n \
+ }\n }\n }\n}\n\n=head2 print_job_status()\n\nPr\
+int status of a job.\n\n &print_job_status($job_i\
+d);\n\n=cut\n\nsub print_job_status {\n print_debu\
+g_message( 'print_job_status', 'Begin', 1 );\n my \
+$jobid = shift;\n print_debug_message( 'print_job_\
+status', 'jobid: ' . $jobid, 1 );\n if ( $outputLe\
+vel > 0 ) {\n print STDERR 'Getting status for jo\
+b ', $jobid, \"\\n\";\n }\n my $result = &rest_get\
+_status($jobid);\n print \"$result\\n\";\n if ( $r\
+esult eq 'FINISHED' && $outputLevel > 0 ) {\n pri\
+nt STDERR \"To get results: $scriptName --polljob \
+--jobid \" . $jobid\n . \"\\n\";\n }\n print_de\
+bug_message( 'print_job_status', 'End', 1 );\n}\n\\
+n=head2 print_result_types()\n\nPrint available re\
+sult types for a job.\n\n &print_result_types($jo\
+b_id);\n\n=cut\n\nsub print_result_types {\n print\
+_debug_message( 'result_types', 'Begin', 1 );\n my\
+ $jobid = shift;\n print_debug_message( 'result_ty\
+pes', 'jobid: ' . $jobid, 1 );\n if ( $outputLevel\
+ > 0 ) {\n print STDERR 'Getting result types for\
+ job ', $jobid, \"\\n\";\n }\n my $status = &rest_\
+get_status($jobid);\n if ( $status eq 'PENDING' ||\
+ $status eq 'RUNNING' ) {\n print STDERR 'Error: \
+Job status is ', $status,\n '. To get result ty\
+pes the job must be finished.', \"\\n\";\n }\n els\
+e {\n my (@resultTypes) = &rest_get_result_types(\
+$jobid);\n if ( $outputLevel > 0 ) {\n print ST\
+DOUT 'Available result types:', \"\\n\";\n }\n f\
+oreach my $resultType (@resultTypes) {\n print S\
+TDOUT $resultType->{'identifier'}, \"\\n\";\n if\
+ ( defined( $resultType->{'label'} ) ) {\n prin\
+t STDOUT \"\\t\", $resultType->{'label'}, \"\\n\";\
+\n }\n if ( defined( $resultType->{'descriptio\
+n'} ) ) {\n print STDOUT \"\\t\", $resultType->\
+{'description'}, \"\\n\";\n }\n if ( defined( \
+$resultType->{'mediaType'} ) ) {\n print STDOUT\
+ \"\\t\", $resultType->{'mediaType'}, \"\\n\";\n \
+ }\n if ( defined( $resultType->{'fileSuffix'} )\
+ ) {\n print STDOUT \"\\t\", $resultType->{'fil\
+eSuffix'}, \"\\n\";\n }\n }\n if ( $status eq \
+'FINISHED' && $outputLevel > 0 ) {\n print STDER\
+R \"\\n\", 'To get results:', \"\\n\",\n \" $\
+scriptName --polljob --jobid \" . $params{'jobid'}\
+ . \"\\n\",\n \" $scriptName --polljob --outf\
+ormat <type> --jobid \"\n . $params{'jobid'} .\
+ \"\\n\";\n }\n }\n print_debug_message( 'result_\
+types', 'End', 1 );\n}\n\n=head2 submit_job()\n\nS\
+ubmit a job to the service.\n\n &submit_job($seq)\
+;\n\n=cut\n\nsub submit_job {\n print_debug_messag\
+e( 'submit_job', 'Begin', 1 );\n\n # Set input seq\
+uence\n $tool_params{'sequence'} = shift;\n\n # Lo\
+ad parameters\n &load_params();\n\n # Submit the j\
+ob\n my $jobid = &rest_run( $params{'email'}, $par\
+ams{'title'}, \\%tool_params );\n\n # Simulate syn\
+c/async mode\n if ( defined( $params{'async'} ) ) \
+{\n print STDOUT $jobid, \"\\n\";\n if ( $output\
+Level > 0 ) {\n print STDERR\n \"To check st\
+atus: $scriptName --status --jobid $jobid\\n\";\n \
+ }\n }\n else {\n if ( $outputLevel > 0 ) {\n p\
+rint STDERR \"JobId: $jobid\\n\";\n }\n sleep 1;\
+\n &get_results($jobid);\n }\n print_debug_messag\
+e( 'submit_job', 'End', 1 );\n}\n\n=head2 multi_su\
+bmit_job()\n\nSubmit multiple jobs assuming input \
+is a collection of fasta formatted sequences.\n\n \
+ &multi_submit_job();\n\n=cut\n\nsub multi_submit_\
+job {\n print_debug_message( 'multi_submit_job', '\
+Begin', 1 );\n my $jobIdForFilename = 1;\n $jobIdF\
+orFilename = 0 if ( defined( $params{'outfile'} ) \
+);\n my (@filename_list) = ();\n\n # Query sequenc\
+e\n if ( defined( $ARGV[0] ) ) { # Bare option\\
+n if ( -f $ARGV[0] || $ARGV[0] eq '-' ) { # Fi\
+le\n push( @filename_list, $ARGV[0] );\n }\n e\
+lse {\n warn 'Warning: Input file \"' . $ARGV[0]\
+ . '\" does not exist'\n }\n }\n if ( $params{'se\
+quence'} ) { # Via --sequence\n \
+ if ( -f $params{'sequence'} || $params{'sequence'\
+} eq '-' ) { # File\n push( @filename_list, $\
+params{'sequence'} );\n }\n else {\n warn 'War\
+ning: Input file \"' . $params{'sequence'} . '\" d\
+oes not exist'\n }\n }\n\n $/ = '>';\n foreach my\
+ $filename (@filename_list) {\n my $INFILE;\n if\
+($filename eq '-') { # STDIN.\n open( $INFILE, '\
+<-' )\n or die 'Error: unable to STDIN (' . $!\
+ . ')';\n } else { # File.\n open( $INFILE, '<'\
+, $filename )\n or die 'Error: unable to open \
+file ' . $filename . ' (' . $! . ')';\n }\n whil\
+e (<$INFILE>) {\n my $seq = $_;\n $seq =~ s/>$\
+//;\n if ( $seq =~ m/(\\S+)/ ) {\n print STDE\
+RR \"Submitting job for: $1\\n\"\n if ( $outp\
+utLevel > 0 );\n $seq = '>' . $seq;\n &print\
+_debug_message( 'multi_submit_job', $seq, 11 );\n \
+ &submit_job($seq);\n $params{'outfile'} = un\
+def if ( $jobIdForFilename == 1 );\n }\n }\n c\
+lose $INFILE;\n }\n print_debug_message( 'multi_su\
+bmit_job', 'End', 1 );\n}\n\n=head2 list_file_subm\
+it_job()\n\nSubmit multiple jobs using a file cont\
+aining a list of entry identifiers as \ninput.\n\n\
+ &list_file_submit_job($list_filename)\n\n=cut\n\\
+nsub list_file_submit_job {\n print_debug_message(\
+ 'list_file_submit_job', 'Begin', 11 );\n my $file\
+name = shift;\n my $jobIdForFilename = 1;\\
+n $jobIdForFilename = 0 if ( defined( $params{'out\
+file'} ) );\n\n # Iterate over identifiers, submit\
+ting each job\n my $LISTFILE;\n if($filename eq '-\
+') { # STDIN.\n open( $LISTFILE, '<-' )\n or d\
+ie 'Error: unable to STDIN (' . $! . ')';\n } else\
+ { # File.\n open( $LISTFILE, '<', $filename )\n \
+ or die 'Error: unable to open file ' . $filenam\
+e . ' (' . $! . ')';\n }\n while (<$LISTFILE>) {\n\
+ my $line = $_;\n chomp($line);\n if ( $line ne\
+ '' ) {\n &print_debug_message( 'list_file_submi\
+t_job', 'line: ' . $line, 2 );\n if ( $line =~ m\
+/\\w:\\w/ ) { # Check this is an identifier\n \
+ print STDERR \"Submitting job for: $line\\n\"\n \
+ if ( $outputLevel > 0 );\n &submit_job($li\
+ne);\n }\n else {\n print STDERR\n\"Warning\
+: line \\\"$line\\\" is not recognised as an ident\
+ifier\\n\";\n }\n }\n $params{'outfile'} = und\
+ef if ( $jobIdForFilename == 1 );\n }\n close $LIS\
+TFILE;\n print_debug_message( 'list_file_submit_jo\
+b', 'End', 11 );\n}\n\n=head2 load_data()\n\nLoad \
+sequence data from file or option specified on the\
+ command-line.\n\n &load_data();\n\n=cut\n\nsub l\
+oad_data {\n print_debug_message( 'load_data', 'Be\
+gin', 1 );\n my $retSeq;\n\n # Query sequence\n if\
+ ( defined( $ARGV[0] ) ) { # Bare option\n if \
+( -f $ARGV[0] || $ARGV[0] eq '-' ) { # File\n \
+ $retSeq = &read_file( $ARGV[0] );\n }\n else { \
+ # DB:ID or seq\
+uence\n $retSeq = $ARGV[0];\n }\n }\n if ( $par\
+ams{'sequence'} ) { # Via --sequ\
+ence\n if ( -f $params{'sequence'} || $params{'se\
+quence'} eq '-' ) { # File\n $retSeq = &read_\
+file( $params{'sequence'} );\n }\n else { # D\
+B:ID or sequence\n $retSeq = $params{'sequence'}\
+;\n }\n }\n print_debug_message( 'load_data', 'En\
+d', 1 );\n return $retSeq;\n}\n\n=head2 load_param\
+s()\n\nLoad job parameters from command-line optio\
+ns.\n\n &load_params();\n\n=cut\n\nsub load_param\
+s {\n print_debug_message( 'load_params', 'Begin',\
+ 1 );\n\n # Database(s) to search\n my (@dbList) =\
+ split /[ ,]/, $params{'database'};\n $tool_params\
+{'database'} = \\@dbList;\n\n # Compatability opti\
+ons, old command-line.\n if(!$tool_params{'viewfil\
+ter'} && $params{'echofilter'}) {\n $tool_params{\
+'viewfilter'} = 'true';\n }\n if(!$tool_params{'al\
+ignments'} && $params{'numal'}) {\n $tool_params{\
+'alignments'} = $params{'numal'};\n }\n # TODO: se\
+t alignment format option to get NCBI BLAST XML.\n\
+ if($params{'appxml'}) {\n $tool_params{'align'} \
+= '';\n }\n\n print_debug_message( 'load_params', \
+'End', 1 );\n}\n\n=head2 client_poll()\n\nClient-s\
+ide job polling.\n\n &client_poll($job_id);\n\n=c\
+ut\n\nsub client_poll {\n print_debug_message( 'cl\
+ient_poll', 'Begin', 1 );\n my $jobid = shift;\n \
+my $status = 'PENDING';\n\n my $errorCount = 0;\n \
+while ($status eq 'RUNNING'\n || $status eq 'PEND\
+ING'\n || ( $status eq 'ERROR' && $errorCount < 2\
+ ) )\n {\n $status = rest_get_status($jobid);\n \
+print STDERR \"$status\\n\" if ( $outputLevel > 0 \
+);\n if ( $status eq 'ERROR' ) {\n $errorCount+\
++;\n }\n elsif ( $errorCount > 0 ) {\n $errorC\
+ount--;\n }\n if ( $status eq 'RUNNING'\n ||\
+ $status eq 'PENDING'\n || $status eq 'ERROR' )\\
+n {\n\n # Wait before polling again.\n sleep \
+$checkInterval;\n }\n }\n print_debug_message( 'c\
+lient_poll', 'End', 1 );\n return $status;\n}\n\n=\
+head2 get_results()\n\nGet the results for a job i\
+dentifier.\n\n &get_results($job_id);\n\n=cut\n\n\
+sub get_results {\n print_debug_message( 'get_resu\
+lts', 'Begin', 1 );\n my $jobid = shift;\n print_d\
+ebug_message( 'get_results', 'jobid: ' . $jobid, 1\
+ );\n\n # Verbose\n if ( $outputLevel > 1 ) {\n p\
+rint 'Getting results for job ', $jobid, \"\\n\";\\
+n }\n\n # Check status, and wait if not finished\n\
+ client_poll($jobid);\n\n # Use JobId if output fi\
+le name is not defined\n unless ( defined( $params\
+{'outfile'} ) ) {\n $params{'outfile'} = $jobid;\\
+n }\n\n # Get list of data types\n my (@resultType\
+s) = rest_get_result_types($jobid);\n\n # Get the \
+data and write it to a file\n if ( defined( $param\
+s{'outformat'} ) ) { # Specified data type\n m\
+y $selResultType;\n foreach my $resultType (@resu\
+ltTypes) {\n if ( $resultType->{'identifier'} eq\
+ $params{'outformat'} ) {\n $selResultType = $r\
+esultType;\n }\n }\n if ( defined($selResultTy\
+pe) ) {\n my $result =\n rest_get_result( $j\
+obid, $selResultType->{'identifier'} );\n if ( $\
+params{'outfile'} eq '-' ) {\n write_file( $par\
+ams{'outfile'}, $result );\n }\n else {\n w\
+rite_file(\n $params{'outfile'} . '.'\n \
+. $selResultType->{'identifier'} . '.'\n . $\
+selResultType->{'fileSuffix'},\n $result\n \
+);\n }\n }\n else {\n die 'Error: unknown re\
+sult format \"' . $params{'outformat'} . '\"';\n \
+}\n }\n else { # Data types available\n \
+# Write a file for each output type\n for my $res\
+ultType (@resultTypes) {\n if ( $outputLevel > 1\
+ ) {\n print STDERR 'Getting ', $resultType->{'\
+identifier'}, \"\\n\";\n }\n my $result = rest\
+_get_result( $jobid, $resultType->{'identifier'} )\
+;\n if ( $params{'outfile'} eq '-' ) {\n writ\
+e_file( $params{'outfile'}, $result );\n }\n e\
+lse {\n write_file(\n $params{'outfile'} . \
+'.'\n . $resultType->{'identifier'} . '.'\n \
+ . $resultType->{'fileSuffix'},\n $result\
+\n );\n }\n }\n }\n print_debug_message( 'ge\
+t_results', 'End', 1 );\n}\n\n=head2 read_file()\n\
+\nRead a file into a scalar. The special filename \
+'-' can be used to read from \nstandard input (STD\
+IN).\n\n my $data = &read_file($filename);\n\n=cu\
+t\n\nsub read_file {\n print_debug_message( 'read_\
+file', 'Begin', 1 );\n my $filename = shift;\n pri\
+nt_debug_message( 'read_file', 'filename: ' . $fil\
+ename, 2 );\n my ( $content, $buffer );\n if ( $fi\
+lename eq '-' ) {\n while ( sysread( STDIN, $buff\
+er, 1024 ) ) {\n $content .= $buffer;\n }\n }\n\
+ else { # File\n open( my $FILE, '<', $filenam\
+e )\n or die \"Error: unable to open input file\
+ $filename ($!)\";\n while ( sysread( $FILE, $buf\
+fer, 1024 ) ) {\n $content .= $buffer;\n }\n c\
+lose($FILE);\n }\n print_debug_message( 'read_file\
+', 'End', 1 );\n return $content;\n}\n\n=head2 wri\
+te_file()\n\nWrite data to a file. The special fil\
+ename '-' can be used to write to \nstandard outpu\
+t (STDOUT).\n\n &write_file($filename, $data);\n\\
+n=cut\n\nsub write_file {\n print_debug_message( '\
+write_file', 'Begin', 1 );\n my ( $filename, $data\
+ ) = @_;\n print_debug_message( 'write_file', 'fil\
+ename: ' . $filename, 2 );\n if ( $outputLevel > 0\
+ ) {\n print STDERR 'Creating result file: ' . $f\
+ilename . \"\\n\";\n }\n if ( $filename eq '-' ) {\
+\n print STDOUT $data;\n }\n else {\n open( my $\
+FILE, '>', $filename )\n or die \"Error: unable\
+ to open output file $filename ($!)\";\n syswrite\
+( $FILE, $data );\n close($FILE);\n }\n print_deb\
+ug_message( 'write_file', 'End', 1 );\n}\n\n=head2\
+ usage()\n\nPrint program usage message.\n\n &usa\
+ge();\n\n=cut\n\nsub usage {\n print STDERR <<EOF\\
+nWU-BLAST\n========\n \nRapid sequence database \
+search programs utilizing the BLAST algorithm\n \
+ \n[Required]\n\n -p, --program : str : BLA\
+ST program to use, see --paramDetail program\n -D\
+, --database : str : database(s) to search, s\
+pace separated. See\n \
+ --paramDetail database\n --stype : st\
+r : query sequence type, see --paramDetail stype\\
+n seqFile : file : query sequence (\"-\
+\" for STDIN, \\@filename for\n \
+ identifier list file)\n\n[Optional]\n\n\
+ -m, --matrix : str : scoring matrix, see \
+--paramDetail matrix\n -e, --exp : real \
+: 0<E<= 1000. Statistical significance threshold \\
+n for reporting datab\
+ase sequence matches.\n -e, --viewfilter : \
+ : display the filtered query sequence\n -f, --fi\
+lter : str : filter the query sequence for \
+low complexity \n reg\
+ions, see --paramDetail filter\n -A, --align \
+ : int : pairwise alignment format, see --param\
+Detail align\n -s, --scores : int : number\
+ of scores to be reported\n -b, --alignments : \
+int : number of alignments to report\n -S, --sen\
+sitivity : str : sensitivity of the search, \n \
+ see --paramDetail sens\
+itivity\n -t, --sort : str : sort order for\
+ hits, see --paramDetail sort\n -T, --stats \
+ : str : statistical model, see --paramDetail st\
+ats\n -d, --strand : str : DNA strand to s\
+earch with,\n see --p\
+aramDetail strand\n -c, --topcombon : str : c\
+onsistent sets of HSPs\n --multifasta : \
+ : treat input as a set of fasta formatted sequen\
+ces\n\n[General]\n\n -h, --help : : \
+prints this help text\n --async : \
+ : forces to make an asynchronous query\n --e\
+mail : str : e-mail address\n --title\
+ : str : title for job\n --status \
+ : : get job status\n --resultTypes :\
+ : get available result types for job\n \
+--polljob : : poll for the status of a j\
+ob\n --jobid : str : jobid that was r\
+eturned when an asynchronous job \n \
+ was submitted.\n --outfile \
+ : str : file name for results (default is jobid\
+;\n \"-\" for STDOUT)\
+\n --outformat : str : result format to r\
+etrieve\n --params : : list input \
+parameters\n --paramDetail : str : display \
+details for input parameter\n --quiet \
+: : decrease output\n --verbose : \
+ : increase output\n \nSynchronous job:\n\n \
+The results/errors are returned as soon as the job\
+ is finished.\n Usage: $scriptName --email <your\\
+\@email> [options...] seqFile\n Returns: results \
+as an attachment\n\nAsynchronous job:\n\n Use thi\
+s if you want to retrieve the results at a later t\
+ime. The results \n are stored for up to 24 hours\
+. \n Usage: $scriptName --async --email <your\\@\
+email> [options...] seqFile\n Returns: jobid\n\n \
+ Use the jobid to query for the status of the job.\
+ If the job is finished, \n it also returns the r\
+esults/errors.\n Usage: $scriptName --polljob --j\
+obid <jobId> [--outfile string]\n Returns: string\
+ indicating the status of the job and if applicabl\
+e, results \n as an attachment.\n\nFurther inform\
+ation:\n\n http://www.ebi.ac.uk/Tools/webservices\
+/services/sss/wu_blast_rest\n http://www.ebi.ac.u\
+k/Tools/webservices/tutorials/perl\n\nSupport/Feed\
+back:\n\n http://www.ebi.ac.uk/support/\nEOF\n}\n\
+\n=head1 FEEDBACK/SUPPORT\n\nPlease contact us at \
+L<http://www.ebi.ac.uk/support/> if you have any \\
+nfeedback, suggestions or issues with the service \
+or this client.\n\n=cut\n","\n\n\nmy $PROBTRESH = \
+0.3;# base pairs below this prob threshold will be\
+ ignored\nmy $WEIGHT = 100.0; # float!!\nmy $NUCAL\
+PH = \"ACGTUNRYMKSWHBVD\";\nuse vars qw($NUCALPH $\
+WEIGHT);\n\nmy $myname = basename($0);\n\nuse stri\
+ct;\nuse warnings;\n\nuse File::Basename;\nuse Get\
+opt::Long;\nuse File::Glob ':glob';\nuse File::Spe\
+c;\nuse File::Temp qw/ tempfile tempdir /;\n\n\n\n\
+\nsub tcoffeelib_header($;$)\n{\n my ($nseq, $f\
+d) = @_;\n if (! defined($fd)) {\n $fd =\
+ *STDOUT;\n }\n printf $fd \"! TC_LIB_FORMAT\
+_01\\n\";\n printf $fd \"%d\\n\", $nseq;\n}\n\n\
+\nsub tcoffeelib_header_addseq($$;$)\n{\n my ($\
+id, $seq, $fd) = @_;\n if (! defined($fd)) {\n \
+ $fd = *STDOUT;\n }\n printf $fd \"%s \
+%d %s\\n\", $id, length($seq), $seq;\n}\n\n\nsub t\
+coffeelib_comment($;$)\n{\n my ($comment, $fd) \
+= @_;\n if (! defined($fd)) {\n $fd = *S\
+TDOUT;\n }\n printf $fd \"!\" . $comment . \\
+"\\n\";\n}\n\n\nsub tcoffeelib_struct($$$;$)\n{\n \
+ my ($nseq, $len, $bpm, $fd) = @_;\n\n if (! \
+defined($fd)) {\n $fd = *STDOUT;\n }\n\n\
+ # output basepair indices with fixed weight\n \
+ printf $fd \"#%d %d\\n\", $nseq, $nseq;\n # \
+output basepairs (only once) and with unit-offset\\
+n for (my $i=0; $i<$len; $i++) {\n for (\
+my $j=$i+1; $j<$len; $j++) {\n if (! de\
+fined($bpm->[$i][$j])) {\n print ST\
+DERR \"ERROR: \\$bpm->[$i][$j] undefined\\n\";\n \
+ }\n if ($bpm->[$i][$j]>0) {\n\
+ print $fd $i+1;\n p\
+rint $fd \" \";\n print $fd $j+1;\n\
+ print $fd \" \" . $bpm->[$i][$j] .\
+ \"\\n\";\n }\n }\n }\n}\n\n\\
+nsub tcoffeelib_footer(;$)\n{\n my ($fd) = @_;\\
+n if (! defined($fd)) {\n $fd = *STDOUT;\
+\n }\n print $fd \"! SEQ_1_TO_N\\n\";\n}\n\n\
+\n \nsub plfold($$$)\n{ \n my ($id, $seq,\
+ $probtresh) = @_;\n my (@struct);# return\n \
+ my ($templ, $fhtmp, $fnametmp, $cmd, $ctr, $windo\
+w_size);\n our $ntemp++;\n \n $templ = $m\
+yname . \".pid-\" . $$ .$ntemp .\".XXXXXX\";\n \
+($fhtmp, $fnametmp) = tempfile($templ, UNLINK => 1\
+); \n print $fhtmp \">$id\\n$seq\\n\";\n\n #\
+ --- init basepair array\n #\n for (my $i=0;\
+ $i<length($seq); $i++) {\n for (my $j=$i+1\
+; $j<length($seq); $j++) {\n $struct[$i\
+][$j]=0;\n }\n }\n\n\n # --- call rna\
+plfold and drop a readme\n #\n $window_size=\
+(length($seq)<70)?length($seq):70;\n $cmd = \"R\
+NAplfold -W $window_size < $fnametmp >/dev/null\";\
+\n system($cmd);\n \n if ($? != 0) {\n \
+ printf STDERR \"ERROR: RNAplfold ($cmd) exite\
+d with error status %d\\n\", $? >> 8;\n ret\
+urn;\n }\n #unlink($fnametmp);\n my $fps \
+= sprintf(\"%s_dp.ps\", $id); # check long name\n \
+ \n if (! -s $fps) {\n {\n\n $fps = spri\
+ntf(\"%s_dp.ps\", substr($id,0,12)); # check short\
+ name\n if (! -s $fps)\n {\n die(\"couldn't\
+ find expected file $fps\\n\");\n return;\n \
+}\n }\n }\n\n \n # --- read base pai\
+rs from created postscript\n #\n open(FH, $f\
+ps);\n while (my $line = <FH>) {\n my ($\
+nti, $ntj, $prob);\n chomp($line); \\
+n # line: bp bp sqrt-prob ubox\n my \
+@match = ($line =~ m/^([0-9]+) +([0-9]+) +([0-9\\.\
+]+) +ubox$/);\n if (scalar(@match)) {\n \
+ $nti=$1;\n $ntj=$2;\n \
+ $prob=$3*$3;# prob stored as square root\n\n \
+ if ($prob>$probtresh) {\n #\
+printf STDERR \"\\$struct[$nti][$ntj] sqrtprob=$3 \
+prob=$prob > $probtresh\\n\";\n $st\
+ruct[$nti-1][$ntj-1] = $WEIGHT\n }\n \
+ # store with zero-offset\n }\n \
+}\n close(FH);\n\n # remove or gzi postscrip\
+t\n #\n unlink($fps);\n #\n # or gzip\\
+n #$cmd = \"gzip -qf $fps\";\n #system($cmd)\
+;\n #if ($? != 0) {\n # printf STDERR \"E\
+RROR: gzip ($cmd) exited with error status %d\\n\"\
+, $? >> 8;\n #}\n\n return \\@struct;\n}\n\n\
+\n\n\n\nsub rnaseqfmt($)\n{\n my ($seq) = @_;\n\
+ # remove gaps\n $seq =~ s/-//g;\n # uppe\
+rcase RNA\n $seq = uc($seq);\n # T -> U\n \
+ $seq =~ s/T/U/g;\n # check for invalid charate\
+rs\n $_ = $seq;\n s/[^$NUCALPH]//g;\n ret\
+urn $_;\n}\n\n\n\n\nsub usage(;$)\n{ \n my (\
+$errmsg) = @_;\n if ($errmsg) {\n print \
+STDERR \"ERROR: $errmsg\\n\";\n }\n print ST\
+DERR << \"EOF\";\n$myname:\n Creates a T-Coffee RN\
+A structure library from RNAplfold prediction.\n S\
+ee FIXME:citation\nUsage:\n $myname -in seq_file -\
+out tcoffee_lib\nEOF\n exit(1);\n}\n\nsub read_\
+fasta_seq \n {\n my $f=$_[0];\n my %hseq;\n\
+ my (@seq, @com, @name);\n my ($a, $s,$nseq)\
+;\n\n open (F, $f);\n while (<F>)\n {\n\
+ $s.=$_;\n }\n close (F);\n\n \n @na\
+me=($s=~/>(\\S*).*\\n[^>]*/g);\n \n @seq =($\
+s=~/>.*.*\\n([^>]*)/g);\n @com =($s=~/>(\\S*)(.\
+*)\\n([^>]*)/g);\n\n\n $nseq=$#name+1;\n \n \
+ for ($a=0; $a<$nseq; $a++)\n {\n my $n=$name\
+[$a];\n my $s;\n $hseq{$n}{name}=$n;\n $s=$seq[$a]\
+;$s=~s/\\s//g;\n \n $hseq{$n}{seq}=$s;\n $hseq{$n}\
+{com}=$com[$a];\n }\n return %hseq;\n }\n\
+\n\n\n\n\n\n\nmy $fmsq = \"\";\nmy $flib = \"\";\n\
+my %OPTS;\nmy %seq;\nmy ($id, $nseq, $i);\nmy @nl;\
+\n\nGetOptions(\"in=s\" => \\$fmsq, \"out=s\" => \\
+\$flib);\n\nif (! -s $fmsq) {\n usage(\"empty o\
+r non-existant file \\\"$fmsq\\\"\")\n}\nif (lengt\
+h($flib)==0) {\n usage(\"empty out-filename\")\\
+n}\n\n\n\n\n\n\n%seq=read_fasta_seq($fmsq);\n\n\n@\
+nl=keys(%seq);\n\n$nseq=$#nl+1;\nopen FD_LIB, \">$\
+flib\" or die \"can't open $flib!\";\ntcoffeelib_h\
+eader($nseq, *FD_LIB);\nforeach $id (keys (%seq))\\
+n {\n my ($seq, $fmtseq);\n \n $seq = $s\
+eq{$id}{seq};\n \n $fmtseq = rnaseqfmt($seq)\
+;# check here, formatting for folding important la\
+ter\n if (length($seq)!=length($fmtseq)) {\n \
+ print STDERR \"ERROR: invalid sequence $id is\
+ not an RNA sequence. read seq is: $seq\\n\";\n \
+ exit\n }\n \n tcoffeelib_header_add\
+seq($id, uc($seq), *FD_LIB);\n }\ntcoffeelib_comm\
+ent(\"generated by $myname on \" . localtime(), *F\
+D_LIB);\n\n\n\n$i=0;\nforeach $id (keys (%seq))\n \
+ {\n my ($cleanid, $seq, $bpm);\n $seq=$seq{\
+$id}{seq};\n $cleanid = $id;\n $cleanid =~ s\
+,[/ ],_,g;# needed for rnaplfold\n $seq = rnase\
+qfmt($seq);\n \n $bpm = plfold($cleanid, rna\
+seqfmt($seq), $PROBTRESH); \n \n tcoff\
+eelib_struct($i+1, length($seq), $bpm, *FD_LIB);\n\
+ $i++;\n}\n\n\ntcoffeelib_footer(*FD_LIB);\nclo\
+se FD_LIB;\nexit (0);\n\n","\n\n\n\n\n$cmd=join ' \
+', @ARGV;\nif ($cmd=~/-infile=(\\S+)/){ $seqfile=$\
+1;}\nif ($cmd=~/-outfile=(\\S+)/){ $libfile=$1;}\n\
+\n\n\n%s=read_fasta_seq ($seqfile);\n\nopen (F, \"\
+>$libfile\");\nforeach $name (keys (%s))\n {\n \
+ my $tclib=\"$name.RNAplfold_tclib\";\n print (\
+F \">$name _F_ $tclib\\n\");\n seq2RNAplfold2tc\
+lib ($name, $s{$name}{seq}, $tclib);\n }\nclose (\
+F);\nexit (EXIT_SUCCESS);\n\nsub seq2RNAplfold2tcl\
+ib\n {\n my ($name, $seq, $tclib)=@_;\n my \
+($tmp);\n $n++;\n $tmp=\"tmp4seq2RNAplfold_t\
+clib.$$.$n.pep\";\n open (RF, \">$tmp\");\n \
+print (RF \">$name\\n$seq\\n\");\n close (RF);\\
+n \n system \"t_coffee -other_pg RNAplfold2t\
+clib.pl -in=$tmp -out=$tclib\";\n \n unlink \
+($tmp);\n return $tclib;\n }\n \n \nsub \
+read_fasta_seq \n {\n my $f=@_[0];\n my %hs\
+eq;\n my (@seq, @com, @name);\n my ($a, $s,$\
+nseq);\n\n open (F, $f);\n while (<F>)\n \
+ {\n $s.=$_;\n }\n close (F);\n\n \n \
+ @name=($s=~/>(\\S*).*\\n[^>]*/g);\n \n @se\
+q =($s=~/>.*.*\\n([^>]*)/g);\n @com =($s=~/>\\S\
+*(.*)\\n([^>]*)/g);\n\n \n $nseq=$#name+1;\n\
+ \n for ($a=0; $a<$nseq; $a++)\n {\n my\
+ $n=$name[$a];\n $hseq{$n}{name}=$n;\n $hseq{$n}{s\
+eq}=$seq[$a];\n $hseq{$n}{com}=$com[$a];\n }\\
+n return %hseq;\n }\n","use Getopt::Long;\nuse\
+ File::Path;\nuse Env;\nuse FileHandle;\nuse Cwd;\\
+nuse Sys::Hostname;\nour $PIDCHILD;\nour $ERROR_DO\
+NE;\nour @TMPFILE_LIST;\nour $EXIT_FAILURE=1;\nour\
+ $EXIT_SUCCESS=0;\n\nour $REFDIR=getcwd;\nour $EXI\
+T_SUCCESS=0;\nour $EXIT_FAILURE=1;\n\nour $PROGRAM\
+=\"tc_generic_method.pl\";\nour $CL=$PROGRAM;\n\no\
+ur $CLEAN_EXIT_STARTED;\nour $debug_lock=$ENV{\"DE\
+BUG_LOCK\"};\nour $LOCKDIR=$ENV{\"LOCKDIR_4_TCOFFE\
+E\"};\nif (!$LOCKDIR){$LOCKDIR=getcwd();}\nour $ER\
+RORDIR=$ENV{\"ERRORDIR_4_TCOFFEE\"};\nour $ERRORFI\
+LE=$ENV{\"ERRORFILE_4_TCOFFEE\"};\n&set_lock ($$);\
+\nif (isshellpid(getppid())){lock4tc(getppid(), \"\
+LLOCK\", \"LSET\", \"$$\\n\");}\n \nour $prin\
+t;\nmy ($fmsq1, $fmsq2, $output, $outfile, $arch, \
+$psv, $hmmtop_home, $trim, $cov, $sample, $mode, $\
+gor_home, $gor_seq, $gor_obs);\n\nGetOptions(\"-in\
+=s\" => \\$fmsq1,\"-output=s\" =>\\$output ,\"-out\
+=s\" => \\$outfile, \"-arch=s\" => \\$arch,\"-psv=\
+s\" => \\$psv, \"-hmmtop_home=s\", \\$hmmtop_home,\
+\"-trim=s\" =>\\$trim ,\"-print=s\" =>\\$print,\"-\
+cov=s\" =>\\$cov , \"-sample=s\" =>\\$sample, \"-m\
+ode=s\" =>\\$mode, \"-gor_home=s\"=>\\$gor_home, \\
+"-gor_seq=s\"=>\\$gor_seq,\"-gor_obs=s\"=>\\$gor_o\
+bs);\n\n\nif (!$mode){$mode = \"hmmtop\"}\nelsif (\
+$mode eq \"hmmtop\"){;}\nelsif ($mode eq \"gor\"){\
+;}\nelse {myexit(flush_error (\"-mode=$mode is unk\
+nown\"));}\n\n\nour $HOME=$ENV{\"HOME\"};\nour $MC\
+OFFEE=($ENV{\"MCOFFEE_4_TCOFFEE\"})?$ENV{\"MCOFFEE\
+_4_TCOFFEE\"}:\"$HOME/.t_coffee/mcoffee\";\n\nif (\
+$mode eq \"hmmtop\")\n {\n check_configuration\
+ (\"hmmtop\");\n if (-e $arch){$ENV{'HMMTOP_ARC\
+H'}=$arch;}\n elsif (-e $ENV{HMMTOP_ARCH}){$arc\
+h=$ENV{HMMTOP_ARCH};}\n elsif (-e \"$MCOFFEE/hm\
+mtop.arch\"){$arch=$ENV{'HMMTOP_ARCH'}=\"$MCOFFEE/\
+hmmtop.arch\";}\n elsif (-e \"$hmmtop_home/hmmt\
+op.arc\"){$arch=$ENV{'HMMTOP_ARCH'}=\"$hmmtop_home\
+/hmmtop.arc\";}\n else {myexit(flush_error ( \"\
+Could not find ARCH file for hmmtop\"));}\n \n \
+ \n if (-e $psv){$ENV{'HMMTOP_PSV'}=$psv;}\n \
+ elsif (-e $ENV{HMMTOP_PSV}){$psv=$ENV{HMMTOP_PS\
+V};}\n elsif (-e \"$MCOFFEE/hmmtop.psv\"){$psv=\
+$ENV{'HMMTOP_PSV'}=\"$MCOFFEE/hmmtop.psv\";}\n \
+elsif (-e \"$hmmtop_home/hmmtop.psv\"){$psv=$ENV{'\
+HMMTOP_PSV'}=\"$hmmtop_home/hmmtop.psv\";}\n el\
+se {myexit(flush_error ( \"Could not find PSV file\
+ for hmmtop\"));}\n }\nelsif ($mode eq \"gor\")\n\
+ {\n our $GOR_SEQ;\n our $GOR_OBS;\n \n \
+ check_configuration (\"gorIV\");\n if (-e $g\
+or_seq){$GOR_SEQ=$gor_seq;}\n elsif (-e $ENV{GO\
+R_SEQ}){$GOR_SEQ=$ENV{GOR_SEQ};}\n elsif (-e \"\
+$MCOFFEE/New_KS.267.seq\"){$GOR_SEQ=\"$MCOFFEE/New\
+_KS.267.seq\";}\n elsif (-e \"$gor_home/New_KS.\
+267.seq\"){$GOR_SEQ=\"$gor_home/New_KS.267.seq\";}\
+\n else {myexit(flush_error ( \"Could not find \
+SEQ file for gor\"));}\n\n if (-e $gor_obs){$GO\
+R_OBS=$gor_obs;}\n elsif (-e $ENV{GOR_OBS}){$GO\
+R_OBS=$ENV{GOR_OBS};}\n elsif (-e \"$MCOFFEE/Ne\
+w_KS.267.obs\"){$GOR_OBS=\"$MCOFFEE/New_KS.267.obs\
+\";}\n elsif (-e \"$gor_home/New_KS.267.obs\"){\
+$GOR_OBS=\"$gor_home/New_KS.267.obs\";}\n else \
+{myexit(flush_error ( \"Could not find OBS file fo\
+r gor\"));}\n }\n\n\nif ( ! -e $fmsq1){myexit(flu\
+sh_error (\"Could Not Read Input file $fmsq1\"));}\
+\n\n\nmy $fmsq2=vtmpnam();\nmy $fmsq3=vtmpnam();\n\
+my $tmpfile=vtmpnam();\nmy $predfile=vtmpnam();\n\\
+nif ($trim){$trim_action=\" +trim _aln_%%$trim\\_K\
+1 \";}\nif ($cov) {$cov_action= \" +sim_filter _al\
+n_c$cov \";}\n&safe_system(\"t_coffee -other_pg se\
+q_reformat -in $fmsq1 -action +convert 'BOUJXZ-' $\
+cov_action $trim_action -output fasta_aln -out $fm\
+sq2\");\nmy (%pred, %seq, %predA);\n\n\n%seq=read_\
+fasta_seq($fmsq2);\n%seq=fasta2sample(\\%seq, $sam\
+ple);\n\nif (1==2 && $mode eq \"hmmtop\" && $outpu\
+t eq \"cons\")\n {\n fasta2hmmtop_cons($outfil\
+e,\\%seq);\n }\nelse\n {\n %pred=fasta2pred(\\
+\%seq, $mode);\n %predA=pred2aln (\\%pred, \\%s\
+eq);\n \n \n if (!$output || $output eq \\
+"prediction\"){output_fasta_seq (\\%predA, $outfil\
+e);}\n elsif ($output eq \"color_html\"){pred2c\
+olor (\\%pred,\\%seq, $outfile);}\n elsif ($out\
+put eq \"cons\"){pred2cons($outfile,\\%predA);}\n \
+ else {flush_error (\"$output is an unknown outp\
+ut mode\");}\n }\n\nsub fasta2sample\n {\n my\
+ $SR=shift;\n my $it=shift;\n my %S=%$SR;\n \
+ \n my $seq=index2seq_name (\\%S, 1);\n my\
+ $l=length($S{$seq}{seq});\n my @sl=keys(%S);\n\
+ my $nseq=$#sl+1;\n my $index=$nseq;\n \n \
+ if (!$sample) {return %S;}\n for (my $a=0; $a\
+<$it; $a++)\n {\n my $newseq=\"\";\n my $nnam\
+e=\"$seq\\_sampled_$index\";\n for (my $p=0; $p<$l\
+; $p++)\n {\n my $i=int(rand($nseq));\n \
+\n my $name = $sl[$i];\n my $seq=$S{$name}\
+{seq};\n my $r=substr ($seq, $p, 1);\n $ne\
+wseq.=$r;\n }\n $S{$nname}{name}=$nname;\n $S{$n\
+name}{seq}=$newseq;\n $S{$nname}{com}=\"sampled\";\
+\n $S{$nname}{index}=++$index;\n }\n retur\
+n %S;\n }\n \nsub fasta2pred\n {\n my $\
+s=shift;\n my $mode=shift;\n\n if ( $mode eq\
+ \"hmmtop\"){return fasta2hmmtop_pred($s);}\n e\
+lsif ($mode eq \"gor\"){return fasta2gor_pred ($s)\
+;}\n }\nsub fasta2hmmtop_cons\n {\n my $outfi\
+le=shift;\n my $SR=shift;\n \n my $o = ne\
+w FileHandle;\n my $i = new FileHandle;\n my\
+ $tmp_in =vtmpnam();\n my $tmp_out=vtmpnam();\n\
+ my %seq=%$SR;\n my %pred;\n my $N=keys(%\
+seq);\n \n output_fasta_seq (\\%seq,$tmp_in,\
+ \"seq\");\n `hmmtop -pi=mpred -if=$tmp_in -sf=\
+FAS -pl 2>/dev/null >$tmp_out`;\n open ($o, \">\
+$outfile\");\n open ($i, \"$tmp_out\");\n wh\
+ile (<$i>)\n {\n my $l=$_;\n if (($l=~/>HP\\:\
+\\s+(\\d+)\\s+(.*)/)){my $line=\">$2 NSEQ: $N\\n\"\
+;print $o \"$line\";}\n elsif ( ($l=~/.*pred(.*)/)\
+) {my $line=\"$1\\n\";print $o \"$line\";}\n \
+ }\n close ($o);\n close ($i);\n return r\
+ead_fasta_seq($tmp);\n }\nsub fasta2hmmtop_pred\n\
+ {\n my $SR=shift;\n my $o = new FileHandle\
+;\n my $i = new FileHandle;\n my $tmp =vt\
+mpnam();\n my $tmp_in =vtmpnam();\n my $tmp_\
+out=vtmpnam();\n my %seq=%$SR;\n my %pred;\n\
+ \n\n output_fasta_seq (\\%seq,$tmp_in, \"se\
+q\");\n `hmmtop -if=$tmp_in -sf=FAS -pl 2>/dev/\
+null >$tmp_out`;\n open ($o, \">$tmp\");\n o\
+pen ($i, \"$tmp_out\");\n while (<$i>)\n {\
+\n my $l=$_;\n if (($l=~/>HP\\:\\s+(\\d+)\\s+(.*)/\
+)){my $line=\">$2\\n\";print $o \"$line\";}\n elsi\
+f ( ($l=~/.*pred(.*)/)) {my $line=\"$1\\n\";print\
+ $o \"$line\";}\n }\n close ($o);\n clo\
+se ($i);\n return read_fasta_seq($tmp);\n }\n \
+ \n \n \n \n \n \n\n \nsub fasta2gor_pred\n \
+ {\n my $SR=shift;\n my $o = new FileHandle;\
+\n my $i = new FileHandle;\n my $tmp =vtm\
+pnam();\n my $tmp_in =vtmpnam();\n my $tmp_o\
+ut=vtmpnam();\n my %seq=%$SR;\n my %pred;\n \
+ \n\n output_fasta_seq (\\%seq,$tmp_in, \"seq\
+\");\n `gorIV -prd $tmp_in -seq $GOR_SEQ -obs $\
+GOR_OBS >$tmp_out`;\n open ($o, \">$tmp\");\n \
+ open ($i, \"$tmp_out\");\n while (<$i>)\n \
+ {\n my $l=$_;\n\n \n if ( $l=~/>/){print $o \"$l\
+\";}\n elsif ( $l=~/Predicted Sec. Struct./){$l=~s\
+/Predicted Sec. Struct\\.//;print $o \"$l\";}\n \
+ }\n close ($o);\n close ($i);\n return\
+ read_fasta_seq($tmp);\n }\n \n \nsub in\
+dex2seq_name\n {\n \n my $SR=shift;\n my\
+ $index=shift;\n \n \n my %S=%$SR;\n \\
+n foreach my $s (%S)\n {\n if ( $S{$s}{ind\
+ex}==$index){return $s;}\n }\n return \"\"\
+;\n }\n\nsub pred2cons\n {\n my $outfile=shif\
+t;\n my $predR=shift;\n my $seq=shift;\n \
+my %P=%$predR;\n my %C;\n my ($s,@r,$nseq);\\
+n my $f= new FileHandle;\n\n open ($f, \">$o\
+utfile\");\n\n if (!$seq){$seq=index2seq_name(\\
+\%P,1);}\n foreach my $s (keys(%P))\n {\n \
+$nseq++;\n $string= $P{$s}{seq};\n $string = uc $s\
+tring;\n my @r=split (//,$string);\n for (my $a=0;\
+ $a<=$#r; $a++)\n {\n if (($r[$a]=~/[OHICE]/\
+)){$C{$a}{$r[$a]}++;}\n }\n }\n @l=keys(\
+%C);\n \n \n $s=$P{$seq}{seq};\n print\
+ $f \">$seq pred based on $nseq\\n\";\n @r=spli\
+t (//,$s);\n \n for (my $x=0; $x<=$#r; $x++)\
+\n {\n if ($r[$x] ne \"-\")\n {\n my $h\
+=$C{$x}{H};\n my $i=$C{$x}{I};\n my $o=$C{\
+$x}{O};\n my $c=$C{$x}{C};\n my $e=$C{$x}{\
+E};\n my $l=$i+$o;\n \n if ($h>=$i && \
+$h>=$o && $h>=$c && $h>=$e){$r[$x]='H';}\n els\
+if ($i>=$o && $i>=$c && $i>=$e){$r[$x]='I';}\n \
+ elsif ($o>=$c && $o>=$e){$r[$x]='O';}\n elsif\
+ ($c>=$e){$r[$x]='C';}\n else {$r[$x]='E';}\n \
+ }\n }\n $j=join ('', @r);\n print $f \
+\"$j\\n\";\n close ($f);\n return $j;\n }\n\
+\nsub pred2aln\n {\n my $PR=shift;\n my $AR\
+=shift;\n \n my $f=new FileHandle;\n my %\
+P=%$PR;\n my %A=%$AR;\n my %PA;\n my $tmp\
+=vtmpnam();\n my $f= new FileHandle;\n \n \
+ open ($f, \">$tmp\");\n foreach my $s (sort{$A\
+{$a}{index}<=>$A{$b}{index}}(keys (%A)))\n {\\
+n my (@list, $seq, @plist, @pseq, $L, $PL, $c, $w)\
+;\n my $seq;\n my $seq=$A{$s}{seq};\n my $pred=$P{\
+$s}{seq};\n $seq=pred2alnS($P{$s}{seq},$A{$s}{seq}\
+);\n print $f \">$s\\n$seq\\n\";\n }\n clo\
+se ($f);\n return read_fasta_seq ($tmp);\n }\n\
+sub pred2alnS\n {\n my $pred=shift;\n my $a\
+ln= shift;\n my ($j,$a,$b);\n my @P=split (/\
+/, $pred);\n my @A=split (//, $aln);\n for (\
+$a=$b=0;$a<=$#A; $a++)\n {\n if ($A[$a] ne \"\
+-\"){$A[$a]=$P[$b++];}\n }\n if ($b!= ($#P\
++1)){add_warning (\"Could not thread sequence: $b \
+$#P\");}\n \n $j= join ('', @A);\n return\
+ $j;\n }\nsub pred2color\n {\n my $predP=shif\
+t;\n my $alnP=shift;\n my $out=shift;\n m\
+y $F=new FileHandle;\n my $struc=vtmpnam();\n \
+ my $aln=vtmpnam();\n \n\n output_fasta_seq\
+ ($alnP, $aln);\n my %p=%$predP;\n \n ope\
+n ($F, \">$struc\");\n \n \n foreach my $\
+s (keys(%p))\n {\n \n print $F \">$s\\n\";\n \
+my $s=uc($p{$s}{seq});\n \n $s=~s/[Oo]/0/g;\n $s=~\
+s/[Ee]/0/g;\n \n $s=~s/[Ii]/5/g;\n $s=~s/[Cc]/5/g;\
+\n \n $s=~s/[Hh]/9/g;\n \n print $F \"$s\\n\";\n \
+ }\n close ($F);\n \n \n \n safe\
+_system ( \"t_coffee -other_pg seq_reformat -in $a\
+ln -struc_in $struc -struc_in_f number_fasta -outp\
+ut color_html -out $out\");\n return;\n }\n \
+\n \nsub display_fasta_seq\n {\n my $SR=shi\
+ft;\n my %S=%$SR;\n \n foreach my $s (sor\
+t{$S{$a}{index}<=>$S{$b}{index}}(keys (%S)))\n \
+ {\n print STDERR \">$s\\n$S{$s}{seq}\\n\";\n \
+ }\n close ($f);\n }\nsub output_fasta_seq\n \
+ {\n my $SR=shift;\n my $outfile=shift;\n \
+ my $mode =shift;\n my $f= new FileHandle;\n \
+ my %S=%$SR;\n \n \n open ($f, \">$outfil\
+e\");\n foreach my $s (sort{$S{$a}{index}<=>$S{\
+$b}{index}}(keys (%S)))\n {\n my $seq=$S{$s}{\
+seq};\n if ( $mode eq \"seq\"){$seq=~s/\\-//g;}\n \
+print $f \">$s\\n$seq\\n\";\n }\n close ($\
+f);\n }\n \nsub read_fasta_seq \n {\n my\
+ $f=$_[0];\n my %hseq;\n my (@seq, @com, @na\
+me);\n my ($a, $s,$nseq);\n my $index;\n \
open (F, $f);\n while (<F>)\n {\n $s.=$_;\\
n }\n close (F);\n\n \n @name=($s=~/\
>(\\S*).*\\n[^>]*/g);\n \n @seq =($s=~/>.*.*\
-\\n([^>]*)/g);\n @com =($s=~/>\\S*(.*)\\n([^>]*\
-)/g);\n\n \n $nseq=$#name+1;\n \n for \
-($a=0; $a<$nseq; $a++)\n {\n my $n=$name[$a];\
-\n $hseq{$n}{name}=$n;\n $hseq{$n}{seq}=$seq[$a];\\
-n $hseq{$n}{com}=$com[$a];\n }\n return %h\
-seq;\n }\n","use Getopt::Long;\nuse File::Path;\n\
-use Env;\nuse FileHandle;\nuse Cwd;\nuse Sys::Host\
-name;\nour $PIDCHILD;\nour $ERROR_DONE;\nour @TMPF\
-ILE_LIST;\nour $EXIT_FAILURE=1;\nour $EXIT_SUCCESS\
-=0;\n\nour $REFDIR=getcwd;\nour $EXIT_SUCCESS=0;\n\
-our $EXIT_FAILURE=1;\n\nour $PROGRAM=\"tc_generic_\
-method.pl\";\nour $CL=$PROGRAM;\n\nour $CLEAN_EXIT\
-_STARTED;\nour $debug_lock=$ENV{\"DEBUG_LOCK\"};\n\
-our $LOCKDIR=$ENV{\"LOCKDIR_4_TCOFFEE\"};\nif (!$L\
-OCKDIR){$LOCKDIR=getcwd();}\nour $ERRORDIR=$ENV{\"\
-ERRORDIR_4_TCOFFEE\"};\nour $ERRORFILE=$ENV{\"ERRO\
-RFILE_4_TCOFFEE\"};\n&set_lock ($$);\nif (isshellp\
-id(getppid())){lock4tc(getppid(), \"LLOCK\", \"LSE\
-T\", \"$$\\n\");}\n \nour $print;\nmy ($fmsq1\
-, $fmsq2, $output, $outfile, $arch, $psv, $hmmtop_\
-home, $trim, $cov, $sample, $mode, $gor_home, $gor\
-_seq, $gor_obs);\n\nGetOptions(\"-in=s\" => \\$fms\
-q1,\"-output=s\" =>\\$output ,\"-out=s\" => \\$out\
-file, \"-arch=s\" => \\$arch,\"-psv=s\" => \\$psv,\
- \"-hmmtop_home=s\", \\$hmmtop_home,\"-trim=s\" =>\
-\\$trim ,\"-print=s\" =>\\$print,\"-cov=s\" =>\\$c\
-ov , \"-sample=s\" =>\\$sample, \"-mode=s\" =>\\$m\
-ode, \"-gor_home=s\"=>\\$gor_home, \"-gor_seq=s\"=\
->\\$gor_seq,\"-gor_obs=s\"=>\\$gor_obs);\n\n\nif (\
-!$mode){$mode = \"hmmtop\"}\nelsif ($mode eq \"hmm\
-top\"){;}\nelsif ($mode eq \"gor\"){;}\nelse {myex\
-it(flush_error (\"-mode=$mode is unknown\"));}\n\n\
-\nour $HOME=$ENV{\"HOME\"};\nour $MCOFFEE=($ENV{\"\
-MCOFFEE_4_TCOFFEE\"})?$ENV{\"MCOFFEE_4_TCOFFEE\"}:\
-\"$HOME/.t_coffee/mcoffee\";\n\nif ($mode eq \"hmm\
-top\")\n {\n check_configuration (\"hmmtop\");\
-\n if (-e $arch){$ENV{'HMMTOP_ARCH'}=$arch;}\n \
- elsif (-e $ENV{HMMTOP_ARCH}){$arch=$ENV{HMMTOP_\
-ARCH};}\n elsif (-e \"$MCOFFEE/hmmtop.arch\"){$\
-arch=$ENV{'HMMTOP_ARCH'}=\"$MCOFFEE/hmmtop.arch\";\
-}\n elsif (-e \"$hmmtop_home/hmmtop.arc\"){$arc\
-h=$ENV{'HMMTOP_ARCH'}=\"$hmmtop_home/hmmtop.arc\";\
-}\n else {myexit(flush_error ( \"Could not find\
- ARCH file for hmmtop\"));}\n \n \n if (-\
-e $psv){$ENV{'HMMTOP_PSV'}=$psv;}\n elsif (-e $\
-ENV{HMMTOP_PSV}){$psv=$ENV{HMMTOP_PSV};}\n elsi\
-f (-e \"$MCOFFEE/hmmtop.psv\"){$psv=$ENV{'HMMTOP_P\
-SV'}=\"$MCOFFEE/hmmtop.psv\";}\n elsif (-e \"$h\
-mmtop_home/hmmtop.psv\"){$psv=$ENV{'HMMTOP_PSV'}=\\
-"$hmmtop_home/hmmtop.psv\";}\n else {myexit(flu\
-sh_error ( \"Could not find PSV file for hmmtop\")\
-);}\n }\nelsif ($mode eq \"gor\")\n {\n our $\
-GOR_SEQ;\n our $GOR_OBS;\n \n check_confi\
-guration (\"gorIV\");\n if (-e $gor_seq){$GOR_S\
-EQ=$gor_seq;}\n elsif (-e $ENV{GOR_SEQ}){$GOR_S\
-EQ=$ENV{GOR_SEQ};}\n elsif (-e \"$MCOFFEE/New_K\
-S.267.seq\"){$GOR_SEQ=\"$MCOFFEE/New_KS.267.seq\";\
-}\n elsif (-e \"$gor_home/New_KS.267.seq\"){$GO\
-R_SEQ=\"$gor_home/New_KS.267.seq\";}\n else {my\
-exit(flush_error ( \"Could not find SEQ file for g\
-or\"));}\n\n if (-e $gor_obs){$GOR_OBS=$gor_obs\
-;}\n elsif (-e $ENV{GOR_OBS}){$GOR_OBS=$ENV{GOR\
-_OBS};}\n elsif (-e \"$MCOFFEE/New_KS.267.obs\"\
-){$GOR_OBS=\"$MCOFFEE/New_KS.267.obs\";}\n elsi\
-f (-e \"$gor_home/New_KS.267.obs\"){$GOR_OBS=\"$go\
-r_home/New_KS.267.obs\";}\n else {myexit(flush_\
-error ( \"Could not find OBS file for gor\"));}\n \
- }\n\n\nif ( ! -e $fmsq1){myexit(flush_error (\"Co\
-uld Not Read Input file $fmsq1\"));}\n\n\nmy $fmsq\
-2=vtmpnam();\nmy $fmsq3=vtmpnam();\nmy $tmpfile=vt\
-mpnam();\nmy $predfile=vtmpnam();\n\nif ($trim){$t\
-rim_action=\" +trim _aln_%%$trim\\_K1 \";}\nif ($c\
-ov) {$cov_action= \" +sim_filter _aln_c$cov \";}\n\
-&safe_system(\"t_coffee -other_pg seq_reformat -in\
- $fmsq1 -action +convert 'BOUJXZ-' $cov_action $tr\
-im_action -output fasta_aln -out $fmsq2\");\nmy (%\
-pred, %seq, %predA);\n\n\n%seq=read_fasta_seq($fms\
-q2);\n%seq=fasta2sample(\\%seq, $sample);\n\nif (1\
-==2 && $mode eq \"hmmtop\" && $output eq \"cons\")\
-\n {\n fasta2hmmtop_cons($outfile,\\%seq);\n \
-}\nelse\n {\n %pred=fasta2pred(\\%seq, $mode);\
-\n %predA=pred2aln (\\%pred, \\%seq);\n \n \
- \n if (!$output || $output eq \"prediction\")\
-{output_fasta_seq (\\%predA, $outfile);}\n elsi\
-f ($output eq \"color_html\"){pred2color (\\%pred,\
-\\%seq, $outfile);}\n elsif ($output eq \"cons\\
-"){pred2cons($outfile,\\%predA);}\n else {flush\
-_error (\"$output is an unknown output mode\");}\n\
- }\n\nsub fasta2sample\n {\n my $SR=shift;\n \
- my $it=shift;\n my %S=%$SR;\n \n my $s\
-eq=index2seq_name (\\%S, 1);\n my $l=length($S{\
-$seq}{seq});\n my @sl=keys(%S);\n my $nseq=$\
-#sl+1;\n my $index=$nseq;\n \n if (!$sample\
-) {return %S;}\n for (my $a=0; $a<$it; $a++)\n \
- {\n my $newseq=\"\";\n my $nname=\"$seq\\_sam\
-pled_$index\";\n for (my $p=0; $p<$l; $p++)\n {\\
-n my $i=int(rand($nseq));\n \n my $nam\
-e = $sl[$i];\n my $seq=$S{$name}{seq};\n m\
-y $r=substr ($seq, $p, 1);\n $newseq.=$r;\n \
-}\n $S{$nname}{name}=$nname;\n $S{$nname}{seq}=$ne\
-wseq;\n $S{$nname}{com}=\"sampled\";\n $S{$nname}{\
-index}=++$index;\n }\n return %S;\n }\n \
- \nsub fasta2pred\n {\n my $s=shift;\n \
-my $mode=shift;\n\n if ( $mode eq \"hmmtop\"){r\
-eturn fasta2hmmtop_pred($s);}\n elsif ($mode eq\
- \"gor\"){return fasta2gor_pred ($s);}\n }\nsub f\
-asta2hmmtop_cons\n {\n my $outfile=shift;\n \
- my $SR=shift;\n \n my $o = new FileHandle;\\
-n my $i = new FileHandle;\n my $tmp_in =vtmp\
-nam();\n my $tmp_out=vtmpnam();\n my %seq=%$\
-SR;\n my %pred;\n my $N=keys(%seq);\n \n \
- output_fasta_seq (\\%seq,$tmp_in, \"seq\");\n \
- `hmmtop -pi=mpred -if=$tmp_in -sf=FAS -pl 2>/dev\
-/null >$tmp_out`;\n open ($o, \">$outfile\");\n\
- open ($i, \"$tmp_out\");\n while (<$i>)\n \
- {\n my $l=$_;\n if (($l=~/>HP\\:\\s+(\\d+)\\s+\
-(.*)/)){my $line=\">$2 NSEQ: $N\\n\";print $o \"$l\
-ine\";}\n elsif ( ($l=~/.*pred(.*)/)) {my $line=\\
-"$1\\n\";print $o \"$line\";}\n }\n close \
-($o);\n close ($i);\n return read_fasta_seq(\
-$tmp);\n }\nsub fasta2hmmtop_pred\n {\n my $S\
-R=shift;\n my $o = new FileHandle;\n my $i =\
- new FileHandle;\n my $tmp =vtmpnam();\n \
-my $tmp_in =vtmpnam();\n my $tmp_out=vtmpnam();\
-\n my %seq=%$SR;\n my %pred;\n \n\n ou\
-tput_fasta_seq (\\%seq,$tmp_in, \"seq\");\n `hm\
-mtop -if=$tmp_in -sf=FAS -pl 2>/dev/null >$tmp_out\
-`;\n open ($o, \">$tmp\");\n open ($i, \"$tm\
-p_out\");\n while (<$i>)\n {\n my $l=$_;\n\
- if (($l=~/>HP\\:\\s+(\\d+)\\s+(.*)/)){my $line=\"\
->$2\\n\";print $o \"$line\";}\n elsif ( ($l=~/.*pr\
-ed(.*)/)) {my $line=\"$1\\n\";print $o \"$line\";\
-}\n }\n close ($o);\n close ($i);\n \
-return read_fasta_seq($tmp);\n }\n \n \n \n \
- \n \n \n\n \nsub fasta2gor_pred\n {\n my $SR\
-=shift;\n my $o = new FileHandle;\n my $i = \
-new FileHandle;\n my $tmp =vtmpnam();\n m\
-y $tmp_in =vtmpnam();\n my $tmp_out=vtmpnam();\\
-n my %seq=%$SR;\n my %pred;\n \n\n out\
-put_fasta_seq (\\%seq,$tmp_in, \"seq\");\n `gor\
-IV -prd $tmp_in -seq $GOR_SEQ -obs $GOR_OBS >$tmp_\
-out`;\n open ($o, \">$tmp\");\n open ($i, \"\
-$tmp_out\");\n while (<$i>)\n {\n my $l=$_\
-;\n\n \n if ( $l=~/>/){print $o \"$l\";}\n elsif (\
- $l=~/Predicted Sec. Struct./){$l=~s/Predicted Sec\
-. Struct\\.//;print $o \"$l\";}\n }\n clos\
-e ($o);\n close ($i);\n return read_fasta_se\
-q($tmp);\n }\n \n \nsub index2seq_name\n\
- {\n \n my $SR=shift;\n my $index=shift;\
-\n \n \n my %S=%$SR;\n \n foreach m\
-y $s (%S)\n {\n if ( $S{$s}{index}==$index){r\
-eturn $s;}\n }\n return \"\";\n }\n\nsub \
-pred2cons\n {\n my $outfile=shift;\n my $pr\
-edR=shift;\n my $seq=shift;\n my %P=%$predR;\
-\n my %C;\n my ($s,@r,$nseq);\n my $f= ne\
-w FileHandle;\n\n open ($f, \">$outfile\");\n\n\
- if (!$seq){$seq=index2seq_name(\\%P,1);}\n \
-foreach my $s (keys(%P))\n {\n $nseq++;\n $st\
-ring= $P{$s}{seq};\n $string = uc $string;\n my @r\
-=split (//,$string);\n for (my $a=0; $a<=$#r; $a++\
-)\n {\n if (($r[$a]=~/[OHICE]/)){$C{$a}{$r[$\
-a]}++;}\n }\n }\n @l=keys(%C);\n \n \
- \n $s=$P{$seq}{seq};\n print $f \">$seq pr\
-ed based on $nseq\\n\";\n @r=split (//,$s);\n \
- \n for (my $x=0; $x<=$#r; $x++)\n {\n if\
- ($r[$x] ne \"-\")\n {\n my $h=$C{$x}{H};\n \
- my $i=$C{$x}{I};\n my $o=$C{$x}{O};\n \
-my $c=$C{$x}{C};\n my $e=$C{$x}{E};\n my $\
-l=$i+$o;\n \n if ($h>=$i && $h>=$o && $h>=\
-$c && $h>=$e){$r[$x]='H';}\n elsif ($i>=$o && \
-$i>=$c && $i>=$e){$r[$x]='I';}\n elsif ($o>=$c\
- && $o>=$e){$r[$x]='O';}\n elsif ($c>=$e){$r[$\
-x]='C';}\n else {$r[$x]='E';}\n }\n }\n\
- $j=join ('', @r);\n print $f \"$j\\n\";\n \
- close ($f);\n return $j;\n }\n\nsub pred2aln\
-\n {\n my $PR=shift;\n my $AR=shift;\n \\
-n my $f=new FileHandle;\n my %P=%$PR;\n m\
-y %A=%$AR;\n my %PA;\n my $tmp=vtmpnam();\n \
- my $f= new FileHandle;\n \n open ($f, \">\
-$tmp\");\n foreach my $s (sort{$A{$a}{index}<=>\
-$A{$b}{index}}(keys (%A)))\n {\n my (@list, $\
-seq, @plist, @pseq, $L, $PL, $c, $w);\n my $seq;\n\
- my $seq=$A{$s}{seq};\n my $pred=$P{$s}{seq};\n $s\
-eq=pred2alnS($P{$s}{seq},$A{$s}{seq});\n print $f \
-\">$s\\n$seq\\n\";\n }\n close ($f);\n \
-return read_fasta_seq ($tmp);\n }\nsub pred2alnS\\
-n {\n my $pred=shift;\n my $aln= shift;\n \
- my ($j,$a,$b);\n my @P=split (//, $pred);\n \
- my @A=split (//, $aln);\n for ($a=$b=0;$a<=$#\
-A; $a++)\n {\n if ($A[$a] ne \"-\"){$A[$a]=$P\
-[$b++];}\n }\n if ($b!= ($#P+1)){add_warni\
-ng (\"Could not thread sequence: $b $#P\");}\n \
-\n $j= join ('', @A);\n return $j;\n }\nsub\
- pred2color\n {\n my $predP=shift;\n my $al\
-nP=shift;\n my $out=shift;\n my $F=new FileH\
-andle;\n my $struc=vtmpnam();\n my $aln=vtmp\
-nam();\n \n\n output_fasta_seq ($alnP, $aln)\
-;\n my %p=%$predP;\n \n open ($F, \">$str\
-uc\");\n \n \n foreach my $s (keys(%p))\n\
- {\n \n print $F \">$s\\n\";\n my $s=uc($p{$s\
-}{seq});\n \n $s=~s/[Oo]/0/g;\n $s=~s/[Ee]/0/g;\n \
-\n $s=~s/[Ii]/5/g;\n $s=~s/[Cc]/5/g;\n \n $s=~s/[H\
-h]/9/g;\n \n print $F \"$s\\n\";\n }\n clo\
-se ($F);\n \n \n \n safe_system ( \"t_\
-coffee -other_pg seq_reformat -in $aln -struc_in $\
-struc -struc_in_f number_fasta -output color_html \
--out $out\");\n return;\n }\n \n \nsub di\
-splay_fasta_seq\n {\n my $SR=shift;\n my %S\
-=%$SR;\n \n foreach my $s (sort{$S{$a}{index\
-}<=>$S{$b}{index}}(keys (%S)))\n {\n print ST\
-DERR \">$s\\n$S{$s}{seq}\\n\";\n }\n close\
- ($f);\n }\nsub output_fasta_seq\n {\n my $SR\
-=shift;\n my $outfile=shift;\n my $mode =shi\
-ft;\n my $f= new FileHandle;\n my %S=%$SR;\n\
- \n \n open ($f, \">$outfile\");\n for\
-each my $s (sort{$S{$a}{index}<=>$S{$b}{index}}(ke\
-ys (%S)))\n {\n my $seq=$S{$s}{seq};\n if ( $\
-mode eq \"seq\"){$seq=~s/\\-//g;}\n print $f \">$s\
-\\n$seq\\n\";\n }\n close ($f);\n }\n \
- \nsub read_fasta_seq \n {\n my $f=$_[0];\n \
- my %hseq;\n my (@seq, @com, @name);\n my (\
-$a, $s,$nseq);\n my $index;\n open (F, $f);\\
-n while (<F>)\n {\n $s.=$_;\n }\n \
-close (F);\n\n \n @name=($s=~/>(\\S*).*\\n[^\
->]*/g);\n \n @seq =($s=~/>.*.*\\n([^>]*)/g);\
-\n @com =($s=~/>.*(.*)\\n([^>]*)/g);\n\n\n $\
-nseq=$#name+1;\n \n \n for ($a=0; $a<$nseq;\
- $a++)\n {\n my $n=$name[$a];\n my $s;\n $hse\
-q{$n}{name}=$n;\n $s=$seq[$a];$s=~s/\\s//g;\n $hse\
-q{$n}{index}=++$index;\n $hseq{$n}{seq}=$s;\n $hse\
-q{$n}{com}=$com[$a];\n }\n return %hseq;\n\
- }\n\n\nsub file2head\n {\n my $file = shift\
-;\n my $size = shift;\n my $f= new FileHandle;\n m\
-y $line;\n open ($f,$file);\n read ($f,$line, $siz\
-e);\n close ($f);\n return $line;\n }\nsub fi\
-le2tail\n {\n my $file = shift;\n my $size = \
-shift;\n my $f= new FileHandle;\n my $line;\n \n o\
-pen ($f,$file);\n seek ($f,$size*-1, 2);\n read ($\
-f,$line, $size);\n close ($f);\n return $line;\n \
- }\n\n\nsub vtmpnam\n {\n my $r=rand(10000\
-0);\n my $f=\"file.$r.$$\";\n while (-e $f)\n {\\
-n $f=vtmpnam();\n }\n push (@TMPFILE_LIST, $\
-f);\n return $f;\n }\n\nsub myexit\n {\n \
-my $code=@_[0];\n if ($CLEAN_EXIT_STARTED==1){r\
-eturn;}\n else {$CLEAN_EXIT_STARTED=1;}\n ##\
-# ONLY BARE EXIT\n exit ($code);\n }\nsub set_\
-error_lock\n {\n my $name = shift;\n \
-my $pid=$$;\n\n \n &lock4tc ($$,\"LERROR\
-\", \"LSET\", \"$$ -- ERROR: $name $PROGRAM\\n\");\
-\n return;\n }\nsub set_lock\n {\n my \
-$pid=shift;\n my $msg= shift;\n my $p=getppi\
-d();\n &lock4tc ($pid,\"LLOCK\",\"LRESET\",\"$p\
-$msg\\n\");\n }\nsub unset_lock\n {\n \n \
- my $pid=shift;\n &lock4tc ($pid,\"LLOCK\",\"LR\
-ELEASE\",\"\");\n }\nsub shift_lock\n {\n my \
-$from=shift;\n my $to=shift;\n my $from_type\
-=shift;\n my $to_type=shift;\n my $action=sh\
-ift;\n my $msg;\n \n if (!&lock4tc($from,\
- $from_type, \"LCHECK\", \"\")){return 0;}\n $m\
-sg=&lock4tc ($from, $from_type, \"LREAD\", \"\");\\
-n &lock4tc ($from, $from_type,\"LRELEASE\", $ms\
-g);\n &lock4tc ($to, $to_type, $action, $msg);\\
-n return;\n }\nsub isshellpid\n {\n my $p=\
-shift;\n if (!lock4tc ($p, \"LLOCK\", \"LCHECK\\
-")){return 0;}\n else\n {\n my $c=lock4tc(\
-$p, \"LLOCK\", \"LREAD\");\n if ( $c=~/-SHELL-/){r\
-eturn 1;}\n }\n return 0;\n }\nsub isroot\
-pid\n {\n if(lock4tc (getppid(), \"LLOCK\", \"\
-LCHECK\")){return 0;}\n else {return 1;}\n }\n\
-sub lock4tc\n {\n my ($pid,$type,$action,$value)\
-=@_;\n my $fname;\n my $host=hostname;\n \n \
- if ($type eq \"LLOCK\"){$fname=\"$LOCKDIR/.$pid.\
-$host.lock4tcoffee\";}\n elsif ( $type eq \"LERR\
-OR\"){ $fname=\"$LOCKDIR/.$pid.$host.error4tcoffee\
-\";}\n elsif ( $type eq \"LWARNING\"){ $fname=\"\
-$LOCKDIR/.$pid.$host.warning4tcoffee\";}\n \n \
-if ($debug_lock)\n {\n print STDERR \"\\\
-n\\t---lock4tc(tcg): $action => $fname =>$value (R\
-D: $LOCKDIR)\\n\";\n }\n\n if ($action eq\
- \"LCHECK\") {return -e $fname;}\n elsif ($actio\
-n eq \"LREAD\"){return file2string($fname);}\n e\
-lsif ($action eq \"LSET\") {return string2file ($v\
-alue, $fname, \">>\");}\n elsif ($action eq \"LR\
-ESET\") {return string2file ($value, $fname, \">\"\
-);}\n elsif ($action eq \"LRELEASE\") \n {\n\
- if ( $debug_lock)\n {\n my $g=new FileH\
-andle;\n open ($g, \">>$fname\");\n print $g\
- \"\\nDestroyed by $$\\n\";\n close ($g);\n \
-safe_system (\"mv $fname $fname.old\");\n }\n \
- else\n {\n unlink ($fname);\n }\n }\n \
- return \"\";\n }\n \nsub file2string\n {\n my \
-$file=@_[0];\n my $f=new FileHandle;\n my $r;\\
-n open ($f, \"$file\");\n while (<$f>){$r.=$_;\
-}\n close ($f);\n return $r;\n }\nsub string2f\
-ile \n {\n my ($s,$file,$mode)=@_;\n my $\
-f=new FileHandle;\n \n open ($f, \"$mode$fil\
-e\");\n print $f \"$s\";\n close ($f);\n }\
-\n\nBEGIN\n {\n srand;\n \n $SIG{'\
-SIGUP'}='signal_cleanup';\n $SIG{'SIGINT'}='s\
-ignal_cleanup';\n $SIG{'SIGQUIT'}='signal_cle\
-anup';\n $SIG{'SIGILL'}='signal_cleanup';\n \
- $SIG{'SIGTRAP'}='signal_cleanup';\n $SIG{\
-'SIGABRT'}='signal_cleanup';\n $SIG{'SIGEMT'}\
-='signal_cleanup';\n $SIG{'SIGFPE'}='signal_c\
-leanup';\n \n $SIG{'SIGKILL'}='signal_cl\
-eanup';\n $SIG{'SIGPIPE'}='signal_cleanup';\n\
- $SIG{'SIGSTOP'}='signal_cleanup';\n $SI\
-G{'SIGTTIN'}='signal_cleanup';\n $SIG{'SIGXFS\
-Z'}='signal_cleanup';\n $SIG{'SIGINFO'}='sign\
-al_cleanup';\n \n $SIG{'SIGBUS'}='signal\
-_cleanup';\n $SIG{'SIGALRM'}='signal_cleanup'\
-;\n $SIG{'SIGTSTP'}='signal_cleanup';\n \
-$SIG{'SIGTTOU'}='signal_cleanup';\n $SIG{'SIG\
-VTALRM'}='signal_cleanup';\n $SIG{'SIGUSR1'}=\
-'signal_cleanup';\n\n\n $SIG{'SIGSEGV'}='sign\
-al_cleanup';\n $SIG{'SIGTERM'}='signal_cleanu\
-p';\n $SIG{'SIGCONT'}='signal_cleanup';\n \
- $SIG{'SIGIO'}='signal_cleanup';\n $SIG{'SIG\
-PROF'}='signal_cleanup';\n $SIG{'SIGUSR2'}='s\
-ignal_cleanup';\n\n $SIG{'SIGSYS'}='signal_cl\
-eanup';\n $SIG{'SIGURG'}='signal_cleanup';\n \
- $SIG{'SIGCHLD'}='signal_cleanup';\n $SIG\
-{'SIGXCPU'}='signal_cleanup';\n $SIG{'SIGWINC\
-H'}='signal_cleanup';\n \n $SIG{'INT'}='\
-signal_cleanup';\n $SIG{'TERM'}='signal_clean\
-up';\n $SIG{'KILL'}='signal_cleanup';\n \
-$SIG{'QUIT'}='signal_cleanup';\n \n our \
-$debug_lock=$ENV{\"DEBUG_LOCK\"};\n \n \\
-n \n \n foreach my $a (@ARGV){$CL.=\
-\" $a\";}\n if ( $debug_lock ){print STDERR \\
-"\\n\\n\\n********** START PG: $PROGRAM **********\
-***\\n\";}\n if ( $debug_lock ){print STDERR \
-\"\\n\\n\\n**********(tcg) LOCKDIR: $LOCKDIR $$ **\
-***********\\n\";}\n if ( $debug_lock ){print\
- STDERR \"\\n --- $$ -- $CL\\n\";}\n \n \
-\n \n \n }\nsub flush_error\n {\n \
- my $msg=shift;\n return add_error ($EXIT_FAILU\
-RE,$$, $$,getppid(), $msg, $CL);\n }\nsub add_err\
-or \n {\n my $code=shift;\n my $rpid=shift;\
-\n my $pid=shift;\n my $ppid=shift;\n my \
-$type=shift;\n my $com=shift;\n \n $ERROR\
-_DONE=1;\n lock4tc ($rpid, \"LERROR\",\"LSET\",\
-\"$pid -- ERROR: $type\\n\");\n lock4tc ($$, \"\
-LERROR\",\"LSET\", \"$pid -- COM: $com\\n\");\n \
- lock4tc ($$, \"LERROR\",\"LSET\", \"$pid -- STACK\
-: $ppid -> $pid\\n\");\n \n return $code;\n \
-}\nsub add_warning \n {\n my $rpid=shift;\n \
- my $pid =shift;\n my $command=shift;\n my $\
-msg=\"$$ -- WARNING: $command\\n\";\n print STD\
-ERR \"$msg\";\n lock4tc ($$, \"LWARNING\", \"LS\
-ET\", $msg);\n }\n\nsub signal_cleanup\n {\n \
-print dtderr \"\\n**** $$ (tcg) was killed\\n\";\n\
- &cleanup;\n exit ($EXIT_FAILURE);\n }\nsub\
- clean_dir\n {\n my $dir=@_[0];\n if ( !-d \
-$dir){return ;}\n elsif (!($dir=~/tmp/)){return\
- ;}#safety check 1\n elsif (($dir=~/\\*/)){retu\
-rn ;}#safety check 2\n else\n {\n `rm -rf \
-$dir`;\n }\n return;\n }\nsub cleanup\n \
-{\n #print stderr \"\\n----tc: $$ Kills $PIDCHI\
-LD\\n\";\n #kill (SIGTERM,$PIDCHILD);\n my $\
-p=getppid();\n $CLEAN_EXIT_STARTED=1;\n \n \
- \n \n if (&lock4tc($$,\"LERROR\", \"LCHECK\
-\", \"\"))\n {\n my $ppid=getppid();\n if (!$\
-ERROR_DONE) \n {\n &lock4tc($$,\"LERROR\", \\
-"LSET\", \"$$ -- STACK: $p -> $$\\n\");\n &loc\
-k4tc($$,\"LERROR\", \"LSET\", \"$$ -- COM: $CL\\n\\
-");\n }\n }\n my $warning=&lock4tc($$, \\
-"LWARNING\", \"LREAD\", \"\");\n my $error=&loc\
-k4tc($$, \"LERROR\", \"LREAD\", \"\");\n #rele\
-ase error and warning lock if root\n \n if (\
-isrootpid() && ($warning || $error) )\n {\n \\
-n print STDERR \"**************** Summary ********\
-*****\\n$error\\n$warning\\n\";\n\n &lock4tc($$,\"\
-LERROR\",\"RELEASE\",\"\");\n &lock4tc($$,\"LWARNI\
-NG\",\"RELEASE\",\"\");\n } \n \n \n \
- foreach my $f (@TMPFILE_LIST)\n {\n if (-e $\
-f){unlink ($f);} \n }\n foreach my $d (@TM\
-PDIR_LIST)\n {\n clean_dir ($d);\n }\n \
- #No More Lock Release\n #&lock4tc($$,\"LLOCK\\
-",\"LRELEASE\",\"\"); #release lock \n\n if ( $\
-debug_lock ){print STDERR \"\\n\\n\\n********** EN\
-D PG: $PROGRAM ($$) *************\\n\";}\n if (\
- $debug_lock ){print STDERR \"\\n\\n\\n**********(\
-tcg) LOCKDIR: $LOCKDIR $$ *************\\n\";}\n \
-}\nEND \n {\n \n &cleanup();\n }\n \n\ns\
-ub safe_system \n{\n my $com=shift;\n my $ntry=s\
-hift;\n my $ctry=shift;\n my $pid;\n my $status\
-;\n my $ppid=getppid();\n if ($com eq \"\"){retu\
-rn 1;}\n \n \n\n if (($pid = fork ()) < 0){retu\
-rn (-1);}\n if ($pid == 0)\n {\n set_lock\
-($$, \" -SHELL- $com (tcg)\");\n exec ($com);\
-\n }\n else\n {\n lock4tc ($$, \"LLOCK\
-\", \"LSET\", \"$pid\\n\");#update parent\n $\
-PIDCHILD=$pid;\n }\n if ($debug_lock){printf S\
-TDERR \"\\n\\t .... safe_system (fasta_seq2hmm) p\
-: $$ c: $pid COM: $com\\n\";}\n\n waitpid ($pid,W\
-TERMSIG);\n\n shift_lock ($pid,$$, \"LWARNING\",\\
-"LWARNING\", \"LSET\");\n\n if ($? == $EXIT_FAILU\
-RE || lock4tc($pid, \"LERROR\", \"LCHECK\", \"\"))\
-\n {\n if ($ntry && $ctry <$ntry)\n {\n \
-add_warning ($$,$$,\"$com failed [retry: $ctry]\")\
-;\n lock4tc ($pid, \"LRELEASE\", \"LERROR\", \"\\
-");\n return safe_system ($com, $ntry, ++$ctry);\
-\n }\n elsif ($ntry == -1)\n {\n if (!shift\
-_lock ($pid, $$, \"LERROR\", \"LWARNING\", \"LSET\\
-"))\n {\n add_warning ($$,$$,\"$com fail\
-ed\");\n }\n else\n {\n lock4tc ($\
-pid, \"LRELEASE\", \"LERROR\", \"\");\n }\n \
-return $?;}\n else\n {\n if (!shift_lock ($\
-pid,$$, \"LERROR\",\"LERROR\", \"LSET\"))\n {\\
-n myexit(add_error ($EXIT_FAILURE,$$,$pid,ge\
-tppid(), \"UNSPECIFIED system\", $com));\n }\n\
- }\n }\n return $?;\n}\n\nsub check_configurat\
-ion \n {\n my @l=@_;\n my $v;\n \
-foreach my $p (@l)\n {\n \n if ( $p eq \"EMA\
-IL\")\n { \n if ( !($EMAIL=~/@/))\n {\n\
- add_warning($$,$$,\"Could Not Use EMAIL\");\n m\
-yexit(add_error ($EXIT_FAILURE,$$,$$,getppid(),\"E\
-MAIL\",\"$CL\"));\n }\n }\n elsif( $p \
-eq \"INTERNET\")\n {\n if ( !&check_inte\
-rnet_connection())\n {\n myexit(add_error ($EX\
-IT_FAILURE,$$,$$,getppid(),\"INTERNET\",\"$CL\"));\
-\n }\n }\n elsif( $p eq \"wget\")\n {\n\
- if (!&pg_is_installed (\"wget\") && !&pg_is\
-_installed (\"curl\"))\n {\n myexit(add_error \
-($EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTALLED:\
-wget\",\"$CL\"));\n }\n }\n elsif( !(&pg_is\
-_installed ($p)))\n {\n myexit(add_error\
- ($EXIT_FAILURE,$$,$$,getppid(),\"PG_NOT_INSTALLED\
-:$p\",\"$CL\"));\n }\n }\n return 1;\n \
- }\nsub pg_is_installed\n {\n my @ml=@_;\n \
-my $r, $p, $m;\n my $supported=0;\n \n my\
- $p=shift (@ml);\n if ($p=~/::/)\n {\n if \
-(safe_system (\"perl -M$p -e 1\")==$EXIT_SUCCESS){\
-return 1;}\n else {return 0;}\n }\n else\n\
- {\n $r=`which $p 2>/dev/null`;\n if ($r eq \\
-"\"){return 0;}\n else {return 1;}\n }\n }\n\
-\n\n\nsub check_internet_connection\n {\n my $\
-internet;\n my $tmp;\n &check_configuration \
-( \"wget\"); \n \n $tmp=&vtmpnam ();\n \n\
- if (&pg_is_installed (\"wget\")){`wget \
-www.google.com -O$tmp >/dev/null 2>/dev/null`;}\n \
- elsif (&pg_is_installed (\"curl\")){`curl w\
-ww.google.com -o$tmp >/dev/null 2>/dev/null`;}\n \
- \n if ( !-e $tmp || -s $tmp < 10){$internet=0\
-;}\n else {$internet=1;}\n if (-e $tmp){unli\
-nk $tmp;}\n\n return $internet;\n }\nsub check\
-_pg_is_installed\n {\n my @ml=@_;\n my $r=&\
-pg_is_installed (@ml);\n if (!$r && $p=~/::/)\n\
- {\n print STDERR \"\\nYou Must Install the p\
-erl package $p on your system.\\nRUN:\\n\\tsudo pe\
-rl -MCPAN -e 'install $pg'\\n\";\n }\n els\
-if (!$r)\n {\n myexit(flush_error(\"\\nProgra\
-m $p Supported but Not Installed on your system\")\
-);\n }\n else\n {\n return 1;\n \
-}\n }\n\n\n\n","\n\n\n\n\nmy $FMODEL =\"\"; \nmy \
-$TMPDIR = \"/tmp\";\n\n\n\n\nmy $NUCALPH = \"ACGTU\
-NRYMKSWHBVD\";\nmy $PRIMNUCALPH = \"ACGTUN\";\nuse\
- vars qw($NUCALPH $PRIMNUCALPH $TMPDIR);\n\n\nmy $\
-errmsg;\nuse vars qw($errmsg);\n\n\n\nuse Getopt::\
-Long;\nuse Cwd;\nuse File::Basename;\nuse File::Te\
-mp qw/ tempfile tempdir /;\nuse File::Copy;\nuse F\
-ile::Path;\n\n\n\nsub usage(;$)\n{\n my ($errms\
-g) = @_;\n my $myname = basename($0);\n\n if\
- ($errmsg) {\n print STDERR \"ERROR: $errms\
-g\\n\";\n }\n\n print STDERR << \"EOF\";\n \
- \n$myname: align two sequences by means of consa\
-n\\'s sfold\nUsage:\n $myname -i file -o file -d p\
-ath\nOptions:\n -i|--in : pairwise input sequence \
-file\n -o|--out: output alignment\n -d|--directory\
- containing data\n\nEOF\n}\n\nsub read_stk_aln \n \
- {\n my $f=$_[0];\n my ($seq, $id);\n \n \
- my %hseq;\n\n open (STK, \"$f\");\n while\
- (<STK>)\n {\n if ( /^#/ || /^\\/\\// || /^\\\
-s*$/){;}\n else\n {\n ($id,$seq)=/(\\S+)\\s+\
-(\\S+)/;\n $hseq{$id}{'seq'}.=$seq;\n }\n \
- }\n close (STK);\n return %hseq;\n }\nsu\
-b read_fasta_seq \n {\n my $f=$_[0];\n my %\
-hseq;\n my (@seq, @com, @name);\n my ($a, $s\
-,$nseq);\n\n open (F, $f);\n while (<F>)\n \
- {\n $s.=$_;\n }\n close (F);\n\n \n\
- @name=($s=~/>(.*).*\\n[^>]*/g);\n \n @se\
-q =($s=~/>.*.*\\n([^>]*)/g);\n @com =($s=~/>.*(\
-.*)\\n([^>]*)/g);\n\n \n $nseq=$#name+1;\n \
- \n for ($a=0; $a<$nseq; $a++)\n {\n my $\
-n=$name[$a];\n $hseq{$n}{name}=$n;\n $hseq{$n}{seq\
-}=$seq[$a];\n $hseq{$n}{com}=$com[$a];\n }\n \
- return %hseq;\n }\n\n\n\nsub sfold_parseoutput\
-($$)\n{\n my ($frawout, $foutfa) = @_;\n my \
-%haln;\n my ($fstk, $cmd, $id);\n open FOUTF\
-A, \">$foutfa\";\n \n $fstk = $frawout . \".\
-stk\";\n \n # first line of raw out contains\
- info\n # remaining stuff is stockholm formatte\
-d\n $cmd = \"sed -e '1d' $frawout\";\n syste\
-m(\"$cmd > $fstk\");\n if ($? != 0) {\n \
-$errmsg = \"command failed with exit status $?.\";\
-\n $errmsg .= \"Command was \\\"$cmd\\\"\"\
-;\n return -1;\n }\n\n # this gives a\
-n error message. just ignore it...\n %haln=read\
-_stk_aln ( $fstk);\n foreach $i (keys (%haln))\\
-n {\n my $s;\n $s=$haln{$i}{'seq'};\n $s =~ s\
-/\\./-/g;\n print FOUTFA \">$i\\n$s\\n\";\n }\
-\n close FOUTFA;\n return 0;\n}\n\n\n\n\nsub\
- sfold_wrapper($$$$)\n{\n \n my ($fs1, $fs2,\
- $fmodel, $foutfa) = @_;\n \n\n my ($cmd, $f\
-rawout, $ferrlog, $freadme, $ftimelog, $fstk);\n\n\
- # add basename($fmsqin) (unknown here!)\n \
-$frawout = \"sfold.log\";\n $ferrlog = \"sfold.\
-err\";\n $ftimelog = \"sfold.time\";\n $frea\
-dme = \"sfold.README\";\n $fstk = \"sfold.stk\\
-";\n \n # prepare execution...\n #\n #\
- ./tmp is essential for dswpalign\n # otherwise\
- you'll get a segfault\n mkdir \"./tmp\";\n \
-\n $cmd = \"sfold -m $fmodel $fs1 $fs2\";\n \
-open(FREADME,\">$freadme\");\n print FREADME \"\
-$cmd\\n\"; \n close(FREADME);\n\n # and go\n\
- #\n system(\"/usr/bin/time -p -o $ftimelog \
-$cmd >$frawout 2>$ferrlog\");\n if ($? != 0) {\\
-n $errmsg = \"command failed with exit stat\
-us $?\";\n $errmsg .= \"command was \\\"$cm\
-d\\\". See \" . getcwd . \"\\n\";\n return \
--1;\n }\n\n return sfold_parseoutput($frawou\
-t, $foutfa);\n}\n\n\n\n\n\n\n\nmy ($help, $fmsqin,\
- $fmsaout);\nGetOptions(\"help\" => \\$help,\n \
- \"in=s\" => \\$fmsqin,\n \"out=s\
-\" => \\$fmsaout,\n \"data=s\" => \\$ref_dir);\\
-n\n\n\nif ($help) {\n usage();\n exit(0);\n}\
-\nif (! defined($fmsqin)) {\n usage('missing in\
-put filename');\n exit(1);\n}\nif (! defined($f\
-msaout)) {\n usage('missing output filename');\\
-n exit(1);\n\n}\nif (scalar(@ARGV)) {\n usag\
-e('Unknown remaining args');\n exit(1);\n}\n\n$\
-FMODEL = \"$ref_dir/mix80.mod\";\nif (! -e \"$FMOD\
-EL\") {\n die(\"couldn't find sfold grammar mod\
-el file. Expected $FMODEL\\n\");\n}\n\n\nmy %hseq=\
-read_fasta_seq ($fmsqin);\nmy $id;\n\nforeach $id \
-(keys(%hseq))\n {\n push(@seq_array, $hseq{$id\
-});\n }\n\nif ( scalar(@seq_array) != 2 ) {\n \
-die(\"Need *exactly* two sequences as input (pairw\
-ise alignment!).\")\n}\n\n\n\nmy ($sec, $min, $hou\
-r, $mday, $mon, $year, $wday, $yday, $isdst) = loc\
-altime(time);\nmy $datei = sprintf(\"%4d-%02d-%02d\
-\", $year+1900, $mon+1, $mday);\nmy $templ = basen\
-ame($0) . \".\" . $datei . \".pid-\" . $$ . \".XXX\
-XXX\";\nmy $wd = tempdir ( $templ, DIR => $TMPDIR)\
-;\n\ncopy($fmsqin, \"$wd/\" . basename($fmsqin) . \
-\".org\"); # for reproduction\ncopy($FMODEL, \"$wd\
-\");\nmy $fmodel = basename($FMODEL);\nmy $orgwd =\
- getcwd;\nchdir $wd;\n\n\n\nmy @sepseqfiles;\nfore\
-ach $id (keys(%hseq)) {\n my ($seq, $orgseq, $f\
-name, $sout);\n $seq=$hseq{$id}{'seq'};\n \n\
- $fname = basename($fmsqin) . \"_$id.fa\";\n \
- # replace funnies in file/id name (e.g. \"/\" \" \
-\" etc)\n $fname =~ s,[/ ],_,g;\n open (PF, \
-\">$fname\");\n print (PF \">$id\\n$seq\\n\");\\
-n close (PF);\n\n push(@sepseqfiles, $fname)\
-;\n}\n\nmy ($f1, $f2, $fout);\n$f1 = $sepseqfiles[\
-0];\n$f2 = $sepseqfiles[1];\n$fout = $wd . basenam\
-e($fmsqin) . \".out.fa\";\nif (sfold_wrapper($f1, \
-$f2, $fmodel, \"$fout\") != 0) {\n printf STDER\
-R \"ERROR: See logs in $wd\\n\";\n exit(1);\n} \
-else {\n chdir $orgwd;\n copy($fout, $fmsaou\
-t);\n rmtree($wd);\n exit(0);\n}\n","\nuse En\
-v qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER);\\
-n\n\n$tmp=clean_cr ($ARGV[0]);\nopen (F, $tmp);\n\\
-nwhile ( <F>)\n {\n my $l=$_;\n if ( $l=~/^\
-# STOCKHOLM/){$stockholm=1;}\n elsif ( $stockho\
-lm && $l=~/^#/)\n {\n $l=~/^#(\\S+)\\s+(\\S+)\
-\\s+(\\S*)/g;\n $l=\"_stockholmhasch_$1\\_stockhol\
-mspace_$2 $3\\n\";\n }\n $file.=$l;\n }\n\
-close (F);\nunlink($tmp);\n$file1=$file;\n\n$file=\
-~s/\\#/_hash_symbol_/g;\n$file=~s/\\@/_arobase_sym\
-bol_/g;\n\n\n$file=~s/\\n[\\.:*\\s]+\\n/\\n\\n/g;\\
-n\n$file=~s/\\n[ \\t\\r\\f]+(\\b)/\\n\\1/g;\n\n\n$\
-file=~s/(\\n\\S+)(\\s+)(\\S)/\\1_blank_\\3/g;\n\n$\
-file=~s/[ ]//g;\n$file=~s/_blank_/ /g;\n\n\n\n$fil\
-e =~s/\\n\\s*\\n/#/g;\n\n$file.=\"#\";\n$file =~s/\
-\\n/@/g;\n\n\n\n\n@blocks=split /\\#/, $file;\nshi\
-ft (@blocks);\n@s=split /\\@/, $blocks[0];\n$nseq=\
-$#s+1;\n\n\n\n$file=join '@', @blocks;\n@lines=spl\
-it /\\@/,$file;\n\n$c=0;\n\nforeach $l (@lines)\n \
- {\n if (!($l=~/\\S/)){next;}\n elsif ($stoc\
-kholm && ($l=~/^\\/\\// || $l=~/STOCKHOLM/)){next;\
-}#get read of STOCHOLM Terminator\n \n $l=~/(\
-\\S+)\\s+(\\S*)/g;\n $n=$1; $s=$2;\n \n $\
-seq[$c].=$s;\n $name[$c]=$n;\n $c++;\n \n\
- if ( $c==$nseq){$c=0;}\n \n } \n\nif ( $c!\
-=0)\n {\n print STDERR \"ERROR: $ARGV[0] is N\
-OT an MSA in Clustalw format: make sure there is n\
-o blank line within a block [ERROR]\\n\";\n exit (\
-EXIT_FAILURE);\n }\n\nfor ($a=0; $a< $nseq; $\
-a++)\n {\n $name[$a]=cleanstring ($name[$a]);\\
-n $seq[$a]=cleanstring ($seq[$a]);\n $seq[$a\
-]=breakstring($seq[$a], 60);\n \n $line=\">$\
-name[$a]\\n$seq[$a]\\n\";\n \n print \"$line\
-\";\n }\nexit (EXIT_SUCCESS);\n\nsub cleanstring\\
-n {\n my $s=@_[0];\n $s=~s/_hash_symbol_/\\\
-#/g;\n $s=~s/_arobase_symbol_/\\@/g;\n $s=~s\
-/[ \\t]//g;\n return $s;\n }\nsub breakstring\\
-n {\n my $s=@_[0];\n my $size=@_[1];\n m\
-y @list;\n my $n,$ns, $symbol;\n \n @list\
-=split //,$s;\n $n=0;$ns=\"\";\n foreach $sy\
-mbol (@list)\n {\n if ( $n==$size)\n {\n \
- $ns.=\"\\n\";\n $n=0;\n }\n $ns.=$symbol;\\
-n $n++;\n }\n return $ns;\n }\n\nsub cl\
-ean_cr\n {\n my $f=@_[0];\n my $file;\n \
-\n $tmp=\"f$.$$\";\n \n \n open (IN, $\
-f);\n open (OUT, \">$tmp\");\n \n while (\
- <IN>)\n {\n $file=$_;\n $file=~s/\\r\\n/\\n/\
-g;\n $file=~s/\\n\\r/\\n/g;\n $file=~s/\\r\\r/\\n/\
-g;\n $file=~s/\\r/\\n/g;\n print OUT \"$file\";\n \
- }\n \n close (IN);\n close (OUT);\n \
- return $tmp;\n }\n","use Env qw(HOST);\nuse En\
-v qw(HOME);\nuse Env qw(USER);\n\n\n$query_start=-\
-1;\n$query_end=-1;\n\nwhile (<>)\n {\n if ( /\\
-\/\\//){$in_aln=1;}\n elsif ( $in_aln && /(\\S+\
-)\\s+(.*)/)\n {\n\n\n $name=$1;\n \n\n $seq=$\
-2;\n $seq=~s/\\s//g;\n $seq=~s/\\~/\\-/g;\n\
- $seq=~s/\\./\\-/g;\n if ( $list{$n}{'name'} && $l\
-ist{$n}{'name'} ne $name)\n {\n print \"$lis\
-t{$n}{'name'} Vs $name\";\n \n exit (EXIT_\
-FAILURE);\n }\n else\n {\n $list{$n}{'name\
-'}= $name;\n }\n\n $list{$n}{'seq'}=$list{$n}{'s\
-eq'}.$seq;\n \n $nseq=++$n;\n \n }\n else\\
-n {$n=0;}\n }\n\n\nfor ($a=0; $a<$nseq; $a++\
-)\n {\n print \">$list{$a}{'name'}\\n$list{$a}\
-{'seq'}\\n\";\n }\n \n","\nuse Env qw(HOST);\
-\nuse Env qw(HOME);\nuse Env qw(USER);\n\n \
- \n\
-use strict; \
- \nuse warnings;\nuse diagnostics;\n\nmy $in_\
-hit_list, my $in_aln=0, my(%name_list)=(),my (%lis\
-t)=(),my $n_seq=0; my $test=0;\nmy($j)=0, my $n=0,\
- my $nom, my $lg_query, my %vu=();\n\nopen (F, \">\
-tmp\");\n\n$/=\"\\n\";\nwhile (<>)\n{\n print F\
- $_;\n if($_ =~ /Query=\\s*(.+?)\\s/i) { $nom=$\
-1;}\n\n if ( /Sequences producing significant a\
-lignments/){$in_hit_list=1;}\n \n if ($_=~ /\
-^pdb\\|/i) { $_=~ s/pdb\\|//g; }\n if ($_=~ /^(\
-1_\\d+)\\s+\\d+/) { $_=~ s/$1/QUERY/;}\n \n \
- if ( /^(\\S+).+?\\s+[\\d.]+\\s+([\\de.-]+)\\s+$/\
- && $in_hit_list) \n {\n my($id)=$1; # \n $id=~\
- s/\\|/_/g; #\n if ($id =~ /.+_$/) { chop($id) }; \
-#\n $name_list{$n_seq++}=$id;\n $name_list{$n_seq-\
-1}=~ s/.*\\|//g; \n }\n \n if (/query/i\
-) {$in_aln=1;}\n if ( /^(\\S+)\\s+(\\d+)\\s+([a\
--zA-Z-]+)\\s+(\\d+)/ || /^(\\S+)(\\s+)(\\-+)(\\s+)\
-/ && ($in_aln == 1))\n {\n my $name=$1;\n my $s\
-tart=$2;\n my $seq=$3;\n my $end=$4;\n \n if ($na\
-me =~ /QUERY/i) { $lg_query=length($seq); }\n\n un\
-less ($test > $n) #m\n {\n my(@seqq)= split(''\
-,$seq);\n my($gap_missing)= scalar(@seqq);\n \
- \n while ($gap_missing != $lg_query) { uns\
-hift (@seqq,\"-\"); $gap_missing= scalar(@seqq); }\
-\n $seq=join('',@seqq); #m\n }\n \n if ($name\
- =~ /QUERY/i)\n {\n $n=0; %vu=(); $j=0;\n \
-$list{$n}{'real_name'}=\"$nom\";\n } \n else\n {\n\
- unless (exists $vu{$name}) { ++$j;} \n $l\
-ist{$n}{'real_name'}=$name_list{$j-1};\n }\n \n $\
-list{$n}{'name'}=$name;\n\n $seq=~tr/a-z/A-Z/;\n $\
-list{$n}{'seq'}=$list{$n}{'seq'};\n $list{$n}{'seq\
-'}.=$seq;\n\n $n++;\n $vu{$name}++;\n $test++;\n \
- } \n \n}\n\nmy @numero=();\n\nfor (my $a=0; $a\
-<$n; $a++) #m\n{\n my $long=length($list{0}{'se\
-q'}); \n my $long1= length($list{$a}{'seq'});\\
-n \n while ($long1 ne $long)\n {\n $list{$a\
-}{'seq'}.=\"-\";\n $long1= length ($list{$a}{'seq'\
-});\n } \n \n push (@numero,\"$list{$a}{'nam\
-e'} $list{$a}{'real_name'}\\n\");\n}\n\nmy %dejavu\
-=();\n\n\nfor (my $i=0; $i<=$#numero; $i++)\n{\n \
- my $s=\">$list{$i}{'real_name'}\\n$list{$i}{'seq\
-'}\\n\";\n my $k=0;\n \n if (exists $deja\
-vu{$numero[$i]}) {next;}\n else\n { \n for (\
-$j=0; $j<$n ; $j++)\n {\n if (\"$numero[$i]\" \
-eq \"$numero[$j]\" && $j != $i )\n {\n ++$k;\\
-n $s .=\">$list{$j}{'real_name'}\\n$list{$j}{'seq\
-'}\\n\";\n }\n } \n }\n \n if ($k>0) \
-\n {\n my $cons;\n open (SOR,\">tempo_aln2cons\\
-"); print SOR $s; close SOR ;\n open (COM,\"t_cof\
-fee -other_pg seq_reformat -in tempo_aln2cons -act\
-ion +aln2cons +upper |\") ; \n while (<COM>)\\
-n { \n if (/^>/) { $cons =\">$list{$i}{'real_n\
-ame'}\\n\"; next;}\n $_=~ s/\\n//g;\n $con\
-s .=$_;\n }\n close COM; unlink (\"tempo_aln2cons\\
-");\n print $cons,\"\\n\"; print F $cons,\"\\n\";\\
-n } \n else { print $s; print F $s; }\n \
- \n $dejavu{$numero[$i]}++;\n} #m\n\nexit;\n\n\\
-n\n\n\n\n\n\n\n\n\n","use Env;\n\n\n$tmp_dir=\"\";\
-\n$init_dir=\"\";\n$program=\"tc_generic_method.pl\
-\";\n\n$blast=@ARGV[0];\n\n$name=\"query\";$seq=\"\
-\";\n%p=blast_xml2profile($name,$seq,100, 0, 0, $b\
-last);\n&output_profile (%p);\n\n\nsub output_prof\
-ile\n {\n my (%profile)=(@_);\n my ($a);\n \
- for ($a=0; $a<$profile{n}; $a++)\n {\n \n \
-print \">$profile{$a}{name} $profile{$a}{comment}\\
-\n$profile{$a}{seq}\\n\";\n }\n return;\n \
- }\nsub file_contains \n {\n my ($file, $tag, \
-$max)=(@_);\n my ($n);\n $n=0;\n \n if\
- ( !-e $file && ($file =~/$tag/)) {return 1;}\n \
- elsif ( !-e $file){return 0;}\n else \n {\
-\n open (FC, \"$file\");\n while ( <FC>)\n {\n \
- if ( ($_=~/$tag/))\n {\n close (FC);\n \
-return 1;\n }\n elsif ($max && $n>$max)\\
-n {\n close (FC);\n return 0;\n }\n \
- $n++;\n }\n }\n close (FC);\n ret\
-urn 0;\n }\n \n \nsub file2string\n {\n \
- my $f=@_[0];\n my $string, $l;\n open (F,\"\
-$f\");\n while (<F>)\n {\n\n $l=$_;\n #cho\
-mp ($l);\n $string.=$l;\n }\n close (F);\n\
- $string=~s/\\r\\n//g;\n $string=~s/\\n//g;\\
-n return $string;\n }\n\n\n\nsub tag2value \n \
- {\n \n my $tag=(@_[0]);\n my $word=(@_[1\
-]);\n my $return;\n \n $tag=~/$word=\"([^\
-\"]+)\"/;\n $return=$1;\n return $return;\n \
- }\n \nsub hit_tag2pdbid\n {\n my $tag=(@\
-_[0]);\n my $pdbid;\n \n $tag=~/id=\"(\
-\\S+)\"/;\n $pdbid=$1;\n $pdbid=~s/_//;\n \
- return $pdbid;\n }\nsub id2pdbid \n {\n my $\
-id=@_[0];\n \n if ($id =~/pdb/)\n {\n $id\
-=~/pdb(.*)/;\n $id=$1;\n }\n $id=~s/[|¦_]/\
-/g;\n return $id;\n }\nsub set_blast_type \n \
-{\n my $file =@_[0];\n if (&file_contains ($\
-file,\"EBIApplicationResult\",100)){$BLAST_TYPE=\"\
-EBI\";}\n elsif (&file_contains ($file,\"NCBI_B\
-lastOutput\",100)) {$BLAST_TYPE=\"NCBI\";}\n el\
-se\n {\n $BLAST_TYPE=\"\";\n }\n retu\
-rn $BLAST_TYPE;\n }\nsub blast_xml2profile \n {\\
-n my ($name,$seq,$maxid, $minid, $mincov, $file\
-)=(@_);\n my (%p, $a, $string, $n);\n \n\n\n\
- if ($BLAST_TYPE eq \"EBI\" || &file_contains (\
-$file,\"EBIApplicationResult\",100)){%p=ebi_blast_\
-xml2profile(@_);}\n elsif ($BLAST_TYPE eq \"NCB\
-I\" || &file_contains ($file,\"NCBI_BlastOutput\",\
-100)){%p=ncbi_blast_xml2profile(@_);}\n else \n\
- {\n print \"************ ERROR: Blast Return\
-ed an unknown XML Format **********************\";\
-\n die;\n }\n for ($a=0; $a<$p{n}; $a++)\n\
- {\n my $name=$p{$a}{name};\n $p{$name}{seq}=\
-$p{$a}{seq};\n }\n return %p;\n }\nsub nc\
-bi_blast_xml2profile \n {\n my ($name,$seq,$ma\
-xid, $minid, $mincov, $string)=(@_);\n my ($L,$\
-l, $a,$b,$c,$d,$nhits,@identifyerL);\n \n \n\
- $seq=~s/[^a-zA-Z]//g;\n $L=length ($seq);\n\
- \n %hit=&xml2tag_list ($string, \"Hit\");\n\
- \n \n for ($nhits=0,$a=0; $a<$hit{n}; $a\
-++)\n {\n my ($ldb,$id, $identity, $expectati\
-on, $start, $end, $coverage, $r);\n my (%ID,%DE,%H\
-SP);\n \n $ldb=\"\";\n\n %ID=&xml2tag_list ($hit{$\
-a}{body}, \"Hit_id\");\n $identifyer=$ID{0}{body};\
-\n \n %DE=&xml2tag_list ($hit{$a}{body}, \"Hit_def\
-\");\n $definition=$DE{0}{body};\n \n %HSP=&xml2ta\
-g_list ($hit{$a}{body}, \"Hsp\");\n for ($b=0; $b<\
-$HSP{n}; $b++)\n {\n my (%START,%END,%E,%I,%\
-Q,%M);\n\n \n %START=&xml2tag_list ($HSP{$b}{\
-body}, \"Hsp_query-from\");\n %HSTART=&xml2tag\
-_list ($HSP{$b}{body}, \"Hsp_hit-from\");\n \n\
- %LEN= &xml2tag_list ($HSP{$b}{body}, \"Hsp_a\
-lign-len\");\n %END= &xml2tag_list ($HSP{$b}{\
-body}, \"Hsp_query-to\");\n %HEND= &xml2tag_l\
-ist ($HSP{$b}{body}, \"Hsp_hit-to\");\n %E=&xm\
-l2tag_list ($HSP{$b}{body}, \"Hsp_evalue\");\n\
- %I=&xml2tag_list ($HSP{$b}{body}, \"Hsp_i\
-dentity\");\n %Q=&xml2tag_list ($HSP{$b}{b\
-ody}, \"Hsp_qseq\");\n %M=&xml2tag_list ($\
-HSP{$b}{body}, \"Hsp_hseq\");\n \n for ($e\
-=0; $e<$Q{n}; $e++)\n\n {\n $qs=$Q{$e}{body\
-};\n $ms=$M{$e}{body};\n if ($seq eq\"\"){$seq=$\
-qs;$L=length($seq);}\n \n $expectation=$E{$e}{bo\
-dy};\n $identity=($LEN{$e}{body}==0)?0:$I{$e}{bod\
-y}/$LEN{$e}{body}*100;\n $start=$START{$e}{body};\
-\n $end=$END{$e}{body};\n $Hstart=$HSTART{$e}{bo\
-dy};\n $Hend=$HEND{$e}{body};\n \n $coverage=(($\
-end-$start)*100)/$L;\n\n \n if ($identity>$maxid \
-|| $identity<$minid || $coverage<$mincov){next;}\n\
- @lr1=(split (//,$qs));\n @lr2=(split (//,$ms));\
-\n $l=$#lr1+1;\n for ($c=0;$c<$L;$c++){$p[$nhits\
-][$c]=\"-\";}\n for ($d=0,$c=0; $c<$l; $c++)\n \
- {\n $r=$lr1[$c];\n if ( $r=~/[A-Za-z]/)\
-\n {\n \n $p[$nhits][$d + $start-1]=$lr\
-2[$c];\n $d++;\n }\n }\n $Qseq[$nhits\
-]=$qs;\n $Hseq[$nhits]=$ms;\n $QstartL[$nhits]=$\
-start;\n $HstartL[$nhits]=$Hstart;\n $identityL[\
-$nhits]=$identity;\n $endL[$nhits]=$end;\n $defi\
-nitionL[$nhits]=$definition;\n $identifyerL[$nhit\
-s]=$identifyer;\n $comment[$nhits]=\"$ldb|$identi\
-fyer [Eval=$expectation][id=$identity%][start=$Hst\
-art end=$Hend]\";\n $nhits++;\n }\n }\n \
- }\n \n $profile{n}=0;\n $profile{$pro\
-file{n}}{name}=$name;\n $profile{$profile{n}}{s\
-eq}=$seq;\n $profile {n}++;\n \n for ($a=\
-0; $a<$nhits; $a++)\n {\n $n=$a+1;\n \n $prof\
-ile{$n}{name}=\"$name\\_$a\";\n $profile{$n}{seq}=\
-\"\";\n $profile{$n}{Qseq}=$Qseq[$a];\n $profile{$\
-n}{Hseq}=$Hseq[$a];\n $profile{$n}{Qstart}=$Qstart\
-L[$a];\n $profile{$n}{Hstart}=$HstartL[$a];\n $pro\
-file{$n}{identity}=$identityL[$a];\n $profile{$n}{\
-definition}=$definitionL[$a];\n $profile{$n}{ident\
-ifyer}=$identifyerL[$a];\n $profile{$n}{comment}=$\
-comment[$a];\n for ($b=0; $b<$L; $b++)\n {\n \
- if ($p[$a][$b])\n {\n $profile{$n}{seq}.=$\
-p[$a][$b];\n }\n else\n {\n $prof\
-ile{$n}{seq}.=\"-\";\n }\n }\n }\n \
- \n $profile{n}=$nhits+1;\n return %profile;\
-\n }\nsub ebi_blast_xml2profile \n {\n my ($n\
-ame,$seq,$maxid, $minid, $mincov, $string)=(@_);\n\
- my ($L,$l, $a,$b,$c,$d,$nhits,@identifyerL,$id\
-entifyer);\n \n\n \n $seq=~s/[^a-zA-Z]//g\
-;\n $L=length ($seq);\n %hit=&xml2tag_list (\
-$string, \"hit\");\n \n for ($nhits=0,$a=0; \
+\\n([^>]*)/g);\n @com =($s=~/>.*(.*)\\n([^>]*)/\
+g);\n\n\n $nseq=$#name+1;\n \n \n for ($\
+a=0; $a<$nseq; $a++)\n {\n my $n=$name[$a];\n\
+ my $s;\n $hseq{$n}{name}=$n;\n $s=$seq[$a];$s=~s/\
+\\s//g;\n $hseq{$n}{index}=++$index;\n $hseq{$n}{s\
+eq}=$s;\n $hseq{$n}{com}=$com[$a];\n }\n r\
+eturn %hseq;\n }\n\n\nsub file2head\n {\n my\
+ $file = shift;\n my $size = shift;\n my $f= new F\
+ileHandle;\n my $line;\n open ($f,$file);\n read (\
+$f,$line, $size);\n close ($f);\n return $line;\n \
+ }\nsub file2tail\n {\n my $file = shift;\
+\n my $size = shift;\n my $f= new FileHandle;\n my\
+ $line;\n \n open ($f,$file);\n seek ($f,$size*-1,\
+ 2);\n read ($f,$line, $size);\n close ($f);\n ret\
+urn $line;\n }\n\n\nsub vtmpnam\n {\n my\
+ $r=rand(100000);\n my $f=\"file.$r.$$\";\n while \
+(-e $f)\n {\n $f=vtmpnam();\n }\n push (@T\
+MPFILE_LIST, $f);\n return $f;\n }\n\nsub mye\
+xit\n {\n my $code=@_[0];\n if ($CLEAN_EXIT\
+_STARTED==1){return;}\n else {$CLEAN_EXIT_START\
+ED=1;}\n ### ONLY BARE EXIT\n exit ($code);\\
+n }\nsub set_error_lock\n {\n my $name = \
+shift;\n my $pid=$$;\n\n \n &lock4t\
+c ($$,\"LERROR\", \"LSET\", \"$$ -- ERROR: $name $\
+PROGRAM\\n\");\n return;\n }\nsub set_lock\
+\n {\n my $pid=shift;\n my $msg= shift;\n \
+ my $p=getppid();\n &lock4tc ($pid,\"LLOCK\",\\
+"LRESET\",\"$p$msg\\n\");\n }\nsub unset_lock\n \
+ {\n \n my $pid=shift;\n &lock4tc ($pid,\
+\"LLOCK\",\"LRELEASE\",\"\");\n }\nsub shift_lock\
+\n {\n my $from=shift;\n my $to=shift;\n \
+ my $from_type=shift;\n my $to_type=shift;\n \
+ my $action=shift;\n my $msg;\n \n if (!&\
+lock4tc($from, $from_type, \"LCHECK\", \"\")){retu\
+rn 0;}\n $msg=&lock4tc ($from, $from_type, \"LR\
+EAD\", \"\");\n &lock4tc ($from, $from_type,\"L\
+RELEASE\", $msg);\n &lock4tc ($to, $to_type, $a\
+ction, $msg);\n return;\n }\nsub isshellpid\n \
+ {\n my $p=shift;\n if (!lock4tc ($p, \"LLOC\
+K\", \"LCHECK\")){return 0;}\n else\n {\n \
+my $c=lock4tc($p, \"LLOCK\", \"LREAD\");\n if ( $c\
+=~/-SHELL-/){return 1;}\n }\n return 0;\n \
+ }\nsub isrootpid\n {\n if(lock4tc (getppid(),\
+ \"LLOCK\", \"LCHECK\")){return 0;}\n else {ret\
+urn 1;}\n }\nsub lock4tc\n {\n my ($pid,$type,$\
+action,$value)=@_;\n my $fname;\n my $host=hos\
+tname;\n \n if ($type eq \"LLOCK\"){$fname=\"$\
+LOCKDIR/.$pid.$host.lock4tcoffee\";}\n elsif ( $\
+type eq \"LERROR\"){ $fname=\"$LOCKDIR/.$pid.$host\
+.error4tcoffee\";}\n elsif ( $type eq \"LWARNING\
+\"){ $fname=\"$LOCKDIR/.$pid.$host.warning4tcoffee\
+\";}\n \n if ($debug_lock)\n {\n pri\
+nt STDERR \"\\n\\t---lock4tc(tcg): $action => $fna\
+me =>$value (RD: $LOCKDIR)\\n\";\n }\n\n if \
+ ($action eq \"LCHECK\") {return -e $fname;}\n \
+ elsif ($action eq \"LREAD\"){return file2string($\
+fname);}\n elsif ($action eq \"LSET\") {return s\
+tring2file ($value, $fname, \">>\");}\n elsif ($\
+action eq \"LRESET\") {return string2file ($value,\
+ $fname, \">\");}\n elsif ($action eq \"LRELEASE\
+\") \n {\n if ( $debug_lock)\n {\n m\
+y $g=new FileHandle;\n open ($g, \">>$fname\");\
+\n print $g \"\\nDestroyed by $$\\n\";\n clo\
+se ($g);\n safe_system (\"mv $fname $fname.old\\
+");\n }\n else\n {\n unlink ($fname);\n\
+ }\n }\n return \"\";\n }\n \nsub file2stri\
+ng\n {\n my $file=@_[0];\n my $f=new FileHandl\
+e;\n my $r;\n open ($f, \"$file\");\n while \
+(<$f>){$r.=$_;}\n close ($f);\n return $r;\n }\
+\nsub string2file \n {\n my ($s,$file,$mode)\
+=@_;\n my $f=new FileHandle;\n \n open ($\
+f, \"$mode$file\");\n print $f \"$s\";\n cl\
+ose ($f);\n }\n\nBEGIN\n {\n srand;\n \
+\n $SIG{'SIGUP'}='signal_cleanup';\n $SI\
+G{'SIGINT'}='signal_cleanup';\n $SIG{'SIGQUIT\
+'}='signal_cleanup';\n $SIG{'SIGILL'}='signal\
+_cleanup';\n $SIG{'SIGTRAP'}='signal_cleanup'\
+;\n $SIG{'SIGABRT'}='signal_cleanup';\n \
+$SIG{'SIGEMT'}='signal_cleanup';\n $SIG{'SIGF\
+PE'}='signal_cleanup';\n \n $SIG{'SIGKIL\
+L'}='signal_cleanup';\n $SIG{'SIGPIPE'}='sign\
+al_cleanup';\n $SIG{'SIGSTOP'}='signal_cleanu\
+p';\n $SIG{'SIGTTIN'}='signal_cleanup';\n \
+ $SIG{'SIGXFSZ'}='signal_cleanup';\n $SIG{'S\
+IGINFO'}='signal_cleanup';\n \n $SIG{'SI\
+GBUS'}='signal_cleanup';\n $SIG{'SIGALRM'}='s\
+ignal_cleanup';\n $SIG{'SIGTSTP'}='signal_cle\
+anup';\n $SIG{'SIGTTOU'}='signal_cleanup';\n \
+ $SIG{'SIGVTALRM'}='signal_cleanup';\n $S\
+IG{'SIGUSR1'}='signal_cleanup';\n\n\n $SIG{'S\
+IGSEGV'}='signal_cleanup';\n $SIG{'SIGTERM'}=\
+'signal_cleanup';\n $SIG{'SIGCONT'}='signal_c\
+leanup';\n $SIG{'SIGIO'}='signal_cleanup';\n \
+ $SIG{'SIGPROF'}='signal_cleanup';\n $SIG\
+{'SIGUSR2'}='signal_cleanup';\n\n $SIG{'SIGSY\
+S'}='signal_cleanup';\n $SIG{'SIGURG'}='signa\
+l_cleanup';\n $SIG{'SIGCHLD'}='signal_cleanup\
+';\n $SIG{'SIGXCPU'}='signal_cleanup';\n \
+ $SIG{'SIGWINCH'}='signal_cleanup';\n \n \
+ $SIG{'INT'}='signal_cleanup';\n $SIG{'TERM'}\
+='signal_cleanup';\n $SIG{'KILL'}='signal_cle\
+anup';\n $SIG{'QUIT'}='signal_cleanup';\n \
+ \n our $debug_lock=$ENV{\"DEBUG_LOCK\"};\n \
+ \n \n \n \n foreach my $a\
+ (@ARGV){$CL.=\" $a\";}\n if ( $debug_lock ){\
+print STDERR \"\\n\\n\\n********** START PG: $PROG\
+RAM *************\\n\";}\n if ( $debug_lock )\
+{print STDERR \"\\n\\n\\n**********(tcg) LOCKDIR: \
+$LOCKDIR $$ *************\\n\";}\n if ( $debu\
+g_lock ){print STDERR \"\\n --- $$ -- $CL\\n\";}\n\
+ \n \n \n \n }\nsub flush_e\
+rror\n {\n my $msg=shift;\n return add_erro\
+r ($EXIT_FAILURE,$$, $$,getppid(), $msg, $CL);\n \
+}\nsub add_error \n {\n my $code=shift;\n m\
+y $rpid=shift;\n my $pid=shift;\n my $ppid=s\
+hift;\n my $type=shift;\n my $com=shift;\n \
+ \n $ERROR_DONE=1;\n lock4tc ($rpid, \"LERR\
+OR\",\"LSET\",\"$pid -- ERROR: $type\\n\");\n l\
+ock4tc ($$, \"LERROR\",\"LSET\", \"$pid -- COM: $c\
+om\\n\");\n lock4tc ($$, \"LERROR\",\"LSET\", \\
+"$pid -- STACK: $ppid -> $pid\\n\");\n \n ret\
+urn $code;\n }\nsub add_warning \n {\n my $rp\
+id=shift;\n my $pid =shift;\n my $command=sh\
+ift;\n my $msg=\"$$ -- WARNING: $command\\n\";\\
+n print STDERR \"$msg\";\n lock4tc ($$, \"LW\
+ARNING\", \"LSET\", $msg);\n }\n\nsub signal_clea\
+nup\n {\n print dtderr \"\\n**** $$ (tcg) was \
+killed\\n\";\n &cleanup;\n exit ($EXIT_FAILU\
+RE);\n }\nsub clean_dir\n {\n my $dir=@_[0];\\
+n if ( !-d $dir){return ;}\n elsif (!($dir=~\
+/tmp/)){return ;}#safety check 1\n elsif (($dir\
+=~/\\*/)){return ;}#safety check 2\n else\n \
+ {\n `rm -rf $dir`;\n }\n return;\n }\ns\
+ub cleanup\n {\n #print stderr \"\\n----tc: $$\
+ Kills $PIDCHILD\\n\";\n #kill (SIGTERM,$PIDCHI\
+LD);\n my $p=getppid();\n $CLEAN_EXIT_STARTE\
+D=1;\n \n \n \n if (&lock4tc($$,\"LERR\
+OR\", \"LCHECK\", \"\"))\n {\n my $ppid=getpp\
+id();\n if (!$ERROR_DONE) \n {\n &lock4tc($$\
+,\"LERROR\", \"LSET\", \"$$ -- STACK: $p -> $$\\n\\
+");\n &lock4tc($$,\"LERROR\", \"LSET\", \"$$ -\
+- COM: $CL\\n\");\n }\n }\n my $warning=\
+&lock4tc($$, \"LWARNING\", \"LREAD\", \"\");\n \
+my $error=&lock4tc($$, \"LERROR\", \"LREAD\", \"\\
+");\n #release error and warning lock if root\n\
+ \n if (isrootpid() && ($warning || $error) \
+)\n {\n \n print STDERR \"**************** Su\
+mmary *************\\n$error\\n$warning\\n\";\n\n \
+&lock4tc($$,\"LERROR\",\"RELEASE\",\"\");\n &lock4\
+tc($$,\"LWARNING\",\"RELEASE\",\"\");\n } \n \
+ \n \n foreach my $f (@TMPFILE_LIST)\n \
+ {\n if (-e $f){unlink ($f);} \n }\n fore\
+ach my $d (@TMPDIR_LIST)\n {\n clean_dir ($d)\
+;\n }\n #No More Lock Release\n #&lock4\
+tc($$,\"LLOCK\",\"LRELEASE\",\"\"); #release lock \
+\n\n if ( $debug_lock ){print STDERR \"\\n\\n\\\
+n********** END PG: $PROGRAM ($$) *************\\n\
+\";}\n if ( $debug_lock ){print STDERR \"\\n\\n\
+\\n**********(tcg) LOCKDIR: $LOCKDIR $$ **********\
+***\\n\";}\n }\nEND \n {\n \n &cleanup();\\
+n }\n \n\nsub safe_system \n{\n my $com=shift;\
+\n my $ntry=shift;\n my $ctry=shift;\n my $pid;\
+\n my $status;\n my $ppid=getppid();\n if ($com\
+ eq \"\"){return 1;}\n \n \n\n if (($pid = fork\
+ ()) < 0){return (-1);}\n if ($pid == 0)\n {\n\
+ set_lock($$, \" -SHELL- $com (tcg)\");\n \
+ exec ($com);\n }\n else\n {\n lock4t\
+c ($$, \"LLOCK\", \"LSET\", \"$pid\\n\");#update p\
+arent\n $PIDCHILD=$pid;\n }\n if ($debug_\
+lock){printf STDERR \"\\n\\t .... safe_system (fas\
+ta_seq2hmm) p: $$ c: $pid COM: $com\\n\";}\n\n w\
+aitpid ($pid,WTERMSIG);\n\n shift_lock ($pid,$$, \
+\"LWARNING\",\"LWARNING\", \"LSET\");\n\n if ($? \
+== $EXIT_FAILURE || lock4tc($pid, \"LERROR\", \"LC\
+HECK\", \"\"))\n {\n if ($ntry && $ctry <$\
+ntry)\n {\n add_warning ($$,$$,\"$com failed [re\
+try: $ctry]\");\n lock4tc ($pid, \"LRELEASE\", \\
+"LERROR\", \"\");\n return safe_system ($com, $n\
+try, ++$ctry);\n }\n elsif ($ntry == -1)\n {\\
+n if (!shift_lock ($pid, $$, \"LERROR\", \"LWARN\
+ING\", \"LSET\"))\n {\n add_warning ($$,\
+$$,\"$com failed\");\n }\n else\n {\n \
+ lock4tc ($pid, \"LRELEASE\", \"LERROR\", \"\")\
+;\n }\n return $?;}\n else\n {\n if (\
+!shift_lock ($pid,$$, \"LERROR\",\"LERROR\", \"LSE\
+T\"))\n {\n myexit(add_error ($EXIT_FAIL\
+URE,$$,$pid,getppid(), \"UNSPECIFIED system\", $co\
+m));\n }\n }\n }\n return $?;\n}\n\nsub ch\
+eck_configuration \n {\n my @l=@_;\n \
+my $v;\n foreach my $p (@l)\n {\n \n if \
+ ( $p eq \"EMAIL\")\n { \n if ( !($EMAIL\
+=~/@/))\n {\n add_warning($$,$$,\"Could Not Use \
+EMAIL\");\n myexit(add_error ($EXIT_FAILURE,$$,$$\
+,getppid(),\"EMAIL\",\"$CL\"));\n }\n }\\
+n elsif( $p eq \"INTERNET\")\n {\n if \
+( !&check_internet_connection())\n {\n myexit(\
+add_error ($EXIT_FAILURE,$$,$$,getppid(),\"INTERNE\
+T\",\"$CL\"));\n }\n }\n elsif( $p eq \"wge\
+t\")\n {\n if (!&pg_is_installed (\"wget\
+\") && !&pg_is_installed (\"curl\"))\n {\n mye\
+xit(add_error ($EXIT_FAILURE,$$,$$,getppid(),\"PG_\
+NOT_INSTALLED:wget\",\"$CL\"));\n }\n }\n e\
+lsif( !(&pg_is_installed ($p)))\n {\n my\
+exit(add_error ($EXIT_FAILURE,$$,$$,getppid(),\"PG\
+_NOT_INSTALLED:$p\",\"$CL\"));\n }\n }\n \
+return 1;\n }\nsub pg_is_installed\n {\n my\
+ @ml=@_;\n my $r, $p, $m;\n my $supported=0;\
+\n \n my $p=shift (@ml);\n if ($p=~/::/)\\
+n {\n if (safe_system (\"perl -M$p -e 1\")==$\
+EXIT_SUCCESS){return 1;}\n else {return 0;}\n \
+ }\n else\n {\n $r=`which $p 2>/dev/null`;\
+\n if ($r eq \"\"){return 0;}\n else {return 1;}\n\
+ }\n }\n\n\n\nsub check_internet_connection\\
+n {\n my $internet;\n my $tmp;\n &check_\
+configuration ( \"wget\"); \n \n $tmp=&vtmpn\
+am ();\n \n if (&pg_is_installed (\"w\
+get\")){`wget www.google.com -O$tmp >/dev/null 2>/\
+dev/null`;}\n elsif (&pg_is_installed (\"cu\
+rl\")){`curl www.google.com -o$tmp >/dev/null 2>/d\
+ev/null`;}\n \n if ( !-e $tmp || -s $tmp < 1\
+0){$internet=0;}\n else {$internet=1;}\n if \
+(-e $tmp){unlink $tmp;}\n\n return $internet;\n\
+ }\nsub check_pg_is_installed\n {\n my @ml=@_\
+;\n my $r=&pg_is_installed (@ml);\n if (!$r \
+&& $p=~/::/)\n {\n print STDERR \"\\nYou Must\
+ Install the perl package $p on your system.\\nRUN\
+:\\n\\tsudo perl -MCPAN -e 'install $pg'\\n\";\n \
+ }\n elsif (!$r)\n {\n myexit(flush_err\
+or(\"\\nProgram $p Supported but Not Installed on \
+your system\"));\n }\n else\n {\n ret\
+urn 1;\n }\n }\n\n\n\n","\n\n\n\n\nmy $FMODE\
+L =\"\"; \nmy $TMPDIR = \"/tmp\";\n\n\n\n\nmy $NUC\
+ALPH = \"ACGTUNRYMKSWHBVD\";\nmy $PRIMNUCALPH = \"\
+ACGTUN\";\nuse vars qw($NUCALPH $PRIMNUCALPH $TMPD\
+IR);\n\n\nmy $errmsg;\nuse vars qw($errmsg);\n\n\n\
+\nuse Getopt::Long;\nuse Cwd;\nuse File::Basename;\
+\nuse File::Temp qw/ tempfile tempdir /;\nuse File\
+::Copy;\nuse File::Path;\n\n\n\nsub usage(;$)\n{\n\
+ my ($errmsg) = @_;\n my $myname = basename(\
+$0);\n\n if ($errmsg) {\n print STDERR \\
+"ERROR: $errmsg\\n\";\n }\n\n print STDERR <\
+< \"EOF\";\n \n$myname: align two sequences by \
+means of consan\\'s sfold\nUsage:\n $myname -i fil\
+e -o file -d path\nOptions:\n -i|--in : pairwise i\
+nput sequence file\n -o|--out: output alignment\n \
+-d|--directory containing data\n\nEOF\n}\n\nsub re\
+ad_stk_aln \n {\n my $f=$_[0];\n my ($seq, \
+$id);\n \n my %hseq;\n\n open (STK, \"$f\\
+");\n while (<STK>)\n {\n if ( /^#/ || /^\\
+\/\\// || /^\\s*$/){;}\n else\n {\n ($id,$se\
+q)=/(\\S+)\\s+(\\S+)/;\n $hseq{$id}{'seq'}.=$s\
+eq;\n }\n }\n close (STK);\n return %\
+hseq;\n }\nsub read_fasta_seq \n {\n my $f=$_\
+[0];\n my %hseq;\n my (@seq, @com, @name);\n\
+ my ($a, $s,$nseq);\n\n open (F, $f);\n w\
+hile (<F>)\n {\n $s.=$_;\n }\n close \
+(F);\n\n \n @name=($s=~/>(.*).*\\n[^>]*/g);\\
+n \n @seq =($s=~/>.*.*\\n([^>]*)/g);\n @c\
+om =($s=~/>.*(.*)\\n([^>]*)/g);\n\n \n $nseq\
+=$#name+1;\n \n for ($a=0; $a<$nseq; $a++)\n\
+ {\n my $n=$name[$a];\n $hseq{$n}{name}=$n;\n\
+ $hseq{$n}{seq}=$seq[$a];\n $hseq{$n}{com}=$com[$a\
+];\n }\n return %hseq;\n }\n\n\n\nsub sfo\
+ld_parseoutput($$)\n{\n my ($frawout, $foutfa) \
+= @_;\n my %haln;\n my ($fstk, $cmd, $id);\n\
+ open FOUTFA, \">$foutfa\";\n \n $fstk = \
+$frawout . \".stk\";\n \n # first line of ra\
+w out contains info\n # remaining stuff is stoc\
+kholm formatted\n $cmd = \"sed -e '1d' $frawout\
+\";\n system(\"$cmd > $fstk\");\n if ($? != \
+0) {\n $errmsg = \"command failed with exit\
+ status $?.\";\n $errmsg .= \"Command was \
+\\\"$cmd\\\"\";\n return -1;\n }\n\n \
+# this gives an error message. just ignore it...\n\
+ %haln=read_stk_aln ( $fstk);\n foreach $i (\
+keys (%haln))\n {\n my $s;\n $s=$haln{$i}{'se\
+q'};\n $s =~ s/\\./-/g;\n print FOUTFA \">$i\\n$s\\
+\n\";\n }\n close FOUTFA;\n return 0;\n\
+}\n\n\n\n\nsub sfold_wrapper($$$$)\n{\n \n m\
+y ($fs1, $fs2, $fmodel, $foutfa) = @_;\n \n\n \
+ my ($cmd, $frawout, $ferrlog, $freadme, $ftimelo\
+g, $fstk);\n\n # add basename($fmsqin) (unknow\
+n here!)\n $frawout = \"sfold.log\";\n $ferr\
+log = \"sfold.err\";\n $ftimelog = \"sfold.time\
+\";\n $freadme = \"sfold.README\";\n $fstk \
+= \"sfold.stk\";\n \n # prepare execution...\
+\n #\n # ./tmp is essential for dswpalign\n \
+ # otherwise you'll get a segfault\n mkdir \"\
+./tmp\";\n \n $cmd = \"sfold -m $fmodel $fs1\
+ $fs2\";\n open(FREADME,\">$freadme\");\n pr\
+int FREADME \"$cmd\\n\"; \n close(FREADME);\n\n\
+ # and go\n #\n system(\"/usr/bin/time -p\
+ -o $ftimelog $cmd >$frawout 2>$ferrlog\");\n i\
+f ($? != 0) {\n $errmsg = \"command failed \
+with exit status $?\";\n $errmsg .= \"comma\
+nd was \\\"$cmd\\\". See \" . getcwd . \"\\n\";\n \
+ return -1;\n }\n\n return sfold_parse\
+output($frawout, $foutfa);\n}\n\n\n\n\n\n\n\nmy ($\
+help, $fmsqin, $fmsaout);\nGetOptions(\"help\" =>\
+ \\$help,\n \"in=s\" => \\$fmsqin,\n \
+ \"out=s\" => \\$fmsaout,\n \"data=s\" =>\
+ \\$ref_dir);\n\n\n\nif ($help) {\n usage();\n \
+ exit(0);\n}\nif (! defined($fmsqin)) {\n usa\
+ge('missing input filename');\n exit(1);\n}\nif\
+ (! defined($fmsaout)) {\n usage('missing outpu\
+t filename');\n exit(1);\n\n}\nif (scalar(@ARGV\
+)) {\n usage('Unknown remaining args');\n ex\
+it(1);\n}\n\n$FMODEL = \"$ref_dir/mix80.mod\";\nif\
+ (! -e \"$FMODEL\") {\n die(\"couldn't find sfo\
+ld grammar model file. Expected $FMODEL\\n\");\n}\\
+n\n\nmy %hseq=read_fasta_seq ($fmsqin);\nmy $id;\n\
+\nforeach $id (keys(%hseq))\n {\n push(@seq_ar\
+ray, $hseq{$id});\n }\n\nif ( scalar(@seq_array) \
+!= 2 ) {\n die(\"Need *exactly* two sequences a\
+s input (pairwise alignment!).\")\n}\n\n\n\nmy ($s\
+ec, $min, $hour, $mday, $mon, $year, $wday, $yday,\
+ $isdst) = localtime(time);\nmy $datei = sprintf(\\
+"%4d-%02d-%02d\", $year+1900, $mon+1, $mday);\nmy \
+$templ = basename($0) . \".\" . $datei . \".pid-\"\
+ . $$ . \".XXXXXX\";\nmy $wd = tempdir ( $templ, D\
+IR => $TMPDIR);\n\ncopy($fmsqin, \"$wd/\" . basena\
+me($fmsqin) . \".org\"); # for reproduction\ncopy(\
+$FMODEL, \"$wd\");\nmy $fmodel = basename($FMODEL)\
+;\nmy $orgwd = getcwd;\nchdir $wd;\n\n\n\nmy @seps\
+eqfiles;\nforeach $id (keys(%hseq)) {\n my ($se\
+q, $orgseq, $fname, $sout);\n $seq=$hseq{$id}{'\
+seq'};\n \n $fname = basename($fmsqin) . \"_\
+$id.fa\";\n # replace funnies in file/id name (\
+e.g. \"/\" \" \" etc)\n $fname =~ s,[/ ],_,g;\n\
+ open (PF, \">$fname\");\n print (PF \">$id\\
+\n$seq\\n\");\n close (PF);\n\n push(@sepseq\
+files, $fname);\n}\n\nmy ($f1, $f2, $fout);\n$f1 =\
+ $sepseqfiles[0];\n$f2 = $sepseqfiles[1];\n$fout =\
+ $wd . basename($fmsqin) . \".out.fa\";\nif (sfold\
+_wrapper($f1, $f2, $fmodel, \"$fout\") != 0) {\n \
+ printf STDERR \"ERROR: See logs in $wd\\n\";\n \
+ exit(1);\n} else {\n chdir $orgwd;\n copy(\
+$fout, $fmsaout);\n rmtree($wd);\n exit(0);\n\
+}\n","\nuse Env qw(HOST);\nuse Env qw(HOME);\nuse \
+Env qw(USER);\n\n\n$tmp=clean_cr ($ARGV[0]);\nopen\
+ (F, $tmp);\n\nwhile ( <F>)\n {\n my $l=$_;\n \
+ if ( $l=~/^# STOCKHOLM/){$stockholm=1;}\n el\
+sif ( $stockholm && $l=~/^#/)\n {\n $l=~/^#(\\
+\S+)\\s+(\\S+)\\s+(\\S*)/g;\n $l=\"_stockholmhasch\
+_$1\\_stockholmspace_$2 $3\\n\";\n }\n $fi\
+le.=$l;\n }\nclose (F);\nunlink($tmp);\n$file1=$f\
+ile;\n\n$file=~s/\\#/_hash_symbol_/g;\n$file=~s/\\\
+@/_arobase_symbol_/g;\n\n\n$file=~s/\\n[\\.:*\\s]+\
+\\n/\\n\\n/g;\n\n$file=~s/\\n[ \\t\\r\\f]+(\\b)/\\\
+n\\1/g;\n\n\n$file=~s/(\\n\\S+)(\\s+)(\\S)/\\1_bla\
+nk_\\3/g;\n\n$file=~s/[ ]//g;\n$file=~s/_blank_/ /\
+g;\n\n\n\n$file =~s/\\n\\s*\\n/#/g;\n\n$file.=\"#\\
+";\n$file =~s/\\n/@/g;\n\n\n\n\n@blocks=split /\\#\
+/, $file;\nshift (@blocks);\n@s=split /\\@/, $bloc\
+ks[0];\n$nseq=$#s+1;\n\n\n\n$file=join '@', @block\
+s;\n@lines=split /\\@/,$file;\n\n$c=0;\n\nforeach \
+$l (@lines)\n {\n if (!($l=~/\\S/)){next;}\n \
+ elsif ($stockholm && ($l=~/^\\/\\// || $l=~/STOC\
+KHOLM/)){next;}#get read of STOCHOLM Terminator\n \
+ \n $l=~/(\\S+)\\s+(\\S*)/g;\n $n=$1; $s=$2\
+;\n \n $seq[$c].=$s;\n $name[$c]=$n;\n \
+ $c++;\n \n if ( $c==$nseq){$c=0;}\n \n \
+} \n\nif ( $c!=0)\n {\n print STDERR \"ERROR:\
+ $ARGV[0] is NOT an MSA in Clustalw format: make s\
+ure there is no blank line within a block [ERROR]\\
+\n\";\n exit (EXIT_FAILURE);\n }\n\nfor ($a=0\
+; $a< $nseq; $a++)\n {\n $name[$a]=cleanstring\
+ ($name[$a]);\n $seq[$a]=cleanstring ($seq[$a])\
+;\n $seq[$a]=breakstring($seq[$a], 60);\n \n\
+ $line=\">$name[$a]\\n$seq[$a]\\n\";\n \n \
+ print \"$line\";\n }\nexit (EXIT_SUCCESS);\n\nsu\
+b cleanstring\n {\n my $s=@_[0];\n $s=~s/_h\
+ash_symbol_/\\#/g;\n $s=~s/_arobase_symbol_/\\@\
+/g;\n $s=~s/[ \\t]//g;\n return $s;\n }\nsu\
+b breakstring\n {\n my $s=@_[0];\n my $size\
+=@_[1];\n my @list;\n my $n,$ns, $symbol;\n \
+ \n @list=split //,$s;\n $n=0;$ns=\"\";\n \
+ foreach $symbol (@list)\n {\n if ( $n==$si\
+ze)\n {\n $ns.=\"\\n\";\n $n=0;\n }\n \
+$ns.=$symbol;\n $n++;\n }\n return $ns;\n \
+ }\n\nsub clean_cr\n {\n my $f=@_[0];\n m\
+y $file;\n \n $tmp=\"f$.$$\";\n \n \n \
+ open (IN, $f);\n open (OUT, \">$tmp\");\n \
+ \n while ( <IN>)\n {\n $file=$_;\n $file=\
+~s/\\r\\n/\\n/g;\n $file=~s/\\n\\r/\\n/g;\n $file=\
+~s/\\r\\r/\\n/g;\n $file=~s/\\r/\\n/g;\n print OUT\
+ \"$file\";\n }\n \n close (IN);\n c\
+lose (OUT);\n return $tmp;\n }\n","use Env qw(\
+HOST);\nuse Env qw(HOME);\nuse Env qw(USER);\n\n\n\
+$query_start=-1;\n$query_end=-1;\n\nwhile (<>)\n \
+{\n if ( /\\/\\//){$in_aln=1;}\n elsif ( $in\
+_aln && /(\\S+)\\s+(.*)/)\n {\n\n\n $name=$1;\
+\n \n\n $seq=$2;\n $seq=~s/\\s//g;\n $seq=~\
+s/\\~/\\-/g;\n $seq=~s/\\./\\-/g;\n if ( $list{$n}\
+{'name'} && $list{$n}{'name'} ne $name)\n {\n \
+ print \"$list{$n}{'name'} Vs $name\";\n \n \
+ exit (EXIT_FAILURE);\n }\n else\n {\n $\
+list{$n}{'name'}= $name;\n }\n\n $list{$n}{'seq'\
+}=$list{$n}{'seq'}.$seq;\n \n $nseq=++$n;\n \n \
+ }\n else\n {$n=0;}\n }\n\n\nfor ($a=0; \
+$a<$nseq; $a++)\n {\n print \">$list{$a}{'name\
+'}\\n$list{$a}{'seq'}\\n\";\n }\n \n","\nuse\
+ Env qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER\
+);\n\n \
+ \nuse strict; \
+ \nuse warnings;\nuse diagnosti\
+cs;\n\nmy $in_hit_list, my $in_aln=0, my(%name_lis\
+t)=(),my (%list)=(),my $n_seq=0; my $test=0;\nmy($\
+j)=0, my $n=0, my $nom, my $lg_query, my %vu=();\n\
+\nopen (F, \">tmp\");\n\n$/=\"\\n\";\nwhile (<>)\n\
+{\n print F $_;\n if($_ =~ /Query=\\s*(.+?)\\
+\s/i) { $nom=$1;}\n\n if ( /Sequences producing\
+ significant alignments/){$in_hit_list=1;}\n \n\
+ if ($_=~ /^pdb\\|/i) { $_=~ s/pdb\\|//g; }\n \
+ if ($_=~ /^(1_\\d+)\\s+\\d+/) { $_=~ s/$1/QUERY/\
+;}\n \n if ( /^(\\S+).+?\\s+[\\d.]+\\s+([\\
+\de.-]+)\\s+$/ && $in_hit_list) \n {\n my($id)=\
+$1; # \n $id=~ s/\\|/_/g; #\n if ($id =~ /.+_$/) {\
+ chop($id) }; #\n $name_list{$n_seq++}=$id;\n $nam\
+e_list{$n_seq-1}=~ s/.*\\|//g; \n }\n \n \
+ if (/query/i) {$in_aln=1;}\n if ( /^(\\S+)\\s\
++(\\d+)\\s+([a-zA-Z-]+)\\s+(\\d+)/ || /^(\\S+)(\\s\
++)(\\-+)(\\s+)/ && ($in_aln == 1))\n {\n my $na\
+me=$1;\n my $start=$2;\n my $seq=$3;\n my $end=$4;\
+\n \n if ($name =~ /QUERY/i) { $lg_query=length($\
+seq); }\n\n unless ($test > $n) #m\n {\n my(@s\
+eqq)= split('',$seq);\n my($gap_missing)= scal\
+ar(@seqq);\n \n while ($gap_missing != $lg\
+_query) { unshift (@seqq,\"-\"); $gap_missing= sc\
+alar(@seqq); }\n $seq=join('',@seqq); #m\n }\\
+n \n if ($name =~ /QUERY/i)\n {\n $n=0; %vu=()\
+; $j=0;\n $list{$n}{'real_name'}=\"$nom\";\n }\
+ \n else\n {\n unless (exists $vu{$name}) { ++\
+$j;} \n $list{$n}{'real_name'}=$name_list{$j-1\
+};\n }\n \n $list{$n}{'name'}=$name;\n\n $seq=~tr\
+/a-z/A-Z/;\n $list{$n}{'seq'}=$list{$n}{'seq'};\n \
+$list{$n}{'seq'}.=$seq;\n\n $n++;\n $vu{$name}++;\\
+n $test++;\n } \n \n}\n\nmy @numero=();\n\nfo\
+r (my $a=0; $a<$n; $a++) #m\n{\n my $long=lengt\
+h($list{0}{'seq'}); \n my $long1= length($list\
+{$a}{'seq'});\n \n while ($long1 ne $long)\n \
+ {\n $list{$a}{'seq'}.=\"-\";\n $long1= length ($\
+list{$a}{'seq'});\n } \n \n push (@numero,\"\
+$list{$a}{'name'} $list{$a}{'real_name'}\\n\");\n}\
+\n\nmy %dejavu=();\n\n\nfor (my $i=0; $i<=$#numero\
+; $i++)\n{\n my $s=\">$list{$i}{'real_name'}\\n\
+$list{$i}{'seq'}\\n\";\n my $k=0;\n \n if\
+ (exists $dejavu{$numero[$i]}) {next;}\n else\n\
+ { \n for ($j=0; $j<$n ; $j++)\n {\n if (\"\
+$numero[$i]\" eq \"$numero[$j]\" && $j != $i )\n \
+ {\n ++$k;\n $s .=\">$list{$j}{'real_name'}\\n\
+$list{$j}{'seq'}\\n\";\n }\n } \n }\n \n\
+ if ($k>0) \n {\n my $cons;\n open (SOR,\">t\
+empo_aln2cons\"); print SOR $s; close SOR ;\n ope\
+n (COM,\"t_coffee -other_pg seq_reformat -in tempo\
+_aln2cons -action +aln2cons +upper |\") ; \n \
+while (<COM>)\n { \n if (/^>/) { $cons =\">$li\
+st{$i}{'real_name'}\\n\"; next;}\n $_=~ s/\\n/\
+/g;\n $cons .=$_;\n }\n close COM; unlink (\"t\
+empo_aln2cons\");\n print $cons,\"\\n\"; print F $\
+cons,\"\\n\";\n } \n else { print $s; prin\
+t F $s; }\n \n $dejavu{$numero[$i]}++;\n} #m\
+\n\nexit;\n\n\n\n\n\n\n\n\n\n\n\n","use Env;\n\n\n\
+$tmp_dir=\"\";\n$init_dir=\"\";\n$program=\"tc_gen\
+eric_method.pl\";\n\n$blast=@ARGV[0];\n\n$name=\"q\
+uery\";$seq=\"\";\n%p=blast_xml2profile($name,$seq\
+,100, 0, 0, $blast);\n&output_profile (%p);\n\n\ns\
+ub output_profile\n {\n my (%profile)=(@_);\n \
+ my ($a);\n for ($a=0; $a<$profile{n}; $a++)\\
+n {\n \n print \">$profile{$a}{name} $profile\
+{$a}{comment}\\n$profile{$a}{seq}\\n\";\n }\n\
+ return;\n }\nsub file_contains \n {\n my \
+($file, $tag, $max)=(@_);\n my ($n);\n $n=0;\
+\n \n if ( !-e $file && ($file =~/$tag/)) {r\
+eturn 1;}\n elsif ( !-e $file){return 0;}\n \
+else \n {\n open (FC, \"$file\");\n while ( <\
+FC>)\n {\n if ( ($_=~/$tag/))\n {\n c\
+lose (FC);\n return 1;\n }\n elsif ($ma\
+x && $n>$max)\n {\n close (FC);\n return 0\
+;\n }\n $n++;\n }\n }\n close \
+(FC);\n return 0;\n }\n \n \nsub file2st\
+ring\n {\n my $f=@_[0];\n my $string, $l;\n\
+ open (F,\"$f\");\n while (<F>)\n {\n\n\
+ $l=$_;\n #chomp ($l);\n $string.=$l;\n }\n \
+ close (F);\n $string=~s/\\r\\n//g;\n $stri\
+ng=~s/\\n//g;\n return $string;\n }\n\n\n\nsub\
+ tag2value \n {\n \n my $tag=(@_[0]);\n \
+my $word=(@_[1]);\n my $return;\n \n $tag\
+=~/$word=\"([^\"]+)\"/;\n $return=$1;\n retu\
+rn $return;\n }\n \nsub hit_tag2pdbid\n {\n\
+ my $tag=(@_[0]);\n my $pdbid;\n \n \
+ $tag=~/id=\"(\\S+)\"/;\n $pdbid=$1;\n $pdbi\
+d=~s/_//;\n return $pdbid;\n }\nsub id2pdbid \\
+n {\n my $id=@_[0];\n \n if ($id =~/pdb/)\\
+n {\n $id=~/pdb(.*)/;\n $id=$1;\n }\n \
+ $id=~s/[|¦_]//g;\n return $id;\n }\nsub set_b\
+last_type \n {\n my $file =@_[0];\n if (&fi\
+le_contains ($file,\"EBIApplicationResult\",100)){\
+$BLAST_TYPE=\"EBI\";}\n elsif (&file_contains (\
+$file,\"NCBI_BlastOutput\",100)) {$BLAST_TYPE=\"NC\
+BI\";}\n else\n {\n $BLAST_TYPE=\"\";\n \
+ }\n return $BLAST_TYPE;\n }\nsub blast_xml2\
+profile \n {\n my ($name,$seq,$maxid, $minid, \
+$mincov, $file)=(@_);\n my (%p, $a, $string, $n\
+);\n \n\n\n if ($BLAST_TYPE eq \"EBI\" || &f\
+ile_contains ($file,\"EBIApplicationResult\",100))\
+{%p=ebi_blast_xml2profile(@_);}\n elsif ($BLAST\
+_TYPE eq \"NCBI\" || &file_contains ($file,\"NCBI_\
+BlastOutput\",100)){%p=ncbi_blast_xml2profile(@_);\
+}\n else \n {\n print \"************ ERROR\
+: Blast Returned an unknown XML Format ***********\
+***********\";\n die;\n }\n for ($a=0; $a<\
+$p{n}; $a++)\n {\n my $name=$p{$a}{name};\n $\
+p{$name}{seq}=$p{$a}{seq};\n }\n return %p\
+;\n }\nsub ncbi_blast_xml2profile \n {\n my (\
+$name,$seq,$maxid, $minid, $mincov, $string)=(@_);\
+\n my ($L,$l, $a,$b,$c,$d,$nhits,@identifyerL);\
+\n \n \n $seq=~s/[^a-zA-Z]//g;\n $L=le\
+ngth ($seq);\n \n %hit=&xml2tag_list ($strin\
+g, \"Hit\");\n \n \n for ($nhits=0,$a=0; \
$a<$hit{n}; $a++)\n {\n my ($ldb,$id, $identi\
ty, $expectation, $start, $end, $coverage, $r);\n \
-my (%Q,%M,%E,%I);\n \n $ldb=&tag2value ($hit{$a}{o\
-pen}, \"database\");\n $identifyer=&tag2value ($hi\
-t{$a}{open}, \"id\");\n\n $description=&tag2value \
-($hit{$a}{open}, \"description\");\n \n %Q=&xml2ta\
-g_list ($hit{$a}{body}, \"querySeq\");\n %M=&xml2t\
-ag_list ($hit{$a}{body}, \"matchSeq\");\n %E=&xml2\
-tag_list ($hit{$a}{body}, \"expectation\");\n %I=&\
-xml2tag_list ($hit{$a}{body}, \"identity\");\n \n\\
-n for ($b=0; $b<$Q{n}; $b++)\n {\n \n \n\
- $qs=$Q{$b}{body};\n $ms=$M{$b}{body};\n \
- if ($seq eq\"\"){$seq=$qs;$L=length($seq);}\n\n\
- $expectation=$E{$b}{body};\n $identity=$I\
-{$b}{body};\n \n \n $start=&tag2v\
-alue ($Q{$b}{open}, \"start\");\n $end=&tag2va\
-lue ($Q{$b}{open}, \"end\");\n $startM=&tag2va\
-lue ($M{$b}{open}, \"start\");\n $endM=&tag2va\
-lue ($M{$b}{open}, \"end\");\n $coverage=(($en\
-d-$start)*100)/$L;\n \n # print \"$id: ID: \
-$identity COV: $coverage [$start $end]\\n\";\n \
- \n \n if ($identity>$maxid || $identity<$\
-minid || $coverage<$mincov){next;}\n # print \\
-"KEEP\\n\";\n\n \n @lr1=(split (//,$qs));\\
-n @lr2=(split (//,$ms));\n $l=$#lr1+1;\n \
- for ($c=0;$c<$L;$c++){$p[$nhits][$c]=\"-\";}\n \
- for ($d=0,$c=0; $c<$l; $c++)\n {\n $r=$\
-lr1[$c];\n if ( $r=~/[A-Za-z]/)\n {\n \n \
- $p[$nhits][$d + $start-1]=$lr2[$c];\n $d\
-++;\n }\n }\n \n \n $identifyer\
-L[$nhits]=$identifyer;\n $comment[$nhits]=\"$l\
-db|$identifyer [Eval=$expectation][id=$identity%][\
-start=$startM end=$endM]\";\n $nhits++;\n }\\
-n }\n \n $profile{n}=0;\n $profile{$\
-profile{n}}{name}=$name;\n $profile{$profile{n}\
-}{seq}=$seq;\n $profile {n}++;\n \n for (\
-$a=0; $a<$nhits; $a++)\n {\n $n=$a+1;\n $prof\
-ile{$n}{name}=\"$name\\_$a\";\n $profile{$n}{seq}=\
-\"\";\n $profile{$n}{identifyer}=$identifyerL[$a];\
-\n \n $profile{$n}{comment}=$comment[$a];\n for ($\
-b=0; $b<$L; $b++)\n {\n if ($p[$a][$b])\n \
- {\n $profile{$n}{seq}.=$p[$a][$b];\n }\\
-n else\n {\n $profile{$n}{seq}.=\"-\";\\
-n }\n }\n }\n $profile{n}=$nhits+1\
-;\n \n return %profile;\n }\n\nsub blast_xm\
-l2hit_list\n {\n my $string=(@_[0]);\n retu\
-rn &xml2tag_list ($string, \"hit\");\n }\nsub xml\
-2tag_list \n {\n my ($string_in,$tag)=@_;\n \
- my $tag_in, $tag_out;\n my %tag;\n \n i\
-f (-e $string_in)\n {\n $string=&file2string \
-($string_in);\n }\n else\n {\n $strin\
-g=$string_in;\n }\n $tag_in1=\"<$tag \";\n\
- $tag_in2=\"<$tag>\";\n $tag_out=\"/$tag>\";\
-\n $string=~s/>/>##1/g;\n $string=~s/</##2</\
-g;\n $string=~s/##1/<#/g;\n $string=~s/##2/#\
->/g;\n @l=($string=~/(\\<[^>]+\\>)/g);\n $ta\
-g{n}=0;\n $in=0;$n=-1;\n \n \n\n foreach $t\
- (@l)\n {\n\n $t=~s/<#//;\n $t=~s/#>//;\n \n \
-if ( $t=~/$tag_in1/ || $t=~/$tag_in2/)\n {\n \n\
- $in=1;\n $tag{$tag{n}}{open}=$t;\n $n\
-++;\n \n }\n elsif ($t=~/$tag_out/)\n {\n \
- \n\n $tag{$tag{n}}{close}=$t;\n $tag{n\
-}++;\n $in=0;\n }\n elsif ($in)\n {\n \\
-n $tag{$tag{n}}{body}.=$t;\n }\n }\n \\
-n return %tag;\n }\n\n\n\n\n","use Env qw(HOST\
-);\nuse Env qw(HOME);\nuse Env qw(USER);\nwhile (<\
->)\n {\n if ( /^>(\\S+)/)\n {\n if ($list\
-{$1})\n {\n print \">$1_$list{$1}\\n\";\n \
- $list{$1}++;\n }\n else\n {\n print $_;\\
-n $list{$1}=1;\n }\n }\n else\n \
- {\n print $_;\n }\n }\n \n","\n\n\nuse\
- Env qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER\
-);\n\n\nopen (F,$ARGV[0]);\nwhile ( <>)\n {\n \
-@x=/([^:,;\\)\\(\\s]+):[^:,;\\)\\(]*/g;\n @list\
-=(@list,@x);\n }\n$n=$#list+1;\nforeach $n(@list)\
-{print \">$n\\nsequence\\n\";}\n\n\nclose (F);\n",\
-"\nopen (F, $ARGV[0]);\n\nwhile ( <F>)\n {\n @\
-l=($_=~/(\\S+)/g);\n \n $name=shift @l;\n \
- \n print STDOUT \"\\n>$name\\n\";\n foreach\
- $e (@l){$e=($e eq \"0\")?\"O\":\"I\";print \"$e\"\
-;}\n }\nclose (F);\n\n \n \n","use Env\
- qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER);\n\
-\n$tmp=\"$ARGV[0].$$\";\nopen (IN, $ARGV[0]);\nope\
-n (OUT, \">$tmp\");\n\nwhile ( <IN>)\n {\n $fi\
-le=$_;\n $file=~s/\\r\\n/\\n/g;\n $file=~s/\\
-\n\\r/\\n/g;\n $file=~s/\\r\\r/\\n/g;\n $fil\
-e=~s/\\r/\\n/g;\n print OUT \"$file\";\n }\ncl\
-ose (IN);\nclose (OUT);\n\nopen (OUT, \">$ARGV[0]\\
-");\nopen (IN, \"$tmp\");\n\nwhile ( <IN>)\n{\n p\
-rint OUT \"$_\";\n}\nclose (IN);\nclose (OUT);\nun\
-link ($tmp);\n\n"};
-/******************************COPYRIGHT NOTICE*******************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
-/*All rights reserved.*/
-/*This file is part of T-COFFEE.*/
-/**/
-/* T-COFFEE is free software; you can redistribute it and/or modify*/
-/* it under the terms of the GNU General Public License as published by*/
-/* the Free Software Foundation; either version 2 of the License, or*/
-/* (at your option) any later version.*/
-/**/
-/* T-COFFEE is distributed in the hope that it will be useful,*/
-/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
-/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
-/* GNU General Public License for more details.*/
-/**/
-/* You should have received a copy of the GNU General Public License*/
-/* along with Foobar; if not, write to the Free Software*/
-/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
-/*............................................... |*/
-/* If you need some more information*/
-/* cedric.notredame@europe.com*/
-/*............................................... |*/
-/**/
-/**/
-/* */
-/******************************COPYRIGHT NOTICE*******************************/
+my (%ID,%DE,%HSP);\n \n $ldb=\"\";\n\n %ID=&xml2ta\
+g_list ($hit{$a}{body}, \"Hit_id\");\n $identifyer\
+=$ID{0}{body};\n \n %DE=&xml2tag_list ($hit{$a}{bo\
+dy}, \"Hit_def\");\n $definition=$DE{0}{body};\n \\
+n %HSP=&xml2tag_list ($hit{$a}{body}, \"Hsp\");\n \
+for ($b=0; $b<$HSP{n}; $b++)\n {\n my (%STAR\
+T,%END,%E,%I,%Q,%M);\n\n \n %START=&xml2tag_l\
+ist ($HSP{$b}{body}, \"Hsp_query-from\");\n %H\
+START=&xml2tag_list ($HSP{$b}{body}, \"Hsp_hit-fro\
+m\");\n \n %LEN= &xml2tag_list ($HSP{$b}{\
+body}, \"Hsp_align-len\");\n %END= &xml2tag_l\
+ist ($HSP{$b}{body}, \"Hsp_query-to\");\n %HEN\
+D= &xml2tag_list ($HSP{$b}{body}, \"Hsp_hit-to\")\
+;\n %E=&xml2tag_list ($HSP{$b}{body}, \"Hs\
+p_evalue\");\n %I=&xml2tag_list ($HSP{$b}{\
+body}, \"Hsp_identity\");\n %Q=&xml2tag_list \
+ ($HSP{$b}{body}, \"Hsp_qseq\");\n %M=&xml2t\
+ag_list ($HSP{$b}{body}, \"Hsp_hseq\");\n \
+\n for ($e=0; $e<$Q{n}; $e++)\n\n {\n $\
+qs=$Q{$e}{body};\n $ms=$M{$e}{body};\n if ($seq \
+eq\"\"){$seq=$qs;$L=length($seq);}\n \n $expecta\
+tion=$E{$e}{body};\n $identity=($LEN{$e}{body}==0\
+)?0:$I{$e}{body}/$LEN{$e}{body}*100;\n $start=$ST\
+ART{$e}{body};\n $end=$END{$e}{body};\n $Hstart=\
+$HSTART{$e}{body};\n $Hend=$HEND{$e}{body};\n \n \
+ $coverage=(($end-$start)*100)/$L;\n\n \n if ($id\
+entity>$maxid || $identity<$minid || $coverage<$mi\
+ncov){next;}\n @lr1=(split (//,$qs));\n @lr2=(sp\
+lit (//,$ms));\n $l=$#lr1+1;\n for ($c=0;$c<$L;$\
+c++){$p[$nhits][$c]=\"-\";}\n for ($d=0,$c=0; $c<\
+$l; $c++)\n {\n $r=$lr1[$c];\n if ( $\
+r=~/[A-Za-z]/)\n {\n \n $p[$nhits][$d +\
+ $start-1]=$lr2[$c];\n $d++;\n }\n }\n\
+ $Qseq[$nhits]=$qs;\n $Hseq[$nhits]=$ms;\n $Qst\
+artL[$nhits]=$start;\n $HstartL[$nhits]=$Hstart;\\
+n $identityL[$nhits]=$identity;\n $endL[$nhits]=\
+$end;\n $definitionL[$nhits]=$definition;\n $ide\
+ntifyerL[$nhits]=$identifyer;\n $comment[$nhits]=\
+\"$ldb|$identifyer [Eval=$expectation][id=$identit\
+y%][start=$Hstart end=$Hend]\";\n $nhits++;\n \
+ }\n }\n }\n \n $profile{n}=0;\n \
+ $profile{$profile{n}}{name}=$name;\n $profile{\
+$profile{n}}{seq}=$seq;\n $profile {n}++;\n \
+\n for ($a=0; $a<$nhits; $a++)\n {\n $n=$a\
++1;\n \n $profile{$n}{name}=\"$name\\_$a\";\n $pro\
+file{$n}{seq}=\"\";\n $profile{$n}{Qseq}=$Qseq[$a]\
+;\n $profile{$n}{Hseq}=$Hseq[$a];\n $profile{$n}{Q\
+start}=$QstartL[$a];\n $profile{$n}{Hstart}=$Hstar\
+tL[$a];\n $profile{$n}{identity}=$identityL[$a];\n\
+ $profile{$n}{definition}=$definitionL[$a];\n $pro\
+file{$n}{identifyer}=$identifyerL[$a];\n $profile{\
+$n}{comment}=$comment[$a];\n for ($b=0; $b<$L; $b+\
++)\n {\n if ($p[$a][$b])\n {\n $profi\
+le{$n}{seq}.=$p[$a][$b];\n }\n else\n \
+ {\n $profile{$n}{seq}.=\"-\";\n }\n }\
+\n }\n \n $profile{n}=$nhits+1;\n re\
+turn %profile;\n }\nsub ebi_blast_xml2profile \n \
+ {\n my ($name,$seq,$maxid, $minid, $mincov, $s\
+tring)=(@_);\n my ($L,$l, $a,$b,$c,$d,$nhits,@i\
+dentifyerL,$identifyer);\n \n\n \n $seq=~\
+s/[^a-zA-Z]//g;\n $L=length ($seq);\n %hit=&\
+xml2tag_list ($string, \"hit\");\n \n for ($\
+nhits=0,$a=0; $a<$hit{n}; $a++)\n {\n my ($ld\
+b,$id, $identity, $expectation, $start, $end, $cov\
+erage, $r);\n my (%Q,%M,%E,%I);\n \n $ldb=&tag2val\
+ue ($hit{$a}{open}, \"database\");\n $identifyer=&\
+tag2value ($hit{$a}{open}, \"id\");\n\n $descripti\
+on=&tag2value ($hit{$a}{open}, \"description\");\n\
+ \n %Q=&xml2tag_list ($hit{$a}{body}, \"querySeq\"\
+);\n %M=&xml2tag_list ($hit{$a}{body}, \"matchSeq\\
+");\n %E=&xml2tag_list ($hit{$a}{body}, \"expectat\
+ion\");\n %I=&xml2tag_list ($hit{$a}{body}, \"iden\
+tity\");\n \n\n for ($b=0; $b<$Q{n}; $b++)\n {\n\
+ \n \n $qs=$Q{$b}{body};\n $ms=$M{\
+$b}{body};\n if ($seq eq\"\"){$seq=$qs;$L=leng\
+th($seq);}\n\n $expectation=$E{$b}{body};\n \
+ $identity=$I{$b}{body};\n \n \n \
+ $start=&tag2value ($Q{$b}{open}, \"start\");\n \
+ $end=&tag2value ($Q{$b}{open}, \"end\");\n $\
+startM=&tag2value ($M{$b}{open}, \"start\");\n \
+ $endM=&tag2value ($M{$b}{open}, \"end\");\n $\
+coverage=(($end-$start)*100)/$L;\n \n # pri\
+nt \"$id: ID: $identity COV: $coverage [$start $en\
+d]\\n\";\n \n \n if ($identity>$maxid \
+|| $identity<$minid || $coverage<$mincov){next;}\n\
+ # print \"KEEP\\n\";\n\n \n @lr1=(spl\
+it (//,$qs));\n @lr2=(split (//,$ms));\n $\
+l=$#lr1+1;\n for ($c=0;$c<$L;$c++){$p[$nhits][\
+$c]=\"-\";}\n for ($d=0,$c=0; $c<$l; $c++)\n \
+ {\n $r=$lr1[$c];\n if ( $r=~/[A-Za-z]/)\n \
+ {\n \n $p[$nhits][$d + $start-1]=$lr2[\
+$c];\n $d++;\n }\n }\n \n \n \
+ $identifyerL[$nhits]=$identifyer;\n $commen\
+t[$nhits]=\"$ldb|$identifyer [Eval=$expectation][i\
+d=$identity%][start=$startM end=$endM]\";\n $n\
+hits++;\n }\n }\n \n $profile{n}=0;\n\
+ $profile{$profile{n}}{name}=$name;\n $profi\
+le{$profile{n}}{seq}=$seq;\n $profile {n}++;\n \
+ \n for ($a=0; $a<$nhits; $a++)\n {\n $n\
+=$a+1;\n $profile{$n}{name}=\"$name\\_$a\";\n $pro\
+file{$n}{seq}=\"\";\n $profile{$n}{identifyer}=$id\
+entifyerL[$a];\n \n $profile{$n}{comment}=$comment\
+[$a];\n for ($b=0; $b<$L; $b++)\n {\n if ($p\
+[$a][$b])\n {\n $profile{$n}{seq}.=$p[$a][$\
+b];\n }\n else\n {\n $profile{$n}\
+{seq}.=\"-\";\n }\n }\n }\n $profi\
+le{n}=$nhits+1;\n \n return %profile;\n }\n\
+\nsub blast_xml2hit_list\n {\n my $string=(@_[\
+0]);\n return &xml2tag_list ($string, \"hit\");\
+\n }\nsub xml2tag_list \n {\n my ($string_in\
+,$tag)=@_;\n my $tag_in, $tag_out;\n my %tag\
+;\n \n if (-e $string_in)\n {\n $string\
+=&file2string ($string_in);\n }\n else\n \
+ {\n $string=$string_in;\n }\n $tag_in1\
+=\"<$tag \";\n $tag_in2=\"<$tag>\";\n $tag_o\
+ut=\"/$tag>\";\n $string=~s/>/>##1/g;\n $str\
+ing=~s/</##2</g;\n $string=~s/##1/<#/g;\n $s\
+tring=~s/##2/#>/g;\n @l=($string=~/(\\<[^>]+\\>\
+)/g);\n $tag{n}=0;\n $in=0;$n=-1;\n \n \n\n\
+ foreach $t (@l)\n {\n\n $t=~s/<#//;\n $t=\
+~s/#>//;\n \n if ( $t=~/$tag_in1/ || $t=~/$tag_in2\
+/)\n {\n \n $in=1;\n $tag{$tag{n}}{open\
+}=$t;\n $n++;\n \n }\n elsif ($t=~/$tag_\
+out/)\n {\n \n\n $tag{$tag{n}}{close}=$t\
+;\n $tag{n}++;\n $in=0;\n }\n elsif ($in\
+)\n {\n \n $tag{$tag{n}}{body}.=$t;\n }\
+\n }\n \n return %tag;\n }\n\n\n\n\n","u\
+se Env qw(HOST);\nuse Env qw(HOME);\nuse Env qw(US\
+ER);\nwhile (<>)\n {\n if ( /^>(\\S+)/)\n \
+ {\n if ($list{$1})\n {\n print \">$1_$list{\
+$1}\\n\";\n $list{$1}++;\n }\n else\n {\n \
+ print $_;\n $list{$1}=1;\n }\n }\n \
+ else\n {\n print $_;\n }\n }\n \
+\n","\n\n\nuse Env qw(HOST);\nuse Env qw(HOME);\nu\
+se Env qw(USER);\n\n\nopen (F,$ARGV[0]);\nwhile ( \
+<>)\n {\n @x=/([^:,;\\)\\(\\s]+):[^:,;\\)\\(]*\
+/g;\n @list=(@list,@x);\n }\n$n=$#list+1;\nfor\
+each $n(@list){print \">$n\\nsequence\\n\";}\n\n\n\
+close (F);\n","\nopen (F, $ARGV[0]);\n\nwhile ( <F\
+>)\n {\n @l=($_=~/(\\S+)/g);\n \n $name=\
+shift @l;\n \n print STDOUT \"\\n>$name\\n\"\
+;\n foreach $e (@l){$e=($e eq \"0\")?\"O\":\"I\\
+";print \"$e\";}\n }\nclose (F);\n\n \n \
+ \n","use Env qw(HOST);\nuse Env qw(HOME);\nuse E\
+nv qw(USER);\n\n$tmp=\"$ARGV[0].$$\";\nopen (IN, $\
+ARGV[0]);\nopen (OUT, \">$tmp\");\n\nwhile ( <IN>)\
+\n {\n $file=$_;\n $file=~s/\\r\\n/\\n/g;\n\
+ $file=~s/\\n\\r/\\n/g;\n $file=~s/\\r\\r/\\\
+n/g;\n $file=~s/\\r/\\n/g;\n print OUT \"$fi\
+le\";\n }\nclose (IN);\nclose (OUT);\n\nopen (OUT\
+, \">$ARGV[0]\");\nopen (IN, \"$tmp\");\n\nwhile (\
+ <IN>)\n{\n print OUT \"$_\";\n}\nclose (IN);\ncl\
+ose (OUT);\nunlink ($tmp);\n\n"};
git://source.jalview.org / jabaws.git / blobdiff