+++ /dev/null
-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$print_\
-sum=0;\n$print_n=0;\nforeach $value ( @ARGV)\n \
-{\n if ($value ne $ARGV[$np]) \n {\n ;\n \
- }\n elsif($value eq \"-print_all\")\n {\n \
- $print_sd=$print_avg=$print_n=$print_sum=1;\n \
- $np++;\n }\n elsif($value eq \"-print_sum\"\
-)\n {\n $print_sum=1;\n $print_avg=0;\\
-n $np++;\n }\n elsif($value eq \"-print_n\\
-")\n {\n $print_n=1;\n $print_avg=0;\n\
- $np++;\n }\n elsif($value eq \"-print_avg\
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-;\n $np++;\n }\n elsif($value eq \"-sd\")\\
-n {\n $print_sd=1;\n $print_avg=0;\n \
- $np++;\n }\n elsif($value eq \"-h\")\n \
-{\n $header=1;\n $np++;\n }\n elsif ($\
-value eq \"-i\")\n {\n $interval= $ARGV[++\
-$np];\n $np++;\n }\n elsif ($value eq \
-\"-r\")\n {\n $min= $ARGV[++$np];\n $m\
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-sif ($value eq \"-x\")\n {\n $x_field= $AR\
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-lue eq \"-y\")\n {\n \n while ($ARGV\
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-_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\" || $val\
-ue eq \"help\")\n {\n print STDOUT \"data_an\
-alyse: Analyse and discretization of data\\n\";\n \
- print STDOUT \" -file: <file containi\
-ng the data to analyze>,.<def=STDIN>\\n\";\n p\
-rint STDOUT \" -x: <field containing the X>,\
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- -y: <field containing the Y>,..............\
-.<Def=1>\\n\";\n print STDOUT \" -i:<Int\
-erval size on the X>,...............<Def=0>\\n\";\\
-n print STDOUT \" -i:<0:only one interva\
-l>\\n\";\n print STDOUT \" -r:<Range of \
-the X>\\n\";\n print STDOUT \" -sd: prin\
-t standard deviation on the Y\";\n print STDOU\
-T \" -h : print column header \\n\";\n \
-exit (0);\n }\n elsif ($value=~/-/)\n {\n \
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- {\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$$\";\n open (F\
-, \">$file\");\n while (<STDIN>)\n {\n print F $\
-_;\n }\n close (F);\n \n ;}\n\n\nopen(F,$file);\\
-n\nif ($interval)\n {\n $interval_size=($max-$\
-min)/$interval;\n }\nwhile (<F>)\n {\n $line=\
-$_;\n if (!/\\S/){next;}\n @list=($line=~/(\\
-\S+)/g);\n \n if ($interval==0){$bin=0;}\n \
- else{$bin=int (($list[$x_field]-$min)/($interval\
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-){$bin--;}\n for ( $a=0; $a<$nyf; $a++)\n \
-{\n $sum{$a}{$bin}+=$list[$y_field[$a]];\n $sum2{$\
-a}{$bin}+=$list[$y_field[$a]]*$list[$y_field[$a]];\
-\n $n{$a}{$bin}++;\n }\n }\n\nif (!$interval\
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- {\n printf ( \"%3d %3d \", $interval_size*$a,\
- $interval_size*($a+1));\n for ( $b=0; $b<$nyf;\
- $b++) \n {\n $i=$interval*$a;\n if ( $n{$b}{\
-$a}==0)\n {\n $avg=0;\n $sd=0;\n }\n e\
-lse\n {\n $avg=$sum{$b}{$a}/$n{$b}{$a};\n \
- $sd=sqrt($sum2{$b}{$a}*$n{$b}{$a}-$sum{$b}{$a}*$\
-sum{$b}{$a})/($n{$b}{$a}*$n{$b}{$a});\n }\n if (\
-$print_n) {printf \"%10.4f \", $n{$b}{$a};}\n if (\
-$print_sum){printf \"%10.4f \", $sum{$b}{$a};}\n i\
-f ($print_avg){printf \"%10.4f \", $avg}\n if ($pr\
-int_sd) {printf \"%10.4f \", $sd;}\n }\n p\
-rintf (\"\\n\");\n }\n\n\nif ( $remove_file){unli\
-nk $file;}\n","use File::Copy;\nuse Env qw(HOST);\\
-nuse Env qw(HOME);\nuse Env qw(USER);\n\nforeach $\
-v (@ARGV){$cl.=$v;}\n\n\nif ( $cl=~/-k(\\d+)/){$k=\
-$1;}\nelse {$k=1;}\nif ( $cl=~/-w(\\d+)/){$w=$1;}\\
-nelse {$w=-1;}\nif ( $cl=~/-p(\\d+)/){$p=$1;}\nels\
-e {$p=-1;}\n\nwhile (<STDIN>)\n {\n @l=($_=~/(\
-\\S+)/g);\n $v=$l[$k-1];\n if ( !$h{$v}){@ll\
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-if ($p!=-1){$print{$v}=$l[$p-1];}\n\n }\nforeach \
-$v (@ll)\n {\n print \"$v $print{$v} $h{$v}\\n\
-\";\n }\n","\nuse Env qw(HOST);\nuse Env qw(HOME)\
-;\nuse Env qw(USER);\n$random_tag=int (rand 10000)\
-+1;\n$unique_prefix=\"$$.$HOST.$random_tag\";\n$qu\
-eue=\"distillery.and.mid\";\n$monitor=0;\n$stderr_\
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-\n elsif ($value eq \"-min_sub_jobs\" )\n {\n \
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-n {\n $queue=$ARGV[++$np];\n $np++;\n \
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-( $var_set eq \"\")\n {\n $var_set=1;\n \
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-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\
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-e \n {\n open (F, $list);\n }\n\nif ($par\
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-n \n \n \n $loc_com=$com;\\
-n if ($check){$loc_check=$check;}\n \n\
- @i_val=($val=~/([^\\s]+)/g);\n \n \
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-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\
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-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\
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- $ARGV[++$np];\n }\n elsif ($value eq \"-a\
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-n }\n elsif ($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 \"/*************\
-*****************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\
-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\
-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\
-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 \
-&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 \
- 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 \" $\
-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=\
-&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=\
-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 \
- `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_\
-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***\
-**************************************************\
-**\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* \
- 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*\
-**************************************************\
-****\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","*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 = \
- \
- \
- 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 (\"$pdb_file.PDB\"))\
-){$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 ($pdb_file))){\
-$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 \"***********\
-**************************************************\
-********\\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\";\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\";\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=$c\
-url_arg;}\n else\n {\n printf stderr \"\\n\
-ERROR: No pg for remote file fetching [wget or cur\
-l][FATAL]\\n\";\n exit ($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 $CDIR\
-;\n return &pg_is_installed ($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 $CACH\
-E = \"$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\"}=\
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-{\"mode\"}=\"mcoffee\";\n$PG{\"proda\"}{\"version\\
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-;\n$PG{\"sap\"}{\"4_TCOFFEE\"}=\"SAP\";\n$PG{\"sap\
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-{\"sap\"}{\"ADDRESS\"}=\"http://mathbio.nimr.mrc.a\
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-;\n$PG{\"TMalign\"}{\"source\"}=\"http://zhang.bio\
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-{\"mode\"}=\"expresso,3dcoffee\";\n$PG{\"TMalign\"\
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-$PG{\"lsqman\"}{\"source\"}=\"empty\";\n$PG{\"lsqm\
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-4_TCOFFEE\"}=\"FUGUE\";\n$PG{\"fugueali\"}{\"type\\
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-\"}{\"ADDRESS\"}=\"http://www-cryst.bioc.cam.ac.uk\
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-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$PG{\"dalilite.pl\"}{\"4_TCOFFEE\"}=\"DALIL\
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-e_pairwise_aligner\";\n$PG{\"dalilite.pl\"}{\"ADDR\
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-}=\"Perl\";\n$PG{\"dalilite.pl\"}{\"source\"}=\"em\
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-never\";\n$PG{\"dalilite.pl\"}{\"mode\"}=\"express\
-o,3dcoffee\";\n$PG{\"probconsRNA\"}{\"4_TCOFFEE\"}\
-=\"PROBCONSRNA\";\n$PG{\"probconsRNA\"}{\"type\"}=\
-\"RNA_multiple_aligner\";\n$PG{\"probconsRNA\"}{\"\
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-"version\"}=\"1.0\";\n$PG{\"sfold\"}{\"4_TCOFFEE\"\
-}=\"CONSAN\";\n$PG{\"sfold\"}{\"type\"}=\"RNA_pair\
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-fold\"}{\"language\"}=\"empty\";\n$PG{\"sfold\"}{\\
-"language2\"}=\"empty\";\n$PG{\"sfold\"}{\"source\\
-"}=\"empty\";\n$PG{\"sfold\"}{\"update_action\"}=\\
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-$PG{\"RNAplfold\"}{\"type\"}=\"RNA_secondarystruct\
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-\"http://www.tbi.univie.ac.at/~ivo/RNA/\";\n$PG{\"\
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-\"}{\"language2\"}=\"C\";\n$PG{\"RNAplfold\"}{\"so\
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-\"http://evolution.gs.washington.edu/phylip/\";\n$\
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-\"}=\"http://evolution.gs.washington.edu/phylip/do\
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-\";\n$PG{\"hmmtop\"}{\"source\"}=\"empty\";\n$PG{\\
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-"ADDRESS\"}=\"built_in\";\n$PG{\"wublast.pl\"}{\"A\
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-"}=\"Perl\";\n$PG{\"wublast.pl\"}{\"source\"}=\"em\
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-ever\";\n$PG{\"wublast.pl\"}{\"mode\"}=\"psicoffee\
-,expresso,accurate\";\n$PG{\"blastpgp.pl\"}{\"4_TC\
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-pl\"}{\"language2\"}=\"Perl\";\n$PG{\"blastpgp.pl\\
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-update_action\"}=\"never\";\n$PG{\"blastpgp.pl\"}{\
-\"mode\"}=\"psicoffee,expresso,accurate\";\n$PG{\"\
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-\"blastcl3\"}{\"type\"}=\"protein_homology_predict\
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-\"language2\"}=\"C\";\n$PG{\"blastcl3\"}{\"source\\
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-\"}{\"ADDRESS\"}=\"ftp://ftp.ncbi.nih.gov/blast/ex\
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-"}=\"C\";\n$PG{\"blastpgp\"}{\"language2\"}=\"C\";\
-\n$PG{\"blastpgp\"}{\"source\"}=\"empty\";\n$PG{\"\
-blastpgp\"}{\"update_action\"}=\"never\";\n$PG{\"b\
-lastpgp\"}{\"mode\"}=\"psicoffee,expresso,3dcoffee\
-\";\n$PG{\"SOAP::Lite\"}{\"4_TCOFFEE\"}=\"SOAPLITE\
-\";\n$PG{\"SOAP::Lite\"}{\"type\"}=\"library\";\n$\
-PG{\"SOAP::Lite\"}{\"ADDRESS\"}=\"http://cpansearc\
-h.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile\
-.PL\";\n$PG{\"SOAP::Lite\"}{\"language\"}=\"Perl\"\
-;\n$PG{\"SOAP::Lite\"}{\"language2\"}=\"Perl\";\n$\
-PG{\"SOAP::Lite\"}{\"source\"}=\"empty\";\n$PG{\"b\
-lastpgp\"}{\"update_action\"}=\"never\";\n$PG{\"SO\
-AP::Lite\"}{\"mode\"}=\"none\";\n$PG{\"XML::Simple\
-\"}{\"4_TCOFFEE\"}=\"XMLSIMPLE\";\n$PG{\"XML::Simp\
-le\"}{\"type\"}=\"library\";\n$PG{\"XML::Simple\"}\
-{\"ADDRESS\"}=\"http://search.cpan.org/~grantm/XML\
--Simple-2.18/lib/XML/Simple.pm\";\n$PG{\"XML::Simp\
-le\"}{\"language\"}=\"Perl\";\n$PG{\"XML::Simple\"\
-}{\"language2\"}=\"Perl\";\n$PG{\"XML::Simple\"}{\\
-"source\"}=\"empty\";\n$PG{\"XML::Simple\"}{\"mode\
-\"}=\"psicoffee,expresso,accurate\";\n$MODE{\"tcof\
-fee\"}{\"name\"}=\"tcoffee\";\n$MODE{\"rcoffee\"}{\
-\"name\"}=\"rcoffee\";\n$MODE{\"3dcoffee\"}{\"name\
-\"}=\"3dcoffee\";\n$MODE{\"mcoffee\"}{\"name\"}=\"\
-mcoffee\";\n$MODE{\"expresso\"}{\"name\"}=\"expres\
-so\";\n$MODE{\"trmsd\"}{\"name\"}=\"trmsd\";\n$MOD\
-E{\"accurate\"}{\"name\"}=\"accurate\";\n$MODE{\"s\
-eq_reformat\"}{\"name\"}=\"seq_reformat\";\n\n\n$P\
-G{C}{compiler}=\"gcc\";\n$PG{C}{compiler_flag}=\"C\
-C\";\n$PG{C}{options}=\"\";\n$PG{C}{options_flag}=\
-\"CFLAGS\";\n$PG{C}{type}=\"compiler\";\n\n$PG{\"C\
-XX\"}{compiler}=\"g++\";\n$PG{\"CXX\"}{compiler_fl\
-ag}=\"CXX\";\n$PG{\"CXX\"}{options}=\"\";\n$PG{\"C\
-XX\"}{options_flag}=\"CXXFLAGS\";\n$PG{CXX}{type}=\
-\"compiler\";\n\n$PG{\"CPP\"}{compiler}=\"g++\";\n\
-$PG{\"CPP\"}{compiler_flag}=\"CPP\";\n$PG{\"CPP\"}\
-{options}=\"\";\n$PG{\"CPP\"}{options_flag}=\"CPPF\
-LAGS\";\n$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$PG{GPP}{type}=\"co\
-mpiler\";\n\n$PG{Fortran}{compiler}=\"g77\";\n$PG{\
-Fortran}{compiler_flag}=\"FCC\";\n$PG{Fortran}{typ\
-e}=\"compiler\";\n\n$PG{Perl}{compiler}=\"CPAN\";\\
-n$PG{Perl}{type}=\"compiler\";\n\n$SUPPORTED_OS{ma\
-cox}=\"Macintosh\";\n$SUPPORTED_OS{linux}=\"Linux\\
-";\n$SUPPORTED_OS{windows}=\"Cygwin\";\n\n\n\n$MOD\
-E{t_coffee}{description}=\" for regular multiple s\
-equence alignments\";\n$MODE{rcoffee} {description\
-}=\" for RNA multiple sequence alignments\";\n\n$M\
-ODE{psicoffee} {description}=\" for Homology Exten\
-ded multiple sequence alignments\";\n$MODE{express\
-o}{description}=\" for very accurate structure bas\
-ed multiple sequence alignments\";\n$MODE{\"3dcoff\
-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 \
- 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\
- = 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\
-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\
-;\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\
-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\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\
-sename;\nuse Data::Dumper;\n\nmy $baseUrl = 'http:\
-//www.ebi.ac.uk/Tools/services/rest/wublast';\n\nm\
-y $checkInterval = 3;\n\nmy $outputLevel = 1;\n\nm\
-y $numOpts = scalar(@ARGV);\nmy %params = ( 'debug\
-Level' => 0 );\n\nmy %tool_params = ();\nGetOption\
-s(\n\n # Tool specific options\n 'program|p=s' \
- => \\$tool_params{'program'}, # BLAST progra\
-m\n 'database|D=s' => \\$params{'database'}, \
- # Search database\n 'matrix|m=s' => \\$tool\
-_params{'matrix'}, # Scoring matrix\n 'exp|E\
-=f' => \\$tool_params{'exp'}, # E\
--value threshold\n 'viewfilter|e' => \\$tool_pa\
-rams{'viewfilter'}, # Display filtered sequence\\
-n 'filter|f=s' => \\$tool_params{'filter'}, \
- # Low complexity filter name\n 'alignments|n=\
-i' => \\$tool_params{'alignments'}, # Number of\
- alignments\n 'scores|s=i' => \\$tool_params{\
-'scores'}, # Number of scores\n 'sensitivity\
-|S=s' => \\$tool_params{'sensitivity'}, # Search \
-sensitivity\n 'sort|t=s' => \\$tool_params{\
-'sort'}, # Sort hits by...\n 'stats|T=s' \
- => \\$tool_params{'stats'}, # Scoring \
-statistic to use\n 'strand|d=s' => \\$tool_pa\
-rams{'strand'}, # Strand to use\n 'topcombon\
-|c=i' => \\$tool_params{'topcombon'}, # Consi\
-stent sets of HSPs\n 'align|A=i' => \\$tool_\
-params{'align'}, # Pairwise alignment format\n '\
-stype=s' => \\$tool_params{'stype'}, # Sequence\
- type 'protein' or 'dna'\n 'sequence=s' => \\$para\
-ms{'sequence'}, # Query sequence file or D\
-B:ID\n 'multifasta' => \\$params{'multifasta'}, \
- # Multiple fasta input\n\n # Compatability opt\
-ions, old command-line.\n 'echofilter|e' => \\$\
-params{'echofilter'}, # Display filtered sequenc\
-e\n 'b=i' => \\$params{'numal'}, # Number \
-of alignments\n 'appxml=s' => \\$params{'ap\
-pxml'}, # Application XML\n\n # Generic opti\
-ons\n 'email=s' => \\$params{'email'}, \
- # User e-mail address\n 'title=s' => \\$\
-params{'title'}, # Job title\n 'outfile=s\
-' => \\$params{'outfile'}, # Output fil\
-e name\n 'outformat=s' => \\$params{'outformat'}\
-, # Output file type\n 'jobid=s' => \\$\
-params{'jobid'}, # JobId\n 'help|h' \
- => \\$params{'help'}, # Usage help\n '\
-async' => \\$params{'async'}, # A\
-synchronous submission\n 'polljob' => \\$par\
-ams{'polljob'}, # Get results\n 'resultType\
-s' => \\$params{'resultTypes'}, # Get result \
-types\n 'status' => \\$params{'status'}, \
- # Get status\n 'params' => \\$params{\
-'params'}, # List input parameters\n 'para\
-mDetail=s' => \\$params{'paramDetail'}, # Get d\
-etails for parameter\n 'quiet' => \\$param\
-s{'quiet'}, # Decrease output level\n 've\
-rbose' => \\$params{'verbose'}, # Inc\
-rease output level\n 'debugLevel=i' => \\$params{\
-'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 \
-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; \
-$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*******************************/
git://source.jalview.org / jabaws.git / blobdiff