Next version of JABA

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / perl_header_lib.h

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","mocca","dalilite.pl","w\
ublast.pl","blastpgp.pl","RNAplfold2tclib.pl","fas\
ta_seq2RNAplfold_templatefile.pl","fasta_seq2hmmto\
p_fasta.pl","fasta_seq2consan_aln.pl","clustalw_al\
n2fasta_aln.pl","msf_aln2fasta_aln.pl","blast_aln2\
fasta_aln.pl","blast_xml2fasta_aln.pl","fasta_aln2\
fasta_aln_unique_name.pl","newick2name_list.pl","e\
xcel2fasta.pl","any_file2unix_file.pl","EndList"};\
char *PerlScriptFile[]={"use File::Copy;\nuse Env \
qw(HOST);\nuse Env qw(HOME);\nuse Env qw(USER);\n$\
x_field=0;\n$y_field=1;\n$interval=0;\n$file=\"std\
in\";\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     $pri\
nt_sd=$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         $n\
p++;\n      }\n elsif($value eq \"-print_avg\")\n        \
   {\n      $print_avg=1;\n         $print_avg=0;\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 e\
q \"-i\")\n         {\n     $interval= $ARGV[++$np];\n\
            $np++;\n                }\n elsif ($value eq \"-r\")\
\n          {\n     $min= $ARGV[++$np];\n           $max= $AR\
GV[++$np];\n        $np++;\n                }\n \n      elsif ($v\
alue eq \"-x\")\n           {\n     $x_field= $ARGV[++$n\
p]-1;\n     $np++;\n                }\n elsif ($value eq \
\"-y\")\n           {\n       \n            while ($ARGV[$np+1]\
 && !($ARGV[$np+1]=~/\\-/))\n         {\n               $y_field[\
$nyf++]=$ARGV[++$np]-1;\n               $y_field_set=1;\n            \
 }\n\n      $np++;\n                }\n elsif ($value eq \\
"-file\")\n         {\n     $file= $ARGV[++$np];\n         \
 $file_set=1;\n     $np++;\n                }       \n  el\
sif ( $value eq \"h\" ||  $value eq \"-h\" || $val\
ue eq \"-H\" || $value eq \"-help\" || $value eq \\
"help\")\n        {\n       print STDOUT \"data_analyse: \
Analyse and discretization of data\\n\";\n          pri\
nt STDOUT \"       -file:    <file containing the \
data to analyze>,.<def=STDIN>\\n\";\n       print ST\
DOUT \"       -x: <field containing the X>,.......\
........<Def=0>\\n\";\n     print STDOUT \"       \
-y: <field containing the Y>,...............<Def=1\
>\\n\";\n           print STDOUT \"       -i:<Interval s\
ize on the X>,...............<Def=0>\\n\";\n        p\
rint STDOUT \"       -i:<0:only one interval>\\n\"\
;\n         print STDOUT \"       -r:<Range of the X>\\
\n\";\n     print STDOUT \"       -sd: print stand\
ard deviation on the Y\";\n         print STDOUT \"   \
    -h  : print column header \\n\";\n      exit (0\
);\n      }\n   elsif ($value=~/-/)\n     {\n       print \\
"$value is not a valid FLAG[FATAL]\\n\";\n          exi\
t (0);\n           } \n elsif ($list eq \"\") \n            {\n \
    $file=$ARGV[$np];\n     $np++;\n        }\n \n      \n\
      }\n\n\n\n\n\nif ($file eq \"stdin\")\n    {\n     $\
remove_file=1;\n        $file=\"tmp$$\";\n      open (F, \">$f\
ile\");\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)/$i\
nterval;\n  }\nwhile (<F>)\n  {\n    $line=$_;\n  \
  if (!/\\S/){next;}\n    @list=($line=~/(\\S+)/g)\
;\n    \n    if ($interval==0){$bin=0;}\n    else{\
$bin=int (($list[$x_field]-$min)/($interval_size))\
;}\n\n    \n    if ($bin && $bin==$interval){$bin-\
-;}\n    for ( $a=0; $a<$nyf; $a++)\n      {\n  $su\
m{$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){$inte\
rval=1;}\nfor ( $a=0; $a<$interval; $a++)\n  {\n  \
  printf ( \"%3d %3d \", $interval_size*$a, $inter\
val_size*($a+1));\n    for ( $b=0; $b<$nyf; $b++)       \
\n      {\n     $i=$interval*$a;\n      if ( $n{$b}{$a}==0)\
\n        {\n       $avg=0;\n       $sd=0;\n      }\n   else\n   \
 {\n        $avg=$sum{$b}{$a}/$n{$b}{$a};\n         $sd=s\
qrt($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       if ($pri\
nt_avg){printf \"%10.4f \", $avg}\n     if ($print_sd)\
 {printf \"%10.4f \", $sd;}\n      }\n    printf (\
\"\\n\");\n  }\n\n\nif ( $remove_file){unlink $fil\
e;}\n","use File::Copy;\nuse Env qw(HOST);\nuse En\
v qw(HOME);\nuse Env qw(USER);\n\nforeach $v (@ARG\
V){$cl.=$v;}\n\n\nif ( $cl=~/-k(\\d+)/){$k=$1;}\ne\
lse {$k=1;}\nif ( $cl=~/-w(\\d+)/){$w=$1;}\nelse {\
$w=-1;}\nif ( $cl=~/-p(\\d+)/){$p=$1;}\nelse {$p=-\
1;}\n\nwhile (<STDIN>)\n  {\n    @l=($_=~/(\\S+)/g\
);\n    $v=$l[$k-1];\n    if ( !$h{$v}){@ll=($v, @\
ll);}\n    \n    if ( $w==-1)\n      {$h{$v}++;}\n\
    else\n      {$h{$v}+=$l[$w-1];}\n\n    if ($p!\
=-1){$print{$v}=$l[$p-1];}\n\n  }\nforeach $v (@ll\
)\n  {\n    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$u\
nique_prefix=\"$$.$HOST.$random_tag\";\n$queue=\"d\
istillery.and.mid\";\n$monitor=0;\n$stderr_file=\"\
/dev/null\";\n$stdio_file=\"/dev/null\";\n$log_fil\
e=\"/dev/null\";\n$pause_time=0;\n$max_sub_jobs=60\
;\n$min_sub_jobs=30;\n$output_all=0;\n$var='\\$';\\
n\nforeach $value ( @ARGV)\n    {\n     if ($value ne \
$ARGV[$np]) \n      {\n     ;\n     }\n elsif ($val\
ue eq \"-max_sub_jobs\")\n          {\n     $max_sub_jo\
bs= $ARGV[++$np];\n         $np++;\n                }   \n      elsi\
f ($value eq \"-min_sub_jobs\" )\n          {\n     $mi\
n_sub_jobs= $ARGV[++$np];\n         $np++;\n                }\
\n      elsif ($value eq \"-para\")\n       {\n     $para\
=1;\n       $monitor=1;\n           $np++;\n                }\n e\
lsif ($value eq \"-monitor\") \n            {\n     $moni\
tor=1;\n            $np++;\n        }\n elsif ($value eq \"-\
no_monitor\") \n            {\n     $monitor=0;\n           $np\
++;\n       }\n elsif ($value eq \"-queue\")\n      {\
\n          $queue=$ARGV[++$np];\n          $np++;\n        }   \\
n       elsif ($value eq \"-stderr_file\")\n        {\n    \
 $stderr_file=$ARGV[++$np];\n       $np++;\n        }\n\
        elsif ($value eq \"-stdio_file\")\n         {\n     $\
stdio_file=$ARGV[++$np];\n          $np++;\n        }\n el\
sif ($value eq \"-output_all\")\n           {\n     $out\
put_all=1;\n        $np++;\n        }\n elsif ($value eq\
 \"-pause\") \n     {\n     $pause_time=$ARGV[++$n\
p];\n       $np++;\n        }\n elsif ($value eq \"-log\
\")\n         {\n              $log=1;\n               \n              \
if ($ARGV[$np+1]=~/\\-\\S+/) \n           {\n             $\
log_file=\"stderr\";\n            }\n          else \\
n                 {\n             $log_file=$ARGV[++$np]; \n              +\
+$np;\n          \n               }\n         }\n       elsif ( $valu\
e eq \"-com\")\n            {\n         \n              if (!$ARGV[$np+1]=~/\
^\\'/) { $com=$ARGV[++$np];}\n          else {$com=$ARGV[+\
+$np];}\n\n          $np++;\n       }\n elsif ( $value e\
q \"-check\")\n   {\n       \n      if (!$ARGV[$np+1]\
=~/^\\'/) { $check=$ARGV[++$np];}\n         else {$che\
ck=$ARGV[++$np];}\n         $np++;\n      }\n   elsif ($com\
 eq \"\") \n        {\n     $com_set=1;\n           $com=$A\
RGV[$np];\n         \n      $np++;\n        }\n elsif ($li\
st eq \"\") \n      {\n     $list_set=1;\n          $lis\
t=$ARGV[$np];\n     $np++;\n        }\n elsif ( $var_\
set eq \"\")\n      {\n     $var_set=1;\n           $var=\
$ARGV[$np];\n       $np++;\n        }\n }\n\n\n\n\nif (\
 $com eq \"\"){print \"You Need to Provide a Comma\
nd [FATAL]\\n\";\n            die;\n         }\n\n\n\nif (\
$list_set==0) \n    {\n    $x= int (rand 100000)+1\
;\n    $tmp_file_name=\"tmp_file_$x\";\n    open (\
 TMP, \">$tmp_file_name\");\n    while (<STDIN>)\n\
      {\n       print TMP $_;\n      }\n    close (TMP);\
\n    open (F, $tmp_file_name);\n    }\nelse \n   \
 {\n    open (F, $list);\n    }\n\nif ($para==0) \\
n    {\n\n     @tc_list= <F>;\n     close (F); \n \
    \n     foreach $val(@tc_list) \n        {\n      \
 \n           \n              \n              $loc_com=$com;\n       \
 if ($check){$loc_check=$check;}\n            \n              \
@i_val=($val=~/([^\\s]+)/g);\n        \n              if (\
 $#i_val==0)\n          {\n               if ($check){$loc_check=~s/$\
var/$i_val[0]/g;}\n               $loc_com=~s/$var/$i_val[0]/\
g;\n            }\n           else\n            {\n               for ($n=1; $n<=$#i_\
val+1;$n++ )\n              {\n               \n                      $sub=\"$v\
ar$n\";\n                     \n                      $loc_com=~s/$sub/$i_val\
[$n-1]/g;\n                   if ($check){$loc_check=~s/$var/\
$i_val[0]/g;}\n             }\n         }\n           if ( $check &&\
 -e $loc_check)\n               {\n               print STDERR \"skipping \
$loc_com...\\n\";\n               }\n         else\n            {\n               sy\
stem \"$loc_com\";\n            }\n         }\n    exit;\n    }\\
n\nelsif ($para==1) \n    {\n    print STDERR \"do\
 parallel execution of: \\\"$com $list\\\"\\n\";\n\
    \n    if ($log==1) \n       {\n     if ($log_file eq \"s\
tdout\" || $log_file eq \"stderr\" ) \n         {\n             $log\
_file=\"\";\n           }\n\n        else \n            {\n             s\
ystem \"echo LOG FILE> $log_file\";\n           \n              \
}\n     }\n    else     \n      {\n     open ( OUT, \">/dev/null\")\
;\n     }\n     \n    \n    $id=0;\n    $n_sub=0;\n    whi\
le ($val=<F>) \n            {               \n      $job_log[$i\
d]=\"$HOME/tmp/$unique_prefix.$id.log_file\";\n   \
  \n        $job=$unique_prefix.\"_$id\";\n         open \
(JOB, \">$job\");\n         \n      $loc_com=$com;\n      \
  chop $val;\n\n            $loc_com=~s/\\$/$val/g;\n    \n\
            print JOB \"#!/bin/csh\\n\";\n          print JOB \
\"#\\$ -cwd\\n\";\n         print JOB \"#\\$ -N $uniqu\
e_prefix\\n\";\n            if ($queue && !($queue eq \" \
\")) {print JOB \"#\\$ -l $queue\\n\";}\n           prin\
t JOB \"#\\n\";     \n            print JOB \"$loc\
_com\\n\";\n        print JOB \"echo FINISHED  >> $jo\
b_log[$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 $st\
derr_file -o $stdio_file >$unique_prefix\";           \
  \n            } \n\n\n\n          print STDERR \"$id: $o\
utput_all\\n\";\n           $n_sub++;\n     if ( $max_su\
b_jobs && $n_sub==$max_sub_jobs) \n             {\n             $n_sub=m\
onitor_process($min_sub_jobs,@job_log);                  \n             \n      \
        }       \n         \n            unlink $unique_prefi\
x;\n        sleep $pause_time;\n            $id++;\n        }\n\
\n    close (OUT);\n    close (F);\n\n    print ST\
DERR \"Your $id Jobs Have Been Submited (NAME=$uni\
que_prefix)\\n\";\n    monitor_process (0, @job_lo\
g);\n    foreach $file(@job_log) {if (-e $file) {u\
nlink($file);}}\n    \n    }\n\nsub monitor_proces\
s ( @job_list)\n    {\n    my (@job_list)=@_;\n   \
 my $min_sub_jobs=shift (@job_list);\n    my $n_su\
b_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_job\
s)|| $n_sub_jobs==-1) ) \n      {\n     $finished=1;\n  $n_s\
ub_jobs=0;\n    $n=0;\n foreach $file (@job_list)\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($tmp_file_name);}\n","\n\n\
foreach ($np=0; $np<=$#ARGV; $np++)\n    {\n    $v\
alue=$ARGV[$np];\n\n    if ($value eq \"-file\")\n\
      {\n      $file= $ARGV[++$np];\n      }\n    \
elsif ($value eq \"-type\")\n      {\n        $typ\
e= $ARGV[++$np];\n      }\n    elsif ($value eq \"\
-institute\")\n      {\n        $institute= $ARGV[\
++$np];\n      }\n    elsif ($value eq \"-author\"\
)\n      {\n        $author= $ARGV[++$np];\n      \
}\n    elsif ($value eq \"-date\")\n      {\n     \
   $date= $ARGV[++$np];\n      }\n     elsif ($val\
ue eq \"-program\")\n      {\n        $program= $A\
RGV[++$np];\n      }\n    elsif ($value eq \"-emai\
l\")\n      {\n        $email= $ARGV[++$np];\n    \
  }\n    else\n      {\n        print \"$value is an unko\
wn argument[FATAL]\\n\";\n      exit (1);\n      }\n  }\
\n\n\n\nopen F, $file || die;\nprint $INSTITUTE;\n\
if ( $type eq \"c\"){print \"/********************\
*************COPYRIGHT NOTICE*********************\
*************/\\n\";}\nif ( $type eq \"perl\"){pri\
nt \"#################################COPYRIGHT NO\
TICE#################################/\\n\";}\nif \
( $type eq \"txt\"){print \"----------------------\
------------COPYRIGHT NOTICE----------------------\
-----------/\\n\";}\n\n\nwhile (<F>)\n  {\n  s/\\$\
INSTITUTE/$institute/g;\n  s/\\$AUTHOR/$author/g;\\
n  s/\\$DATE/$date/g;\n  s/\\$PROGRAM/$program/g; \
 \n  s/\\$EMAIL/$email/g;  \n  if ( $type eq \"txt\
\"){print $_;}\n  elsif ($type eq \"c\"){chop $_; \
print \"\\/*$_*\\/\\n\";}\n  elsif ($type eq \"per\
l\"){print \"\\#$_\";}\n}\nclose (F);\nif ( $type \
eq \"c\"){print \"/*******************************\
**COPYRIGHT NOTICE********************************\
**/\\n\";}\nif ( $type eq \"perl\"){print \"######\
###########################COPYRIGHT NOTICE#######\
##########################/\\n\";}\nif ( $type eq \
\"txt\"){print \"---------------------------------\
-COPYRIGHT NOTICE---------------------------------\
/\\n\";}\n\n","\nwhile (<>)     \n      {\n     s/\\=cc/1234567\
89/g;\n s/\\bcc/\\$\\(CC\\)/g;\n        s/123456789/\\=cc\
/g;\n   print $_;\n     }\n\n","$version=\"1.00\";\n$rse\
ed= int(rand(100000))+1;\n\n\nif ( $#ARGV==-1)\n  \
{\n    print \"msa2bootstrap -i <input_file> -o <o\
ut_file> -input <seq|msa|matrix|tree> -n <N-Boostr\
ap> -o <outtree> -tmode <nj|upgma|parsimony|ml> -d\
mode <kimura> -alignpg <t_coffee | muscle | clusta\
lw> -rtree <file> -stype <prot|cdna|dna> -recomput\
e -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 di\
rectly to method -tmode [caveat: tmode=nj or upgma\
]\";\n    print \"\\n\\t\\ttree: list of newick tr\
ees directly fed to consence in order to generate \
a bootstraped tree\";\n    \n    print \"\\n\\t-n:\
 number of bootstrap replicates\";\n    print \"\\\
n\\t-o: name of the output tree. Files are not ove\
rwritten. Use -recompute to overwrite existing fil\
e\";\n    print \"\\n\\t-tmode: tree mode: nj|upgm\
a|parsimony|ml\";\n    print \"\\n\\t-dmode: dista\
nce mode\";\n    print \"\\n\\t-alignpg: program f\
or aligning sequences (t_coffee=default)\";\n    p\
rint \"\\n\\t-rtree: replicate tree file (default:\
 no file)\";\n    print \"\\n\\t-rmsa: replicate m\
sa file (default: no file)\";\n    print \"\\n\\t-\
rmat: replicate matrix file (default: no file)\";\\
n    print \"\\n\\t-stype: sequence type: protein,\
 dna or cdna\";\n    print \"\\n\\t-recompute: for\
ce files to be overwritten\";\n    print \"\\n\\t-\
system: cygwin|unix\";\n      \n\n    \n    &my_ex\
it (EXIT_FAILURE);\n  }\nforeach $arg (@ARGV){$com\
mand.=\"$arg \";}\n\nprint \"CLINE: $command\\n\";\
\n$threshold=100;\n$trim_msa=0;\n$stype=\"prot\";\\
nprint \"msa2bootstrap \";\n\n$system=\"cygwin\";\\
nif(($command=~/\\-system (\\S+)/))\n  {\n    $sys\
tem=$1;\n    if ( $system eq \"cygwin\")\n      {\\
n       $exec_extension=\".exe\";\n      }\n    elsif ( \
$system eq \"unix\")\n      {\n $exec_extension=\"\
\";\n   print \"system=Unix\";die;\n      }\n    els\
e\n      {\n    print \"msa2boostrap: -system=$system\
 is an unknown mode [FATAL]\\n\"; die;\n      }\n \
   \n    print \"-system $system \";\n  }\nif(($co\
mmand=~/\\-stype (\\S+)/))\n  {\n    $stype=$1;\n \
 }\nprint \"-stype=$stype \";\n\n\n\nif(($command=\
~/\\-i (\\S+)/))\n  {\n    $msa=$1;\n    print \"-\
i $msa \";\n  }\n\nif(($command=~/\\-rtree (\\S+)/\
))\n  {\n    $rtree=$1;\n    print \"-rtree=$rtree\
 \";\n  }\n\nif(($command=~/\\-rmsa (\\S+)/))\n  {\
\n    $rmsa=$1;\n  }\nif(($command=~/\\-rmat (\\S+\
)/))\n  {\n    $rmat=$1;\n  }\n$input=\"seq\";\nif\
(($command=~/\\-input (\\S+)/))\n  {\n    $input=$\
1;\n  }\nprint \"-input=$input \";\n\n$dmode=\"kim\
ura\";\nif(($command=~/\\-dmode (\\S+)/))\n  {\n  \
  $dmode=$1;\n  }\nprint \"-dmode=$dmode \";\n$ali\
gnpg=\"muscle\";\nif(($command=~/\\-alignpg (\\S+)\
/))\n  {\n    $alignpg=$1;\n  }\nprint \"-alignpg=\
$dmode \";\n\n$tmode=\"nj\";\nif(($command=~/\\-tm\
ode (\\S+)/))\n  {\n    $tmode=$1;\n  }\nprint \"-\
tmode=$tmode \";\n$recompute=0;\nif(($command=~/\\\
-recompute/))\n  {\n    $recompute=1;\n    print \\
"-recompute \";\n  }\n\n$out=$msa;\n$out=~s/\\..*/\
/;\n$out.=\".bph\";\nif(($command=~/\\-o (\\S+)/))\
\n  {\n    $out=$1;\n    \n  }\nprint \"-out=$out \
\";\nif (-e $out && !$recompute)\n  {\n    print \\
"\\nNo Computation Required $out already exists\\n\
\";\n    &my_exit (EXIT_SUCCESS);\n    \n  }\n\n$n\
=100;\nif(($command=~/\\-n (\\d+)/))\n  {\n    $n=\
$1;\n  }\nprint \"-n=$n \";\n$seed=3;\nif(($comman\
d=~/\\-s (\\d+)/))\n  {\n    $seed=$1;\n  }\nprint\
 \"-s=$seed\";\n\nif(($command=~/\\-run_name (\\d+\
)/))\n  {\n    $suffix=$1;\n  }\nelse\n  {\n    $m\
sa=~/([^.]+)/;\n    $suffix=$1;\n  }\nprint \"-run\
_name=$suffix\";\n\n\nif ( $input eq \"seq\")\n  {\
\n    $seq=$msa;\n    $msa=\"$suffix.prot_msa\";\n\
    \n    if ($stype eq \"cdna\")\n      {\n    $cdna\
_seq=$seq;\n    $clean_cdna_seq=&vtmpnam();\n   $seq=&v\
tmpnam();\n     `t_coffee -other_pg seq_reformat -in $\
cdna_seq -action +clean_cdna >$clean_cdna_seq`;\n       \
`t_coffee -other_pg seq_reformat -in $clean_cdna_s\
eq -action +translate >$seq`;\n \n      }\n\n    i\
f (!-e $msa || $recompute)\n      {\n   print \"\\n#\
####   Compute an MSA With $alignpg\\n\";\n     \n      if \
( $alignpg eq \"t_coffee\")\n     {`$alignpg $seq -o\
utfile=$msa >/dev/null 2>/dev/null`;}\n elsif ( $a\
lignpg eq \"muscle\")\n   {\n       `$alignpg -in $s\
eq > $msa 2>/dev/null`;\n         }\n   elsif ( $alignpg e\
q \"clustalw\")\n         {\n       `$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=$seq -outfile=\
$msa`;\n          }\n      }\n    if (!-e $msa)\n      {\\
n       print \"\\nError: $alignpg Could Not produce the\
 MSA $msa [FATAL]\\n\";\n      }\n\n    if ($stype\
 eq \"cdna\")\n      {\n        $msa2=\"$suffix.cdna_msa\\
";\n    `t_coffee -other_pg seq_reformat -in $clean_c\
dna_seq -in2 $msa -action +thread_dna_on_prot_aln \
-output fasta_aln  >$msa2`;\n   $msa=$msa2;\n      }\
\n    \n    $input=\"msa\";\n  }\n\n\n\n$seqboot_o\
=&vtmpnam();\n$seqboot_c=&vtmpnam();\n\n$protdist_\
o=&vtmpnam();\n$protdist_c=&vtmpnam();\nif ( $inpu\
t eq \"msa\")\n  {\n    if ($tmode eq \"nj\" || $t\
mode eq \"upgma\"){$input=\"matrix\";}\n    \n    \
$lmsa= &vtmpnam ();\n    `t_coffee -other_pg seq_r\
eformat -in $msa -output phylip_aln > $lmsa`;\n   \
 \n    if ( -e \"outfile\"){unlink (\"outfile\");}\
\n    # run seqboot\n  \n    if ( $n>1)\n      {\n\
        print \"Run SeqBoot .....\";\n  open (F, \">$seqbo\
ot_c\");\n      print F \"$lmsa\\nR\\n$n\\nY\\n$seed\\n\
\";\n   close (F);\n    `seqboot$exec_extension  < $seq\
boot_c`;\n      if ( -e \"outfile\"){ print \"[OK]\\n\"\
;}\n    else { print \"[FAILED]\\n\";&my_exit (EXIT_F\
AILURE);}\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 \"upgma\")\n  \
    {\n if ( $stype eq \"prot\")\n        {\n       # run\
 protdist\n         print \"Run Protdist [dmode=$dmode\
]\";\n      if ($dmode eq \"kimura\")\n       {\n               \
$dmode=\"P\\nP\\nP\";\n       }\n           else\n           \
 {\n            print \"\\n$dmode is an unknown mode for Pro\
tdist [FATAL:msa2bootstrap.pl]\\n\";\n          &my_exit (\
EXIT_FAILURE);\n              }\n           open (F, \">$protdi\
st_c\");\n          if ($n>1){print F \"$seqboot_o\\n$d\
mode\\nM\\nD\\n$n\\nY\\n\";}\n      else {printf F \
\"$seqboot_o\\n$dmode\\nY\\n\";}\n          close (F);\\
n           `cp $protdist_c pd_comm`;\n     `protdist$ex\
ec_extension  < $protdist_c`;\n     if ( -e \"outf\
ile\"){ print \"[OK]\\n\";}\n       else { print \"[\
FAILED]\\n\";&my_exit (EXIT_FAILURE);}\n            `mv o\
utfile $protdist_o`;\n   \n       }\n   elsif ( $stype eq\
 \"cdna\" || $stype eq \"dna\")\n         {\n       print \
\"Run dnadist [dmode=default\";\n           open (F, \">\
$protdist_c\");\n           if ($n>1){print F \"$seqboot\
_o\\nM\\nD\\n$n\\nY\\n\";}\n        else {printf F \"\
$seqboot_o\\nY\\n\";}\n     close (F);\n            `prot\
dist$exec_extension  < $protdist_c`;\n      if ( -e\
 \"outfile\"){ print \"[OK]\\n\";}\n        else { pr\
int \"[FAILED]\\n\";&my_exit (EXIT_FAILURE);}\n   \
  `mv outfile $protdist_o`;\n     }\n      }\n  }\ne\
lsif ( $input eq \"matrix\")\n  {\n    $protdist_o\
=&vtmpnam();\n    print \"MSA: $msa\\n\";\n    `cp\
 $msa $protdist_o`;\n    $n=1;\n  }\n\n\n\n\n\n$nb\
_o=&vtmpnam();\n$nb_c=&vtmpnam();\nif ($input eq \\
"matrix\" && $tmode ne \"parsimony\" && $tmode ne \
\"ml\")\n  {\n    print \"Run neighbor [tmode=$tmo\
de]\";\n\n    if ($tmode eq \"nj\")\n      {\n  $tm\
ode=\"\\nN\\nN\";\n      }\n    elsif ( $tmode eq \
\"upgma\")\n      {\n   $tmode = \"\\nN\";\n      }\\
n    else\n      {\n    print \"\\n ERROR: $tmode is \
an unknown tree computation mode\\n\";\n        &my_exit \
(EXIT_FAILURE);\n      }\n\n    open (F, \">$nb_c\\
");\n    if ($n>1){print F \"$protdist_o$tmode\\nM\
\\n$n\\n$seed\\nY\\n\";}\n    else {print F \"$pro\
tdist_o$tmode\\nY\\n\";}\n    close (F);\n\n    `n\
eighbor$exec_extension  < $nb_c`;\n    if ( -e \"o\
uttree\"){ print \"[Neighbor OK]\\n\";}\n    else \
{ print \"[FAILED]\\n\";&my_exit (EXIT_FAILURE);}\\
n    `mv outtree $nb_o`;\n    unlink (\"outfile\")\
;\n  }\nelsif ($input eq \"msa\" && $tmode eq \"pa\
rsimony\")\n  {\n    if ( -e \"outfile\"){unlink (\
\"outfile\");}\n    if ( -e \"outtree\"){unlink (\\
"outtree\");}\n    \n    if ($stype eq \"prot\")\n\
      {\n       print \"Run protpars [tmode=$tmode]\";\n\
        open (F, \">$nb_c\");\n if ($n>1){print F \"$seqb\
oot_o\\nM\\nD\\n$n\\n$seed\\n10\\nY\\n\";}\n    else \
{print F \"$seqboot_o\\nY\\n\";}\n      close (F);\n    `p\
rotpars$exec_extension  < $nb_c`;\n      }\n    el\
sif ( $stype eq \"dna\" || $stype eq \"cdna\")\n  \
    {\n print \"Run dnapars [tmode=$tmode]\";\n op\
en (F, \">$nb_c\");\n   if ($n>1){print F \"$seqboot\
_o\\nM\\nD\\n$n\\n$seed\\n10\\nY\\n\";}\n       else {pr\
int F \"$seqboot_o\\nY\\n\";}\n close (F);\n    `dnap\
ars$exec_extension  < $nb_c`;\n      }\n    if ( -\
e \"outtree\"){ print \"[OK]\\n\";}\n    else { pr\
int \"[FAILED]\\n\";&my_exit (EXIT_FAILURE);}\n   \
 `mv outtree $nb_o`;\n   unlink (\"outfile\");\n  \
}\nelsif ($input eq \"msa\" && $tmode eq \"ml\")\n\
  {\n    if ( -e \"outfile\"){unlink (\"outfile\")\
;}\n    if ( -e \"outtree\"){unlink (\"outtree\");\
}\n    \n    if ($stype eq \"prot\")\n      {\n pr\
int \"Error: ML impossible with Protein Sequences \
[ERROR]\";\n    &my_exit (EXIT_FAILURE);\n      }\n  \
  elsif ( $stype eq \"dna\" || $stype eq \"cdna\")\
\n      {\n     print \"Run dnaml [tmode=$tmode]\";\n   \
open (F, \">$nb_c\");\n if ($n>1){print F \"$seqbo\
ot_o\\nM\\nD\\n$n\\n$seed\\n10\\nY\\n\";}\n     else {\
print F \"$seqboot_o\\nY\\n\";}\n       close (F);\n    `dn\
aml$exec_extension  < $nb_c`;\n      }\n    if ( -\
e \"outtree\"){ print \"[OK]\\n\";}\n    else { pr\
int \"[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 \"\\nOut\
put List of $n Replicate MSA: $rmsa\\n\";`cp $seqb\
oot_o $rmsa`;}\nif ($rmat && -e $protdist_o){print\
 \"\\nOutput List of $n Replicate MATRICES: $rmat\\
\n\";`cp $protdist_o $rmat`;}\nif ($rtree && -e $n\
b_o){print \"\\nOutput List of $n Replicate TREES:\
 $rtree\\n\";`cp $nb_o $rtree`;}\n\n\n\n$con_o=&vt\
mpnam();\n$con_c=&vtmpnam();\nif ($n >1)\n  {\n   \
 print \"Run Consense.....\";\n    open (F, \">$co\
n_c\");\n    print F \"$nb_o\\nY\\n\";\n    close \
(F);\n    `consense$exec_extension  < $con_c`;\n  \
  if ( -e \"outfile\"){ print \"[OK]\\n\";}\n    e\
lse { print \"[FAILED]\\n\";&my_exit (EXIT_FAILURE\
);}\n    `mv outtree $con_o`;\n    unlink (\"outfi\
le\");\n  }\nelse\n  {\n    `cp $nb_o $con_o`;\n  \
}\n\n\n`cp $con_o $out`;\nif ( !-e $out)\n  {\n   \
 print \"Tree Computation failed [FAILED]\\n\";\n \
   &my_exit (EXIT_FAILURE);\n  }\nelsif ($n>1)\n  \
{\n    print \"\\nOutput Bootstrapped Tree: $out\\\
n\";\n    $avg=`t_coffee -other_pg seq_reformat -i\
n $out -action +avg_bootstrap`;\n    $avg=~s/\\n//\
g;\n    print \"$avg\\n\";\n  }\nelse\n  {\n    pr\
int \"\\nOutput Tree: $out\\n\";\n  }\n\nopen (F, \
\"$out\");\nwhile (<F>)\n  {\n    \n    $tree.=$_;\
\n  }\nclose (F);\n$tree=~s/\\n//g;\nprint \"BPH: \
$tree\\n\";\n\n\n&my_exit (EXIT_SUCCESS);\n\nsub m\
y_exit \n  {\n    my $m=@_[0];\n    &clean_vtmpnam\
();\n    exit ($m);\n  }\nsub vtmpnam \n  {\n    m\
y $file;\n\n\n    $ntmp++;\n    $file=\"tmp4msa2bo\
otstrap.$rseed.$$.$ntmp\";\n    \n    push (@tmpfi\
le, $file);\n    return $file;\n  }\nsub clean_vtm\
pnam \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 -ver\
sion`);$tc_version=~s/PROGRAM: //;\n\n\nprint STDE\
RR \"\\n******************************************\
***********************\";\nprint STDERR \"\\n*   \
        HIGH LEVEL PROGRAM: T-COFFEE_DPA Version $\
VersionTag\";\nprint 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 obtain a list\\n\";\n    print \"Requ\
ires $TC_VERSION\\n\";\n    print \"Requires \";\n\
    print \"t_coffee_dpa specific flags:\\n\";\n  \
  print \"\\t-dpa_master_aln....................Ma\
ster alignment: provided OR computed\\n\";\n    pr\
int \"\\t-dpa_master_aln....................By def\
ault, Computed with t_coffee -very_fast\\n\";\n   \
 print \"\\t-dpa_master_aln=<file>.............Use\
 file, (must be an aln in Fasta or ClustalW\\n\";\\
n    print \"\\t-dpa_master_aln=<program>.........\
.Compute aln with pg -in seq -out aln`\\n\";\n    \
print \"\\t-dpa_maxnseq.......................Maxi\
mum number of sequences in subgroups\\n\";\n    pr\
int \"\\t-dpa_min_score1....................Minimu\
m Id for two sequences to be grouped in ref_aln\\n\
\";\n    print \"\\t-dpa_min_score2...............\
.....Minimum Id within a subgroup\\n\";\n    print\
 \"\\t-dpa_debug.........................Keep Tmp \
File (for debug purpose)\\n\\n\";\n    \n    exit \
(0);\n  }\nforeach $arg (@ARGV)\n  {\n    $arg_lis\
t.=\" $arg\";\n  }\n$arg_list=~s/[=,;]/ /g;\n\n\n(\
$seq0, $arg_list)=&extract_val_from_arg_list(\"^\"\
,$arg_list, \"SPLICE\",\"unset\");\n($seq1, $arg_l\
ist)=&extract_val_from_arg_list(\"-seq\",$arg_list\
, \"SPLICE\",\"unset\");\n($seq2, $arg_list)=&extr\
act_val_from_arg_list(\"-in\",$arg_list, \"KEEP\",\
\"unset\");\n($seq3, $arg_list)=&extract_val_from_\
arg_list(\"-infile\",$arg_list, \"SPLICE\",\"unset\
\");\n($prf,  $arg_list)=&extract_val_from_arg_lis\
t(\"-profile\",$arg_list, \"SPLICE\",\"unset\");\n\
\n$gl{'Seq'}=$seq=&vtmpnam();#file containing all \
the sequences\n\n   #1-remove sequences from -in\n\
if ( $arg_list =~/\\-in\\b/)\n  {\n    my $save, $\
name;\n    while($arg_list=~/\\-in\\b[^-]+(\\bS[\\\
w.]+)/)\n      {\n      $name=$1;$name=~s/^.//;\n       if ( \
!-e $name){$save.=\" S$name \";}\n\n    $arg_list=~s/\
S$name/ /;\n      }\n    $arg_list=~s/\\-in\\b/\\-\
in $save /;\n  }\n   #2-prepare \n\nif (!($arg_lis\
t=~/\\-outorder/))\n  {\n    \n    $output_cl .=\"\
 -outorder=$seq\";\n  }\n@output_flag=(\"-output\"\
,\"-outfile\", \"-run_name\", \"-outorder\"); \nfo\
reach $v1 (@output_flag)\n  {\n    ($v2, $arg_list\
)=&extract_val_from_arg_list($v1,$arg_list, \"SPLI\
CE\",\"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_lis\
t)  =&extract_val_from_arg_list(\"-dpa_master_aln\\
",$arg_list, \"SPLICE\", \"t_coffee\");\n$dpa_mast\
er_aln=~s/\\s//g;\n($nseqT, $arg_list)           =\
&extract_val_from_arg_list(\"-dpa_maxnseq\",$arg_l\
ist, \"SPLICE\", 30);\n($scoreT1, $arg_list)      \
   =&extract_val_from_arg_list(\"-dpa_min_score1\"\
,$arg_list, \"SPLICE\", 80);\n($scoreT2, $arg_list\
)         =&extract_val_from_arg_list(\"-dpa_min_s\
core2\"    ,$arg_list, \"SPLICE\", 30);\n($dpa_lim\
it, $arg_list)       =&extract_val_from_arg_list(\\
"-dpa_limit\"        ,$arg_list, \"SPLICE\", 0);\n\
($dpa_delta_id, $arg_list)    =&extract_val_from_a\
rg_list(\"-dpa_delta_id\"        ,$arg_list, \"SPL\
ICE\", 1);\n($dpa_debug, $arg_list)       =&extrac\
t_val_from_arg_list(\"-dpa_debug\"           ,$arg\
_list, \"SPLICE\", 0);\n\n\n$in_seq=$seq0.\" \".$s\
eq1.\" \".$seq2.\" \".$seq3;\n$in_prf=(($prf ne $u\
nset)?\"$prf \":\"\");\n&exit_dpa (($in_seq eq \"\\
" && $in_prf eq \"\")?1:0, \"ERROR: You did not Pr\
ovide any sequences. Use the -seq flag [FATAL: t_c\
offee_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 $s\
tep: Gather all the sequences into the tmp file: [\
$seq]\";$step++;        \n    &my_system (\"t_coffee $in_\
seq -convert -quiet -output fasta_seq -outfile=$se\
q -maxnseq 0\");\n  }\n\nif ( !-e $seq){$seq=\"\";\
}\n\nif ($in_prf=~/\\S+/)\n  {\n    $seq_in_type=\\
"profile\"; \n    $seq.= $in_prf; \n  }\nif ($seq \
eq \"\"){ &exit_dpa (1, \"\\nERROR: No Sequence FO\
und. Provide Sequences with the -seq flag [FATAL: \
t_coffee_dpa]\", EXIT_FAILURE);}\n\n \n\nif ( $run\
_name)\n  {\n    $suffix=$run_name;\n  }\nelsif ($\
in_seq=~/\\b(S[\\w.]+\\b)/)\n  {\n    my $suffix1,\
 $sufffix2;\n    $suffix1=$suffix2=$1;\n    $suffi\
x2=~s/^S//;\n    if ( -e $suffix1){$suffix=$suffix\
1;}\n    elsif ( -e $suffix2){$suffix=$suffix2;}\n\
    else\n      {\n     $suffix=&vtmpnam();     \n      }\\
n    $suffix=~s/\\.\\w+//;\n  }\n\nelse\n  {\n    \
$suffix=&vtmpnam();\n  }\n\n\nif (!$run_name){$out\
put_cl.=\" -run_name $suffix \";}\n\n\n$gl{'Tree'}\
=&seq2dpa_tree ($seq, \"$suffix.dpadnd\");\n\nprin\
t STDERR \"\\n Step $step: Prepare guide tree: $gl\
{'Tree'}\";$step++;\n\nprint STDERR \"\\n Step $st\
ep: Identify and Align Closely Related Groups\";$s\
tep++;\n%gl=&make_one_pass (0, $scoreT1,\"Align\",\
%gl);\n\nprint STDERR \"\\n Step $step: Make Multi\
ple Group Alignment\";$step++;\nwhile (!%gl ||$gl{\
'Ng'}>$nseqT)\n  {\n    %gl=&make_one_pass ($nseqT\
, $scoreT2,\"t_coffee\",%gl);\n    if ( $gl{'Newgr\
oups'}==0){$scoreT2--;}    \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&align_groups (\"t_coffee\",'0', $arg_li\
st, \" \", %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=&vtmpnam ();\n\n    &my_system (\"t_coff\
ee -special_mode quickaln -in $seq -outfile $aln -\
quiet\");\n    &my_system (\"$seq_reformat -in $al\
n -action +aln2tree +tree2dpatree -output newick >\
$newtree\");\n    return $newtree;\n  } \nsub seq2\
dpa_tree_old \n  {\n    my $aln=@_[0];\n    my $ne\
wtree=@_[1];\n    \n    \n    &my_system(\"$seq_re\
format -in $aln -action +seq2dpatree -output newic\
k > $newtree\");\n    return $newtree;\n  }\nsub a\
ln2dpa_tree \n  {\n    my $aln=@_[0];\n    my $new\
tree=&vtmpnam();\n    \n    &my_system(\"$seq_refo\
rmat -in $aln -action +aln2tree +tree2dpatree -out\
put newick > $newtree\");\n    return $newtree;\n \
 }\nsub group_file2ngroups\n  {\n    my $file=@_[0\
];\n    my $n;\n    \n    open ( F, $file);\n    w\
hile (<F>)\n      {\n   $n+=/\\>/;\n      }\n    clo\
se (F);\n    return $n;\n  }\n\nsub make_one_pass\\
n  {\n    my ($N, $ID,$pg, %gl)=@_;\n    my $a;\n\\
n    %gl=&tree2group ($N,$ID,%gl);\n    if (!$gl{'\
Newgroups'}){return %gl;}\n    else\n      {\n  for\
 ( $a=0; $a< $ng; $a++)\n         {\n       if ($gl{$gl{$a\
}{'File'}}{'Ng'}>1){&display_group($a, %gl);}\n   \
  &align_groups ($pg, $a, $arg_list, \" -quiet=qui\
et \", %gl);\n    }\n   return %gl;\n      }\n  }\n\n\
sub tree2group \n  {\n    my ($N, $ID, %gl)=@_;\n \
   my $prefix=&vtmpnam();\n    my $group_file=&vtm\
pnam();\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 extract the groups\n    &my_system (\"$se\
q_reformat -in $tree -action +tree2group $N $ID $p\
refix > $group_file\");\n    $n=group_file2ngroups\
($group_file);\n    \n    \n    $gl{'Newgroups'}=1\
;\n    if ( $n==$gl{'Ng'})\n      {\n   $gl{'Newgrou\
ps'}=0;\n       return %gl;\n      }\n    $gl{'Iteration\
'}++;\n    $gl{'MaxNseq'}=$N;$gl{'MinID'}=$ID;\n  \
  $gl{'GroupFile'}=$group_file;$gl{'Ng'}=$ng=0;\n \
   #2 Process the group list into the hash\n    op\
en (F, $group_file);\n    while (<F>)\n      {\n        $\
gl{'File'}.=$_;\n       if (/\\>/)\n      {\n       $line=$_;\
\n          $line=~s/\\>//;\n       @list=($line=~/(\\S+)\
/g);\n      $file=$gl{$ng}{'File'}=shift @list;\n        \
   $gl{$file}{'Output'}=$file;\n            \n      $gl{$f\
ile}{'Ng'}=$#list+1;\n      if ($gl{$file}{'Ng'}>1)\
{ $gl{$file}{'Tlist'}=$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}{'Ng'}=1;\n            }\n           $gl{$file}{'Tlist'\
}.=\"$gl{$l}{'Tlist'},\";\n             $gl{$file}{'Alist'}.=\
\"$gl{$l}{'Tlist'}|\";\n                $gl{$file}{'Nseq'}+=$gl{\
$l}{'Nseq'};\n        }\n           \n\n            chop($gl{$fi\
le}{'Tlist'});chop($gl{$file}{'Alist'});\n          if \
($gl{$file}{'Ng'}>1){$gl{$file}{'Tlist'}.=\")\"; $\
gl{$file}{'Alist'}.=\");\";}\n      $ng++;\n      }     \n\
      }\n    $gl{'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 newick > $gl{'Tree'}\");\n    \n    r\
eturn %gl;\n  }\n\nsub display_group \n  {\n    my\
 ($g,%gl)=@_;\n    my $f;\n    \n    if ( $g==-1)\\
n      {\n      print STDERR \"\\nIteration $gl{'Iterat\
ion'} [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[$action][MaxN=$gl{'MaxNseq'}][MinID=$gl{'\
MinID'}][File $f][Nseq=$gl{$f}{'Nseq'}][Ngroups=$g\
l{$f}{'Ng'}][$gl{$f}{'Alist'}]\";\n      }\n  }\n \
     \n\n\nsub align_groups\n  {\n    my ($pg, $g,\
 $arg, $extra_arg,%gl)=@_;\n    my $f;\n    my $Ou\
tput,$Outflag;\n    \n    \n    $f=$gl{$g}{'File'}\
;\n    $Output=($gl{$f}{'Output'});\n    \n    if \
( $pg eq \"Align\")\n      {\n  if ( !-e $f)\n    {\\
n           $command=\"$seq_reformat -in $gl{'Seq'}  -ac\
tion +extract_aln $gl{'GroupFile'}\";\n     if ($g\
l{$f}{'Ng'}>1)\n              {\n               &my_system ($command);\
\n              $command=\"t_coffee -special_mode quick_aln  S\
$f -outfile=$Output -quiet\";\n       }\n         }\n   el\
se \n     {$command=\"\";}\n      }\n    elsif ( -e \
$f)\n      {    \n      $Outflag=($Output)?\"-outfile=$Out\
put\":\"\";\n   $command=\"$pg -infile $f $Outflag -\
quiet stdout $arg $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=$Output\":\"\";\n    $command=\"$pg -profi\
le $gl{$f}{'List'} $Outflag $arg $extra_arg -maxns\
eq 0\";\n      }\n    \n    &my_system ($command);\
\n    return $outfile;\n  }\n    \nsub my_system \\
n  {\n    my $command=@_[0];\n    my $force=@_[1];\
\n    my $status;\n\n    if ( $dpa_debug) {print S\
TDERR \"\\nCOMMAND: $command\";}\n    $status=syst\
em ($command);\n\n    if (!$force)\n       {\n   &e\
xit_dpa (($status==1), \"Failed in Command:\\n$com\
mand\\n[FATAL: t_coffee_dpa]\\n\", EXIT_FAILURE);\\
n       }\n    \n    return $status;\n  }\n\nsub v\
tmpnam\n  {\n    my $prefix=@_[0];\n    my $tmp_fi\
le_name;\n\n    $tmp_prefix=($prefix)?$prefix:\"dp\
a_tmp_file_$$\";\n   \n    $tmp_count++;\n    $tmp\
_file_name=\"$tmp_prefix\".\"$tmp_count\";\n    $t\
l[$#tl+1]=$tmp_file_name;\n    return $tmp_file_na\
me;\n  }\n\nsub clean_tmp_file\n  {\n\n    my $lis\
t;\n    my $file;\n    \n    if ($dpa_debug){retur\
n;}\n    $list=vtmpnam();\n    `ls -1 | grep $tmp_\
prefix>$list`;\n    \n    open (F,$list);\n    whi\
le ( <F>)\n      {\n    $file=$_;\n     chop $file;\n   if \
( -e $file){unlink $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 extract_val_from_arg_list\n  {\n    \
my $arg=@_[0];\n    my $arg_list=@_[1];\n    my $k\
eep_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_lis\
t=~/^([^@]*)/;\n        $val=$1;\n      }\n    else\n    \
  {$arg_list=~/$arg ([^@]*)/;$val=$1;}\n    \n    \
#remove trailing spaces\n    $val=~s/\\s*$//;\n   \
 \n    #remove the parsed sequence if needed\n    \
if (($val ne \"\") && $keep_flag ne \"KEEP\")\n   \
   {\n  if ( $arg eq \"^\"){$arg_list=~s/$val/ /;}\\
n       else {$arg_list=~s/($arg [^@]*)/ /;}\n      }\n \
\n    #unprotect\n    $arg_list=~s/\\@/-/g;\n    $\
arg=~s/\\@/-/g;\n    \n    if (($val eq \"\") && $\
default_value ne \"unset\"){$val=$default_value;}\\
n    \n    return $val, $arg_list;\n  }\n$program=\
\"T-COFFEE (Version_7.90)\";\\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 (@ARG\
V)\n  {\n    $arg_list.=\" $arg\";\n  }\n$max_nseq\
=10;\n($seq0, $arg_list)=&extract_val_from_arg_lis\
t(\"^\",$arg_list);\n($seq1, $arg_list)=&extract_v\
al_from_arg_list(\"-seq\",$arg_list);\n($seq2, $ar\
g_list)=&extract_val_from_arg_list(\"-in\",$arg_li\
st, \"KEEP\");\n($seq3, $arg_list)=&extract_val_fr\
om_arg_list(\"-infile\",$arg_list);\n$in_seq=$seq0\
.\" \".$seq1.\" \".$seq2.\" \".$seq3;\n\n$seq=vtmp\
nam();\n`t_coffee $in_seq -convert -output fasta_s\
eq -outfile=$seq`;\n\n\n($dpa_nseq, $arg_list)=&ex\
tract_val_from_arg_list(\"-dpa_nseq\",$arg_list);\\
n($master_aln, $arg_list)=&extract_val_from_arg_li\
st(\"-master_aln\",$arg_list);\n($sim_matrix, $arg\
_list)=&extract_val_from_arg_list(\"-sim_matrix\",\
$arg_list);\n($core_seq, $arg_list)=&extract_val_f\
rom_arg_list(\"-core_seq\",$arg_list);\n($dpa_sim,\
 $arg_list)=&extract_val_from_arg_list(\"-dpa_sim\\
",$arg_list);\n($run_name, $arg_list)=&extract_val\
_from_arg_list(\"-run_name\",$arg_list);\n($output\
, $arg_list)=&extract_val_from_arg_list(\"-output\\
",$arg_list);\n\n\n\nif (!$sim_mat && !$master_aln\
)#Compute the fast alignment\n  {\n    $ref_aln=vt\
mpnam();\n    `t_coffee -seq=$seq -very_fast -outf\
ile=$ref_aln -quiet`;\n    \n  }\n\nif (!$sim_mat)\
\n  {\n    $sim_mat=vtmpnam();\n    `seq_reformat \
-in $ref_aln -output sim > $sim_mat`;\n  }\n\nif (\
 !$core_seq)\n  {\n    $core_seq=vtmpnam();\n    `\
seq_reformat -in $ref_aln -action +trimTC N$max_ns\
eq -output fasta_seq > $core_seq`;\n  }\n@core_nam\
e=`seq_reformat -in $core_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 $s (@tot_name){$s=~s/\\s//g;}\nprint \
STDERR \"T-Coffee_dpa:\\n\";\nprint STDERR \"\\tTO\
TAL  SEQ: @tot_name\\n\";\nprint STDERR \"\\tCHOSE\
N SEQ: @core_name\\n\";\n\n\n\nopen (F, $sim_mat);\
\nwhile ( <F>)\n  {\n    @l=($_=~/(\\b[\\S]+\\b)/g\
);\n    if (($l[0] eq \"TOP\" || $l[0] eq \"BOT\")\
)\n      {\n    $s1=$l[1];$s2=$l[2];$v=$l[3];\n if ($\
hcore{$s1} && !$hcore{$s2})\n     {\n       if (!$hseq\
{$s2}{\"sim\"} || $v>$hseq{$s2}{\"sim\"})\n           \
{\n             $hseq{$s2}{\"sim\"}=$v;$hseq{$s2}{\"seq\"}=$s\
1;\n          }\n         }\n      }\n  }\nclose (F);\nfore\
ach $s (@tot_name)\n  {\n\n    if ( !$hseq{$s}{\"s\
eq\"}){;}\n    else\n      {\n  $s2=$hseq{$s}{\"seq\
\"};\n  $v=$hseq{$s}{\"sim\"};\n                \n      if ($v>$dpa_si\
m)\n      {\n       $hseq{$s}{'used'}=1;\n          $seq_lis\
t{$s2}{$seq_list{$s2}{'nseq'}++}=$s;\n    }\n      \
}\n  }\nforeach $s (@core_name){$seq_list{$s}{$seq\
_list{$s}{'nseq'}++}=$s;$hseq{$s}{'used'}=1;}\nfor\
each $s (@tot_name){if (!$hseq{$s}{'used'}){$seq_l\
ist{'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_li\
st=(), $a=0; $a<$n; $a++){@g_list=(@g_list,$seq_li\
st{$s}{$a});}\n\n    $g_seq=vtmpnam();\n    $g_aln\
=vtmpnam();\n    \n    print STDERR \"Group $ng: $\
#g_list Seq: @g_list: \";\n    \n    \n    `seq_re\
format -in $seq -action +lower +keep_name +extract\
_seq  @g_list -output fasta_seq > $g_seq`;\n    \n\
    \n    if ( $#g_list==0)\n      {\n  print STDER\
R \"[No aln]\\n\";\n    $g_aln=$g_seq;\n      }\n    \
elsif ($#g_list<$max_nseq) \n      {\n  print STDER\
R \"[t_coffee]\\n\";\n  `t_coffee $g_seq -outfile=$\
g_aln -quiet $arg_list`;\n      }\n    else\n     \
 {\n    print STDERR \"[t_coffee_dpa]\\n\";\n   `t_coff\
ee_dpa2 $g_seq -outfile=$g_aln $arg_list -sim_matr\
ix $sim_matrix -dpa_nseq $dpa_nseq`;\n      }\n   \
 @profile_list=(@profile_list, $g_aln);\n  }\n\n\n\
print \"UNUSED $seq_list{'unused'}{'nseq'}\";\n\ni\
f ($seq_list{'unused'}{'nseq'})\n    {\n      $prf\
=vtmpnam();\n      \n      `t_coffee -profile @pro\
file_list $arg_list -outfile=$prf -quiet`;\n      \
$n=$seq_list{\"unused\"}{'nseq'};\n      $new_seq=\
vtmpnam();\n      $new_prf=vtmpnam();\n      for (\
$a=0; $a<$n-1; $a++)\n  {\n       $s=$seq_list{\"unused\
\"}{$a};\n        print STDERR \"\\nADD Sequence $s\";\\
n         \n      `seq_reformat -in $seq -action +lower +ke\
ep_name +extract_seq $s  -output fasta_seq > $new_\
seq`;\n   `t_coffee -profile $prf $new_seq $arg_li\
st -outfile=$new_prf`;\n          `cp $new_prf $prf`;\n }\
\n      $s=$seq_list{\"unused\"}{$a};\n      `seq_\
reformat -in $seq -action +lower +keep_name +extra\
ct_seq $s  -output fasta_seq > $new_seq`;\n      @\
profile_list=($prf, $new_seq);\n    }\n    \n     \
 \nif ($run_name){$arg_list.=\" -run_name $run_nam\
e\";}\nelse \n  {\n    $in_seq=~/([\\w-]+)/;\n    \
$arg_list.=\" -run_name $1\";\n  }\nif ( $output){\
$arg_list.=\" -output $output \";}\n\n`t_coffee -p\
rofile @profile_list $arg_list`;\n\n\n&clean (@tmp\
_file_list);\n\n\nsub vtmpnam\n  {\n    my $tmp_fi\
le_name;\n    $tmp_name_counter++;\n    $tmp_file_\
name=\"tmp_file_$tmp_name_counter\\_Pid$$\";\n    \
$tmp_file_list[$ntmp_file++]=$tmp_file_name;\n    \
return $tmp_file_name;\n  }\nsub clean\n  {\n  my \
@fl=@_;\n  my $file;\n  return;\n\n  foreach $file\
 ( @fl)\n    {\n      if ( -e $file){unlink($file)\
;}\n    }\n}\nsub extract_val_from_arg_list\n  {\n\
    my $arg=@_[0];\n    my $arg_list=@_[1];\n    m\
y $keep_flag=@_[2];\n    #protect\n    $arg_list=~\
s/\\s-/ \\@/g;\n    $arg=~s/-/\\@/g;\n    \n    #s\
earch\n    if ($arg eq \"^\")\n      {\n        $arg_list\
=~/^([^@]*)/;\n $val=$1;\n      }\n    else\n     \
 {$arg_list=~/$arg ([^@]*)/;$val=$1;}\n    \n    #\
remove the parsed sequence if needed\n    if ($val\
 && $keep_flag ne \"KEEP\")\n      {\n  if ( $arg e\
q \"^\"){$arg_list=~s/$val/ /;}\n       else {$arg_list=\
~s/($arg [^@]*)/ /;}\n      }\n \n    #unprotect\n\
    $arg_list=~s/\\@/-/g;\n    $arg=~s/\\@/-/g;\n \
   \n    return $val, $arg_list;\n  }\n\n","use En\
v;\n\n$BLAST_MAX_NRUNS=2;\n$EXIT_SUCCESS=0;\n$EXIT\
_FAILURE=1;\n\nuse Cwd;\n$REF_EMAIL=\"\";\n\n\n$tm\
p_dir=\"\";\n$init_dir=\"\";\n$program=\"tc_generi\
c_method.pl\";\n\n$test=0;\nif ($test==1)\n  {\n  \
  $SERVER=\"NCBI\";\n    $query=$ARGV[0];\n    $hi\
tf=$ARGV[1];\n    %s=read_fasta_seq($query);\n    \
@sl=keys(%s);\n    &blast_xml2profile (\"xx\", $s{\
$sl[0]}{seq},$maxid,$minid,$mincov, $hitf);\n    m\
yexit ($EXIT_FAILURE);\n  }\n\nforeach $v(@ARGV){$\
cl.=\"$v \";}\n($mode)=&my_get_opt ( $cl, \"-mode=\
\",1,0);\n\n($A)=(&my_get_opt ( $cl, \"-name1=\",0\
,0));\n($B)=(&my_get_opt ( $cl, \"-name2=\",0,0));\
\n($TMPDIR)=(&my_get_opt ( $cl, \"-tmpdir=\",0,0))\
;\n($CACHE)=(&my_get_opt ( $cl, \"-cache=\",0,0));\
\n($SERVER)=((&my_get_opt ( $cl, \"-server=\",0,0)\
));\n($EMAIL)=((&my_get_opt ( $cl, \"-email=\",0,0\
)));\n\nif (!$A){$A=\"A\";}\nif (!$B){$B=\"B\";}\n\
\n\nif (!$TMPDIR)\n  {\n    $HOME=$ENV{HOME};\n   \
 if ($ENV{TMP_4_TCOFFEE}){$TMPDIR=$ENV{TMP_4_TCOFF\
EE};}\n    else{$TMPDIR=\"$HOME/.t_coffee/tmp/\";}\
\n  }\nif ( ! -d $TMPDIR)\n  {\n    mkdir $TMPDIR;\
\n  }\nif ( ! -d $TMPDIR)\n  {\n    print \"ERROR:\
 Could not create temporary dir: $TMPDIR\\n\";\n  \
  myexit ($EXIT_FAILURE);\n  }\n\n$EMAIL=~s/XEMAIL\
X/\\@/g;\nif (!$EMAIL)\n  {\n    if ($ENV{EMAIL_4_\
TCOFFEE}){$EMAIL=$ENV{EMAIL_4_TCOFFEE};}\n    elsi\
f ($ENV{EMAIL}){$EMAIL=$ENV{EMAIL};}\n    else {$E\
MAIL=$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 (!$cl=~/\\-minid\\=/){$minid=35;}\n\
if (!$cl=~/\\-mincov\\=/){$mincov=80;}\n\n\n\nif (\
$mode eq \"seq_msa\")\n  {\n    &seq2msa($mode,&my\
_get_opt ( $cl, \"-infile=\",1,1, \"-method=\",1,2\
, \"-param=\",0,0, \"-outfile=\",1,0));\n  }\n\nel\
sif ( $mode eq \"thread_pair\")\n  {\n    &seq2thr\
ead_pair($mode,&my_get_opt ( $cl, \"-infile=\",1,1\
, \"-pdbfile1=\",1,1, \"-method=\",1,2,\"-param=\"\
,0,0, \"-outfile=\",1,0, ));\n  }\nelsif ( $mode e\
q \"pdbid_pair\")\n  {\n    &seq2pdbid_pair($mode,\
&my_get_opt ( $cl, \"-pdbfile1=\",1,0, \"-pdbfile2\
=\",1,0, \"-method=\",1,2,\"-param=\",0,0, \"-outf\
ile=\",1,0, ));\n  }\nelsif ( $mode eq \"pdb_pair\\
")\n  {\n    &seq2pdb_pair($mode,&my_get_opt ( $cl\
, \"-pdbfile1=\",1,1, \"-pdbfile2=\",1,1, \"-metho\
d=\",1,2,\"-param=\",0,0, \"-outfile=\",1,0, ));\n\
  }\nelsif ( $mode eq \"profile_pair\")\n  {\n    \
 &seq2profile_pair($mode,&my_get_opt ( $cl, \"-pro\
file1=\",1,1, \"-profile2=\",1,1, \"-method=\",1,2\
,\"-param=\",0,0, \"-outfile=\",1,0, ));\n  }\nels\
if ( $mode eq \"pdb_template\")\n  {\n    &blast2p\
db_template ($mode,&my_get_opt ( $cl, \"-infile=\"\
,1,1, \"-database=\",1,0, \"-method=\",1,0, \"-out\
file=\",1,0));\n  }\nelsif ( $mode eq \"profile_te\
mplate\")\n  {\n    &psiblast2profile_template ($m\
ode,&my_get_opt ( $cl, \"-infile=\",1,1, \"-databa\
se=\",1,0, \"-method=\",1,0, \"-outfile=\",1,0));\\
n  }\nelsif ( $mode eq \"psiprofile_template\")\n \
 {\n    &psiblast2profile_template ($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_te\
mplate ($mode,&my_get_opt ( $cl, \"-infile=\",1,1,\
 \"-outfile=\",1,0));\n  }\nelsif ( $mode eq \"tm_\
template\")\n  {\n    &seq2tm_template ($mode,&my_\
get_opt ( $cl, \"-infile=\",1,1,\"-arch=\",1,1,\"-\
psv=\",1,1, \"-outfile=\",1,0,));\n  }\nelsif ( $m\
ode eq \"psitm_template\")\n  {\n    &seq2tm_templ\
ate ($mode,&my_get_opt ( $cl, \"-infile=\",1,1,\"-\
arch=\",1,1,\"-psv=\",1,1, \"-outfile=\",1,0,));\n\
  }\nelsif ( $mode eq \"ssp_template\")\n  {\n    \
&seq2ssp_template ($mode,&my_get_opt ( $cl, \"-inf\
ile=\",1,1,\"-seq=\",1,1,\"-obs=\",1,1, \"-outfile\
=\",1,0));\n  }\nelsif ( $mode eq \"psissp_templat\
e\")\n  {\n    &seq2ssp_template ($mode,&my_get_op\
t ( $cl, \"-infile=\",1,1,\"-seq=\",1,1,\"-obs=\",\
1,1, \"-outfile=\",1,0));\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}elsif ( $mode eq \"calc_rna_template\")\n\
{\n    &calc_rna_template($mode,&my_get_opt ( $cl,\
 \"-infile=\",1,1,\"-pdbfile=\",1,1, \"-outfile=\"\
,1,0));\n}\nelse\n  {\n    print STDERR \"$mode is\
 an unknown mode of tc_generic_method.pl [FATAL]\\\
n\";\n  }\nmyexit ($EXIT_SUCCESS);\nsub seq2ssp_te\
mplate\n  {\n  my ($mode, $infile,$gor_seq,$gor_ob\
s,$outfile)=@_;\n  my %s, %h;\n  my $result;\n  my\
 (@profiles);\n  &set_temporary_dir (\"set\",$infi\
le,\"seq.pep\");\n  %s=read_fasta_seq (\"seq.pep\"\
);\n\n  \n  open (R, \">result.aln\");\n  \n  #pri\
nt stdout \"\\n\";\n  foreach $seq (keys(%s))\n   \
 {\n      \n      open (F, \">seqfile\");\n      $\
s{$seq}{seq}=uc$s{$seq}{seq};\n      print (F \">$\
s{$seq}{name}\\n$s{$seq}{seq}\\n\");\n      close \
(F);\n      $lib_name=\"$s{$seq}{name}.ssp\";\n   \
   $lib_name=&clean_file_name ($lib_name);\n      \
\n      if ($mode eq \"ssp_template\"){&seq2gor_pr\
ediction ($s{$seq}{name},$s{$seq}{seq}, \"seqfile\\
", $lib_name,$gor_seq, $gor_obs);}\n      elsif ($\
mode eq \"psissp_template\")\n  {\n       &seq2msa_gor_\
prediction ($s{$seq}{name},$s{$seq}{seq},\"seqfile\
\", $lib_name,$gor_seq, $gor_obs);\n    }\n    \n    \
  if ( !-e $lib_name)\n {\n       print STDERR (\"GORI\
V failed to compute the secondary structure of $s{\
$seq}{name} [FATAL:$mode/$method/$program]\\n\");\\
n         myexit ($EXIT_FAILURE);\n     }\n      else\n {\n     \
  print stdout \"\\tProcess: >$s{$seq}{name} _E_ $\
lib_name \\n\";\n         print R \">$s{$seq}{name} _E_ \
$lib_name\\n\";\n       }\n      unshift (@profiles, $li\
b_name);\n    }\n  close (R);\n  &set_temporary_di\
r (\"unset\",$mode, $method,\"result.aln\",$outfil\
e, @profiles);\n}\n\nsub seq2tm_template\n  {\n  m\
y ($mode, $infile,$arch,$psv,$outfile)=@_;\n  my %\
s, %h;\n  my $result;\n  my (@profiles);\n  &set_t\
emporary_dir (\"set\",$infile,\"seq.pep\");\n  %s=\
read_fasta_seq (\"seq.pep\");\n\n  \n  open (R, \"\
>result.aln\");\n  \n  #print stdout \"\\n\";\n  f\
oreach $seq (keys(%s))\n    {\n      open (F, \">s\
eqfile\");\n      print (F \">$s{$seq}{name}\\n$s{\
$seq}{seq}\\n\");\n      close (F);\n      $lib_na\
me=\"$s{$seq}{name}.tmp\";\n      $lib_name=&clean\
_file_name ($lib_name);\n\n      if ($mode eq \"tm\
_template\")\n  {\n       &safe_system (\"t_coffee -oth\
er_pg fasta_seq2hmmtop_fasta.pl -in=seqfile -out=$\
lib_name -arch=$arch -psv=$psv\");\n    }\n      elsi\
f ( $mode eq \"psitm_template\")\n      {\n       &seq2msa_\
tm_prediction ($s{$seq}{name},$s{$seq}{seq},\"seqf\
ile\", $lib_name,$arch, $psv);\n        }\n      if ( !-e\
 $lib_name)\n   {\n       print STDERR (\"RNAplfold fail\
ed to compute the secondary structure of $s{$seq}{\
name} [FATAL:$mode/$method/$program]\\n\");\n     my\
exit ($EXIT_FAILURE);\n }\n      else\n {\n       prin\
t stdout \"\\tProcess: >$s{$seq}{name} _T_ $lib_na\
me\\n\";\n        print R \">$s{$seq}{name} _T_ $lib_na\
me\\n\";\n      }\n      unshift (@profiles, $lib_name)\
;\n    }\n  close (R);\n  &set_temporary_dir (\"un\
set\",$mode, $method,\"result.aln\",$outfile, @pro\
files);\n}\n\nsub seq2RNA_template\n  {\n  my ($mo\
de, $infile,$outfile)=@_;\n  my %s, %h, ;\n  my $r\
esult;\n  my (@profiles);\n  &set_temporary_dir (\\
"set\",$infile,\"seq.pep\");\n  %s=read_fasta_seq \
(\"seq.pep\");\n\n  \n  open (R, \">result.aln\");\
\n  \n  #print stdout \"\\n\";\n  foreach $seq (ke\
ys(%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}{n\
ame}.rfold\";\n      $lib_name=&clean_file_name ($\
lib_name);\n      &safe_system (\"t_coffee -other_\
pg RNAplfold2tclib.pl -in=seqfile -out=$lib_name\"\
);\n      \n      if ( !-e $lib_name)\n {\n       prin\
t STDERR (\"RNAplfold failed to compute the second\
ary structure of $s{$seq}{name} [FATAL:$mode/$meth\
od/$program]\\n\");\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      unsh\
ift (@profiles, $lib_name);\n    }\n  close (R);\n\
  &set_temporary_dir (\"unset\",$mode, $method,\"r\
esult.aln\",$outfile, @profiles);\n}\n\nsub psibla\
st2profile_template \n  {\n  my ($mode, $infile, $\
db, $method, $outfile)=@_;\n  my %s, %h, ;\n  my (\
$result,$psiblast_output,$profile_name,@profiles);\
\n  \n  &set_temporary_dir (\"set\",$infile,\"seq.\
pep\");\n  %s=read_fasta_seq (\"seq.pep\");\n  ope\
n (R, \">result.aln\");\n  \n  #print stdout \"\\n\
\";\n  foreach $seq (keys(%s))\n    {\n      open \
(F, \">seqfile\");\n      print (F \">$A\\n$s{$seq\
}{seq}\\n\");\n      close (F);\n      $psiblast_o\
utput=&run_blast ($s{$seq}{name},$method, $db, \"s\
eqfile\",\"outfile\");\n      if ( -e $psiblast_ou\
tput)\n {\n       %profile=blast_xml2profile($s{$seq}{\
name}, $s{$seq}{seq},$maxid, $minid,$mincov,$psibl\
ast_output);\n    unlink ($psiblast_output);\n    \n\
          $profile_name=\"$s{$seq}{name}.prf\";\n         $prof\
ile_name=&clean_file_name ($profile_name);\n      uns\
hift (@profiles, $profile_name);\n        output_profil\
e ($profile_name, %profile);\n    print stdout \"\\\
tProcess: >$s{$seq}{name} _R_ $profile_name [$prof\
ile{n} Seq.] [$SERVER/blast/$db][$CACHE_STATUS]\\n\
\";\n     print R \">$s{$seq}{name} _R_ $profile_nam\
e\\n\";\n       }\n    }\n  close (R);\n  &set_temporary\
_dir (\"unset\",$mode, $method,\"result.aln\",$out\
file, @profiles);\n}\n\nsub blast2pdb_template \n \
 {\n  my ($mode, $infile, $db, $method, $outfile)=\
@_;\n  my %s, %h, ;\n  my ($result,$blast_output);\
\n  &set_temporary_dir (\"set\",$infile,\"seq.pep\\
");\n  %s=read_fasta_seq (\"seq.pep\");\n  open (R\
, \">result.aln\");\n  \n \n  #print stdout \"\\n\\
";\n  foreach $seq (keys(%s))\n    {\n      open (\
F, \">seqfile\");\n      print (F \">$A\\n$s{$seq}\
{seq}\\n\");\n      close (F);\n      \n      $bla\
st_output=&run_blast ($s{$seq}{name},$method, $db,\
 \"seqfile\",\"outfile\");\n      %p=blast_xml2pro\
file($s{$seq}{name}, $s{$seq}{seq},$maxid, $minid,\
$mincov,$blast_output);\n      unlink ($blast_outp\
ut);\n      if ($p{n}>1)\n      {\n       $pdbid=id2pdbid($\
p{1}{identifyer});\n      if ( length ($pdbid)>5){$pd\
bid=id2pdbid($p{1}{definition});}\n       \n      print R\
 \">$s{$seq}{name} _P_ $pdbid\\n\";\n     print stdo\
ut \"\\tProcess: >$s{$seq}{name} _P_ $pdbid [$SERV\
ER/blast/$db][$CACHE_STATUS]\\n\";\n    }\n      else\
\n      {\n       print R \">$s{$seq}{name}\\n\";\n       print\
 stdout \"\\tProcess: >$s{$seq}{name} _P_ No Templ\
ate Found [$SERVER/blast/$db][$CACHE_STATUS]\\n\";\
\n      }\n    }\n  close (R);\n  &set_temporary_dir (\\
"unset\",$mode, $method,\"result.aln\",$outfile);\\
n}\nsub blast_msa\n  {\n    my ($infile,$outfile)=\
@_;\n    my ($a, %seq);\n    %s1=&read_fasta_seq (\
$infile);\n    foreach $s (keys (%s1))\n      {\n       \
$i=$s1{$s}{order};\n    $s{$i}{name}=$s;\n      $s{$i}{seq\
}=$s1{$s}{seq};\n       $s{$i}{len}=length( $s{$i}{seq})\
;\n     $s{n}++;\n      }\n    `formatdb -i $infile`;\\
n    `blastpgp -i $infile -d $infile -m7 -j4 > io`\
;\n    &set_blast_type (\"io\");\n    \n    %FB=&x\
ml2tag_list (\"io\", \"BlastOutput\");\n    \n    \
open (F, \">$outfile\");\n    print F \"! TC_LIB_F\
ORMAT_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=blas\
t_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}{Qseq});\n          my $hi\
t=$p{$b}{definition};\n     my $Qstart=$p{$b}{Qsta\
rt};\n      my $Hstart=$p{$b}{Hstart};\n            my $id\
entity=$p{$b}{identity};\n          my @lrQ=split (//,$\
p{$b}{Qseq});\n     my @lrH=split (//,$p{$b}{Hseq}\
);\n        my $i= $s1{$s{$a}{name}}{order}+1;\n            \
my $j= $s1{$hit}{order}+1;\n        #if ( $j==$i){nex\
t;}\n       printf F \"# %d %d\\n\", $i, $j;\n      #\
  print  F \"\\n$p{$b}{Qseq} ($Qstart)\\n$p{$b}{Hs\
eq} ($Hstart)\";\n          for ($c=0; $c<$l; $c++)\n    \
     {\n                my $rQ=$lrQ[$c];\n              my $rH=$lrH[$c];\n              \
my $n=0;\n              \n              if ($rQ ne \"-\"){$n++, $Qstart++;\
}\n             if ($rH ne \"-\"){$n++; $Hstart++;}\n           \n              if\
 ( $n==2)\n               {\n               printf F \"\\t%d %d %d\\n\\
", $Qstart-1, $Hstart-1,$identity;\n              }\n         \
}\n       }\n      }\n    print F \"! SEQ_1_TO_N\\n\";\
\n    close (F);\n    return $output;\n  \n  }\n\n\
sub seq2msa\n  {\n    my ($mode, $infile, $method,\
 $param, $outfile)=@_;\n    &set_temporary_dir (\"\
set\",$infile,\"seq.pep\");\n    $param.=\" >/dev/\
null 2>&1 \";\n    \n    #make sure test.pep is in\
 FASTA\n    &safe_system (\"t_coffee -other_pg seq\
_reformat -in seq.pep -output fasta_seq > x\");\n \
   `mv x seq.pep`;\n    \n    if ( $method eq \"bl\
astpgp\")\n      {\n    &blast_msa (\"seq.pep\", \"re\
sult.aln\");\n      }\n    elsif ( $method eq \"mu\
scle\")\n      {\n      `muscle -in seq.pep -out result\
.aln $param`;\n      }\n    elsif ( $method eq \"p\
robcons\")\n      {\n   `probcons seq.pep >result.al\
n 2>/dev/null`;\n      }\n    elsif ( $method eq \\
"mafft\")\n      {\n    `mafft --quiet --localpair --\
maxiterate 1000 seq.pep> result.aln  2>/dev/null`\\
n      }\n    elsif ( $method=~/prank/)\n      {\n\
        `$method -d=seq.pep -o=result.aln -quiet 2>/dev/n\
ull`;\n `mv result.aln.1.fas result.aln`;\n      }\
\n    else\n      {\n   `$method -infile=seq.pep -ou\
tfile=result.aln`;\n      }\n    \n    &set_tempor\
ary_dir (\"unset\",$mode, $method,\"result.aln\",$\
outfile);\n    myexit ($EXIT_SUCCESS);\n  }\n\nsub\
 seq2thread_pair\n  {\n    my ($mode, $infile, $pd\
bfile1, $method, $param, $outfile)=@_;\n    &set_t\
emporary_dir (\"set\",$infile,\"seq.pep\",$pdbfile\
1,\"struc.pdb\");\n    if ($method eq \"fugueali\"\
)\n      {\n    #Env Variable that need to be defined\
 for Fugue\n    if (!$ENV{FUGUE_LIB_LIST}){$ENV{FUGUE\
_LIB_LIST}=\"DUMMY\";}\n        if (!$ENV{HOMSTRAD_PATH})\
  {$ENV{HOMSTRAD_PATH}=\"DUMMY\";}\n    if (!$ENV{HOM\
S_PATH}){$ENV{HOMS_PATH}=\"DUMMY\";}\n  \n      `joy str\
uc.pdb >x 2>x`;\n       &check_file(\"struc.tem\", \"Joy\
 failed [FATAL:$program/$method]\");\n  `melody -t \
struc.tem >x 2>x`;\n    &check_file(\"struc.tem\", \"\
Melody failed [FATAL:$program/$method]\");\n    `fugu\
eali -seq seq.pep -prf struc.fug -print > tmp_resu\
lt.aln`;\n      \n      &check_file(\"tmp_result.aln\", \"Fu\
gue failed [FATAL:$program/$method]\");\n       &safe_sy\
stem (\"t_coffee -other_pg seq_reformat -in tmp_re\
sult.aln -output fasta_aln >result.aln\");\n      \
}\n    elsif ( $method eq \"t_coffee\")\n      {\n\
        &safe_system (\"t_coffee -in Pstruc.pdb Sseq.pep \
Mslow_pair -outfile result.aln -quiet\");\n      }\
\n    else\n      {\n   &safe_system (\"$method -inf\
ile=seq.pep -pdbfile1=struc.pdb -outfile=result.al\
n $param>x 2>x\");\n      }\n    &set_temporary_di\
r (\"unset\",$mode,$method,\"result.aln\",$outfile\
);\n    myexit ($EXIT_SUCCESS);\n  }\nsub seq2pdbi\
d_pair\n  {\n    my ($mode, $pdbfile1, $pdbfile2, \
$method, $param, $outfile)=@_;\n    my ($name);\n\\
n    \n    &set_temporary_dir (\"set\");\n    $nam\
e=$pdbfile1.\" \".$pdbfile2;\n\n    if (    &cache\
_file(\"GET\",\"\",\"$name\",\"$method\",\"dali\",\
$outfile,\"EBI\"))\n      {return $outfile;}\n    \
else\n      {\n if ($method eq \"dalilite\")\n    {\
\n          $pdbfile1=~/(....)(.)/;\n       $id1=$1; $c1=\
$2;\n       \n      $pdbfile2=~/(....)(.)/;\n       $id\
2=$1; $c2=$2;\n     \n      $command=\"t_coffee -ot\
her_pg dalilite.pl --pdb1 $id1 --chainid1 $c1 --pd\
b2 $id2 --chainid2 $c2 --email=$EMAIL  >dali_stder\
r 2>dali_stderr\";\n        $dali=`$command`;\n     \\
n           open (F, \"dali_stderr\");\n            while (<F>)\
\n            {\n               if ( /JobId: dalilite-(\\S+)/)\n                {\\
n                 $jobid=$1;\n          }\n           }\n           close (F);\n        \
    unlink (\"dali_stderr\");\n     \n      $output\
1=\"dalilite-$jobid.txt\";\n        if ( -e $output1)\
\n            {\n               unlink ($output1);\n            &url2file (\"h\
ttp://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cg\
i/dalilite/dalilite-$jobid/aln.html\", \"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=~/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 (\\
"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\",\"$met\
hod\",\"dali\",\"result.aln\",\"EBI\");\n    &set_\
temporary_dir (\"unset\",$mode, $method, \"result.\
aln\",$outfile);\n    myexit ($EXIT_SUCCESS);\n  }\
\nsub seq2pdb_pair\n  {\n    my ($mode, $pdbfile1,\
 $pdbfile2, $method, $param, $outfile)=@_;\n    \n\
    &set_temporary_dir (\"set\",$pdbfile1,\"pdb1.p\
db\",$pdbfile2,\"pdb2.pdb\");\n    if ($method eq \
\"t_coffee\")\n      {\n        &safe_system (\"t_coffee \
-in Ppdb1.pdb Ppdb2.pdb -quiet -outfile=result.aln\
\");\n      }\n    elsif ( $method eq \"TMalign\")\
\n      {\n     if ( &safe_system (\"TMalign pdb1.pdb \
pdb2.pdb >tmp1\")==$EXIT_SUCCESS)\n       {\n       `tai\
l -4 tmp1 > tmp2`;\n        \n      open (F, \"tmp2\")\
;\n         while (<F>)\n             {\n               unshift(@l, $_);\\
n             }\n           close (F);\n            open (F, \">resul\
t.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 faile\
d to align the considered structures[tc_generic_me\
thod.pl]\\n\";\n            `rm result.aln >/dev/null 2>/\
dev/null`;\n      }\n      }\n    elsif ( $method eq \
\"mustang\")\n      {\n if ( &safe_system (\"musta\
ng -i pdb1.pdb pdb2.pdb -F fasta >/dev/null 2>/dev\
/null\")==$EXIT_SUCCESS)\n        {\n       `mv results.a\
fasta result.aln`;\n      }\n   else\n    {\n       print \
\"ERROR: mustang failed to align the considered st\
ructures[tc_generic_method.pl]\\n\";\n      `rm res\
ult.aln >/dev/null 2>/dev/null`;\n        }\n      }\n \
   else\n      {\n      if ( &safe_system (\"$method -p\
dbfile1=pdb1.pep -pdbfile2=pdb2.pdb -outfile=resul\
t.aln $param>x 2>x\")==$EXIT_SUCCESS)\n   {\n       \
`mv results.afasta result.aln`;\n         }\n   else\n    {\
\n          print \"ERROR: $method failed to align the \
considered structures[tc_generic_method.pl]\\n\";\\
n           `rm result.aln >/dev/null 2>/dev/null`;\n     \
}\n      }\n    &set_temporary_dir (\"unset\",$mod\
e, $method, \"result.aln\",$outfile);\n    myexit \
($EXIT_SUCCESS);\n  }\n\nsub seq2profile_pair\n  {\
\n    my ($mode, $profile1, $profile2, $method, $p\
aram, $outfile)=@_;\n    \n    \n    if ($method e\
q \"clustalw\")\n      {\n      &set_temporary_dir (\"s\
et\",$profile1,\"prf1.aln\",$profile2,\"prf2.aln\"\
);\n    `clustalw -profile1=prf1.aln -profile2=prf2.a\
ln -outfile=result.aln`;\n      &set_temporary_dir (\"u\
nset\",$mode, $method, \"result.aln\",$outfile);\n\
      }\n    elsif ( $method eq \"hhalign\")\n    \
  {\n   hhalign ( $profile1,$profile2,$outfile,$para\
m);\n      }\n    else\n      {\n       \n      `$method -pro\
file1=prf1.aln -profile2=prf2.aln -outfile=result.\
aln $param>x 2>x`;\n      }\n   \n    myexit ($EXI\
T_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    $r=`which $p\
 2>/dev/null`;\n    if ($r eq \"\"){return 0;}\n  \
  else {return 1;}\n  }\nsub check_pg_is_installed\
\n  {\n    my @ml=@_;\n    my $r=&pg_is_installed \
(@ml);\n    if (!$r)\n      {\n print STDERR \"\\n\
Program $p Supported but Not Installed on your sys\
tem [FATAL:tc_generic_method]\\n\";\n   myexit ($EXI\
T_FAILURE);\n      }\n    else\n      {\n       return 1\
;\n      }\n  }\nsub set_temporary_dir\n  {\n    m\
y @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       srand;\n        $ra\
nd=rand (100000);\n         $tmp_dir=\"$TMPDIR/tmp4tco\
ffee_profile_pair_dir_$$_P_$rand\";\n     }\n   if ( !\
-d $tm_dir)\n     {\n       `mkdir $tmp_dir`;\n   }\n   \
\n      for ( $a=0; $a<=$#list; $a+=2)\n              {\n               `cp\
 $list[$a] $tmp_dir/$list[$a+1]`;\n           }\n       chdi\
r $tmp_dir;\n      }\n    elsif ( $dir_mode eq \"u\
nset\")\n      {\n      $mode=shift (@list);\n  $method=\
shift (@list);\n        \n      if (!-e $list[0])\n       {\n       \
print STDERR (\"Program $method failed to produce \
$list[1] [FATAL:$mode/$method/$program]\\n\");\n         \
   myexit ($EXIT_FAILURE);\n      }\n   else\n    {\n     \
  chdir $initial_dir;\n     # `t_coffee -other_pg \
seq_reformat -in $tmp_dir/$list[0] -output fasta_a\
ln -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/re\
sult2.aln $list[1]`;\n        }\n           shift (@list)\
; shift (@list);\n          foreach $f (@list)\n              \
{\n             `mv $tmp_dir/$f .`;\n         }\n         }\n      }\\
n  }\nsub clean_dir\n  {\n    my $dir=@_[0];\n    \
if ( !-d $dir){return ;}\n    elsif (!($dir=~/tmp/\
)){return ;}#safety check 1\n    elsif (($dir=~/\\\
*/)){return ;}#safety check 2\n    else\n      {\n\
        `rm -rf $dir`;\n      }\n    return;\n  }\n\nsub \
myexit\n  {\n    my $code=@_[0];\n    &clean_dir (\
$tmp_dir);\n    exit ($code);\n  }\n\nsub my_get_o\
pt\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  $op\
tion=$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 b\
e an existing file\n    #$status: 2=>must be an insta\
lled package\n  \n\n    if ($optional==0){;}\n  elsif (\
 $optional==1 && $argv eq \"\")\n         {\n       print \
STDERR \"ERROR: Option $option must be set [FATAL:\
$program/$mode/$method]\\n\";\n     myexit ($EXIT_\
FAILURE);\n       }\n   if ($status==0){;}\n    elsif ($sta\
tus ==1 && $argv ne \"\" && !-e $argv)\n          {\n      \
 print STDERR \"ERROR: File $argv must exist [FATA\
L:$program/$mode/$method]\\n\";\n           myexit ($EXI\
T_FAILURE);\n     }\n   elsif ( $status==2 && $argv ne\
 \"\" && &check_pg_is_installed ($argv)==0)\n     {\\
n           print STDERR \"ERROR: $argv is not installed\
 [FATAL:$program/$mode/$method]\\n\";\n     myexit\
 ($EXIT_FAILURE);\n       }\n      }\n\n    return @ar\
gl;\n    }\n\nsub check_file \n  {\n    my ($file,\
 $msg)=@_;\n\n    if ( !-e $file)\n      {\n    print\
 \"\\n$msg\\n\";\n      myexit ($EXIT_FAILURE);\n      \
}\n    }\nsub hhalign\n  {\n    my ($aln1, $aln2, \
$outfile, $param)=@_;\n    my $h1, $h2;\n    \n   \
 $h{0}{index}=0;\n    $h{1}{index}=1;\n    \n    $\
h{0}{aln}=$aln1;\n    $h{1}{aln}=$aln2;\n\n   \n\n\
    %{$h{0}}=aln2psi_profile (%{$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.tmp -rank 1 -\
mapt 0 $param\";\n    `$command`;\n    \n  #  `hha\
lign -i $h{0}{a3m} -t $h{1}{a3m} -tc $outfile.tmp \
-rank 1 -mapt 0 -gapf 0.8 -gapg 0.8`;\n    \n\n   \
 # To run global use the following\n    \n    open\
 (I, \"$outfile.tmp\");\n    open (O, \">$outfile\\
");\n    $h{0}{cons}=s/\\./x/g;\n    $h{1}{cons}=s\
/\\./x/g;\n\n    print O \"! TC_LIB_FORMAT_01\\n2\\
\n$h{0}{name} $h{0}{len} $h{0}{seq}\\n$h{1}{name} \
$h{1}{len} $h{1}{seq}\\n#1 2\\n\";\n    \n    whil\
e (<I>)\n      {\n      if (/(\\d+)\\s+(\\d+)\\s+(\\d+)\
/)\n      {\n       print O \"\\t$h{0}{$1}\\t$h{1}{$2}\\
\t$3\\n\";\n      }\n      }\n    print O \"! SEQ_1_T\
O_N\\n\";\n\n    close (O);\n    close (I);\n  }\n\
\nsub aln2psi_profile\n  {\n    my (%h)=@_;\n    m\
y ($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 seq_reformat -\
in $aln -output hasch\";\n    $hv=`$command`;chomp\
 ($hv);\n    \n    $h{a2m}=\"$tmp/$hv.tmp4hhpred.a\
2m\";\n    $h{a3m}=\"$tmp/$hv.tmp4hhpred.a3m\";\n \
   if ( -e $h{a3m}){;}\n    else\n      {\n     `hhcon\
sensus  -M 50 -i $h{aln} -oa2m $h{a2m}`;\n      if (!-e\
 $h{a2m})\n       {\n       print STDERR \"Program tc_ge\
neric_method.pl FAILED to run:\\n\\thhconsensus  -\
M 50 -i $h{aln} -oa2m $h{a2m}\";\n          myexit ($EX\
IT_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_method.pl FAIL\
ED to run:\\n\\thhconsensus  -M 50 -i $h{aln} -oa3\
m $h{a3m}\";\n      myexit ($EXIT_FAILURE);\n     }\n\
       `buildali.pl $h{a3m} -n 1`;\n      }\n    \\
n    \n    $h{a2m_seq}=`head -n 2 $h{a2m} | grep -\
v \">\"`;chomp ($h{a2m_seq});\n    $h{a3m_seq}=`he\
ad -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{l\
en}=$#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    $na\
me=`head -n 2 $h{aln} | grep \">\"`;\n    $name=~/\
\\>(\\S+)/;\n    $h{name}=$1;\n    \n    `cp $h{a2\
m} $i.a2m`;\n    `cp $h{a3m} $i.a3m`;\n    `cp $h{\
aln} $i.hh_aln`;\n    \n    return %h;\n  }\n\nsub\
 read_fasta_seq \n  {\n    my $f=@_[0];\n    my %h\
seq;\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    @s\
eq =($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        m\
y $s;\n my $n=$name[$a];\n      $hseq{$n}{name}=$n;\n   $\
seq[$a]=~s/[^A-Za-z]//g;\n      $hseq{$n}{order}=$a;\n  \
$hseq{$n}{seq}=$seq[$a];\n      $hseq{$n}{com}=$com[$a]\
;\n     \n      }\n    return %hseq;\n  }\n\nsub 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    return 0;\n  }\n\
            \n    \nsub file2string\n  {\n    my $f=@_[0];\
\n    my $string, $l;\n    open (F,\"$f\");\n    w\
hile (<F>)\n      {\n\n $l=$_;\n        #chomp ($l);\n  $s\
tring.=$l;\n      }\n    close (F);\n    $string=~\
s/\\r\\n//g;\n    $string=~s/\\n//g;\n    return $\
string;\n  }\n\n\nsub my_get_opt\n  {\n    my @lis\
t=@_;\n    my $cl, $a, $argv, @argl;\n    \n    @a\
rgl=();\n    $cl=shift @list;\n    for ( $a=0; $a<\
=$#list; $a+=3)\n      {\n      $option=$list[$a];\n    $o\
ptional=$list[$a+1];\n  $status=$list[$a+2];\n  $arg\
v=\"\";\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 req\
uirement\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 && $ar\
gv eq \"\")\n     {\n       print STDERR \"ERROR: Opti\
on $option must be set [FATAL:$program/$mode/$meth\
od]\\n\";\n         myexit ($EXIT_FAILURE);\n     }\n   if\
 ($status==0){;}\n      elsif ($status ==1 && $argv ne \
\"\" && !-e $argv)\n      {\n       print STDERR \"ERRO\
R: File $argv must exist [FATAL:$program/$mode/$me\
thod]\\n\";\n       myexit ($EXIT_FAILURE);\n     }\n   \
elsif ( $status==2 && $argv ne \"\" && &check_pg_i\
s_installed ($argv)==0)\n         {\n       print STDERR \\
"ERROR: $argv is not installed [FATAL:$program/$mo\
de/$method]\\n\";\n         myexit ($EXIT_FAILURE);\n   \
  }\n      }\n\n    return @argl;\n    }\n\nsub ta\
g2value \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    $t\
ag=~/id=\"(\\S+)\"/;\n    $pdbid=$1;\n    $pdbid=~\
s/_//;\n    return $pdbid;\n  }\nsub id2pdbid \n  \
{\n    my $in=@_[0];\n    my $id;\n    \n    $in=~\
/(\\S+)/;\n    $id=$in;\n    \n    if ($id =~/pdb/\
)\n      {\n    $id=~/pdb(.*)/;\n       $id=$1;\n      }\n \
   $id=~s/[|��_]//g;\n    return $id;\n  }\nsu\
b set_blast_type \n  {\n    my $file =@_[0];\n    \
if (&file_contains ($file,\"EBIApplicationResult\"\
,100)){$BLAST_TYPE=\"EBI\";}\n    elsif (&file_con\
tains ($file,\"NCBI_BlastOutput\",100)) {$BLAST_TY\
PE=\"NCBI\";}\n    else\n      {\n      $BLAST_TYPE=\"\\
";\n      }\n    return $BLAST_TYPE;\n  }\nsub bla\
st_xml2profile \n  {\n    my ($name,$seq,$maxid, $\
minid, $mincov, $file)=(@_);\n    my (%p, $a, $str\
ing, $n);\n    \n\n\n    if ($BLAST_TYPE eq \"EBI\\
" || &file_contains ($file,\"EBIApplicationResult\\
",100)){%p=ebi_blast_xml2profile(@_);}\n    elsif \
($BLAST_TYPE eq \"NCBI\" || &file_contains ($file,\
\"NCBI_BlastOutput\",100)){%p=ncbi_blast_xml2profi\
le(@_);}\n    else \n      {\n  print \"***********\
* ERROR: Blast Returned an unknown XML Format ****\
******************\";\n myexit ($EXIT_FAILURE);\n \
     }\n    for ($a=0; $a<$p{n}; $a++)\n      {\n       \
my $name=$p{$a}{name};\n        $p{$name}{seq}=$p{$a}{seq\
};\n      }\n    return %p;\n  }\nsub ncbi_blast_x\
ml2profile \n  {\n    my ($name,$seq,$maxid, $mini\
d, $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, $expectation, $start\
, $end, $coverage, $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  $de\
finition=$DE{0}{body};\n        \n      %HSP=&xml2tag_list ($h\
it{$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}, \"H\
sp_query-from\");\n         %HSTART=&xml2tag_list ($HS\
P{$b}{body}, \"Hsp_hit-from\");\n           \n      %LEN=\
  &xml2tag_list ($HSP{$b}{body}, \"Hsp_align-len\"\
);\n        %END=  &xml2tag_list ($HSP{$b}{body}, \"H\
sp_query-to\");\n           %HEND=  &xml2tag_list ($HSP{\
$b}{body}, \"Hsp_hit-to\");\n       %E=&xml2tag_list\
     ($HSP{$b}{body}, \"Hsp_evalue\");\n            %I=&x\
ml2tag_list     ($HSP{$b}{body}, \"Hsp_identity\")\
;\n         %Q=&xml2tag_list     ($HSP{$b}{body}, \"Hs\
p_qseq\");\n        %M=&xml2tag_list     ($HSP{$b}{bo\
dy}, \"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              $en\
d=$END{$e}{body};\n             $Hstart=$HSTART{$e}{body};\n    \
        $Hend=$HEND{$e}{body};\n        \n              $coverage=(($end-$st\
art)*100)/$L;\n\n       \n              if ($identity>$maxid || $ide\
ntity<$minid || $coverage<$mincov){next;}\n             @lr1=\
(split (//,$qs));\n             @lr2=(split (//,$ms));\n                $l=\
$#lr1+1;\n              for ($c=0;$c<$L;$c++){$p[$nhits][$c]=\\
"-\";}\n                for ($d=0,$c=0; $c<$l; $c++)\n            {\n            \
   $r=$lr1[$c];\n                   if ( $r=~/[A-Za-z]/)\n                 \
   {\n                  \n                      $p[$nhits][$d + $start-1]=$lr2[$c];\\
n                       $d++;\n               }\n                 }\n           $Qseq[$nhits]=$qs;\\
n               $Hseq[$nhits]=$ms;\n            $QstartL[$nhits]=$start;\\
n               $HstartL[$nhits]=$Hstart;\n             $identityL[$nhits]\
=$identity;\n           $endL[$nhits]=$end;\n           $definitionL\
[$nhits]=$definition;\n         $identifyerL[$nhits]=$ide\
ntifyer;\n              $comment[$nhits]=\"$ldb|$identifyer [E\
val=$expectation][id=$identity%][start=$Hstart end\
=$Hend]\";\n            $nhits++;\n           }\n         }\n      }\n\
    \n    $profile{n}=0;\n    $profile{$profile{n}\
}{name}=$name;\n    $profile{$profile{n}}{seq}=$se\
q;\n    $profile {n}++;\n    \n    for ($a=0; $a<$\
nhits; $a++)\n      {\n $n=$a+1;\n      \n      $profile{$n}\
{name}=\"$name\\_$a\";\n        $profile{$n}{seq}=\"\";\n\
        $profile{$n}{Qseq}=$Qseq[$a];\n $profile{$n}{Hseq\
}=$Hseq[$a];\n  $profile{$n}{Qstart}=$QstartL[$a];\\
n       $profile{$n}{Hstart}=$HstartL[$a];\n    $profile{$n\
}{identity}=$identityL[$a];\n   $profile{$n}{definit\
ion}=$definitionL[$a];\n        $profile{$n}{identifyer}=\
$identifyerL[$a];\n     $profile{$n}{comment}=$comment\
[$a];\n for ($b=0; $b<$L; $b++)\n         {\n       if ($p\
[$a][$b])\n           {\n               $profile{$n}{seq}.=$p[$a][$\
b];\n         }\n           else\n            {\n               $profile{$n}\
{seq}.=\"-\";\n       }\n         }\n      }\n    \n    \
$profile{n}=$nhits+1;\n    return %profile;\n  }\n\
sub ebi_blast_xml2profile \n  {\n    my ($name,$se\
q,$maxid, $minid, $mincov, $string)=(@_);\n    my \
($L,$l, $a,$b,$c,$d,$nhits,@identifyerL,$identifye\
r);\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, $ex\
pectation, $start, $end, $coverage, $r);\n      my (%Q,\
%M,%E,%I);\n    \n      $ldb=&tag2value ($hit{$a}{open}, \\
"database\");\n $identifyer=&tag2value ($hit{$a}{o\
pen}, \"id\");\n\n      $description=&tag2value ($hit{$\
a}{open}, \"description\");\n   \n      %Q=&xml2tag_list \
($hit{$a}{body}, \"querySeq\");\n       %M=&xml2tag_list\
 ($hit{$a}{body}, \"matchSeq\");\n      %E=&xml2tag_lis\
t ($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     $qs=$Q{$b}{bod\
y};\n       $ms=$M{$b}{body};\n     \n      $expectat\
ion=$E{$b}{body};\n         $identity=$I{$b}{body};\n   \
    \n              \n      $start=&tag2value ($Q{$b}{o\
pen}, \"start\");\n         $end=&tag2value ($Q{$b}{op\
en}, \"end\");\n            $startM=&tag2value ($M{$b}{op\
en}, \"start\");\n          $endM=&tag2value ($M{$b}{op\
en}, \"end\");\n            $coverage=(($end-$start)*100)\
/$L;\n      \n     # print \"$id: ID: $identity COV:\
 $coverage [$start $end]\\n\";\n            \n      \n     \
 if ($identity>$maxid || $identity<$minid || $cove\
rage<$mincov){next;}\n      # print \"KEEP\\n\";\n\\
n           \n      @lr1=(split (//,$qs));\n        @lr2=(sp\
lit (//,$ms));\n            $l=$#lr1+1;\n           for ($c=0;$\
c<$L;$c++){$p[$nhits][$c]=\"-\";}\n         for ($d=0,\
$c=0; $c<$l; $c++)\n          {\n               $r=$lr1[$c];\n          if\
 ( $r=~/[A-Za-z]/)\n              {\n               \n              $p[$nhits\
][$d + $start-1]=$lr2[$c];\n                $d++;\n               }\n    \
     }\n          \n        \n      $identifyerL[$nhits]=$ide\
ntifyer;\n          $comment[$nhits]=\"$ldb|$identifyer\
 [Eval=$expectation][id=$identity%][start=$startM \
end=$endM]\";\n     $nhits++;\n   }\n      }\n    \
\n    $profile{n}=0;\n    $profile{$profile{n}}{na\
me}=$name;\n    $profile{$profile{n}}{seq}=$seq;\n\
    $profile {n}++;\n    \n    for ($a=0; $a<$nhit\
s; $a++)\n      {\n     $n=$a+1;\n      $profile{$n}{name}=\
\"$name\\_$a\";\n       $profile{$n}{seq}=\"\";\n       $profi\
le{$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               $prof\
ile{$n}{seq}.=$p[$a][$b];\n           }\n           else\n       \
     {\n                $profile{$n}{seq}.=\"-\";\n           }\n         \
}\n      }\n    $profile{n}=$nhits+1;\n    \n    r\
eturn %profile;\n  }\nsub output_profile\n  {\n   \
 my ($name,%profile)=(@_);\n    my ($a);\n    open\
 (P, \">$name\");\n    for ($a=0; $a<$profile{n}; \
$a++)\n      {\n        print P \">$profile{$a}{name} $pr\
ofile{$a}{comment}\\n$profile{$a}{seq}\\n\";\n    \
  }\n    close (P);\n    return;\n  }\nsub blast_x\
ml2hit_list\n  {\n    my $string=(@_[0]);\n    ret\
urn &xml2tag_list ($string, \"hit\");\n  }\nsub xm\
l2tag_list  \n  {\n    my ($string_in,$tag)=@_;\n \
   my $tag_in, $tag_out;\n    my %tag;\n    \n    \
if (-e $string_in)\n      {\n   $string=&file2string\
 ($string_in);\n      }\n    else\n      {\n    $stri\
ng=$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    $t\
ag{n}=0;\n    $in=0;$n=-1;\n  \n \n\n    foreach $\
t (@l)\n      {\n\n     $t=~s/<#//;\n   $t=~s/#>//;\n   \n\
        if ( $t=~/$tag_in1/ || $t=~/$tag_in2/)\n          {\n    \\
n           $in=1;\n        $tag{$tag{n}}{open}=$t;\n       $\
n++;\n      \n    }\n   elsif ($t=~/$tag_out/)\n          {\n\
            \n\n            $tag{$tag{n}}{close}=$t;\n      $tag{\
n}++;\n     $in=0;\n      }\n   elsif ($in)\n     {\n      \
\n          $tag{$tag{n}}{body}.=$t;\n    }\n      }\n  \
\n    return %tag;\n  }\n\n\nsub seq2gor_predictio\
n \n  {\n    my ($name, $seq,$infile, $outfile, $g\
or_seq, $gor_obs)=(@_);\n    my ($l);\n    \n    `\
gorIV -prd $infile -seq $gor_seq -obs $gor_obs > g\
or_tmp`;\n    open (GR, \">$outfile\");\n    open \
(OG, \"gor_tmp\");\n\n    while (<OG>)\n      {\n       \
\n      $l=$_;\n        if ($l=~/\\>/){print GR \"$l\";}\n      els\
if ( $l=~/Predicted Sec. Struct./)\n      {\n       $l=\
~s/Predicted Sec. Struct\\.//;\n            print GR \"$l\
\";\n     }\n      }\n    close (GR);\n    close (OG\
);\n    return;\n  }\nsub seq2msa_tm_prediction \n\
  {\n    my ($name, $seq,$infile, $outfile, $arch,\
 $psv)=(@_);\n    my (%p,%gseq,%R, $blast_output, \
%s, $l);\n    \n    $blast_output=&run_blast ($nam\
e,\"blastp\", \"uniprot\", $infile, \"outfile\");\\
n    \n    \n    %p=blast_xml2profile($name,$seq,$\
maxid, $minid,$mincov,$blast_output);\n    \n    \\
n    open (F, \">tm_input\");\n    for ($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_seq2hmmt\
op_fasta.pl -in=tm_input -out=tm_output -arch=$arc\
h -psv=$psv\");\n    unlink (\"tm_input\");\n    %\
gs=read_fasta_seq(\"tm_output\");\n    foreach $s \
(keys(%gs))\n      {\n  my (@list, $seq, @plist, @p\
seq, $L, $PL);\n        \n      \n      #Prediction\n   $seq=$gs{$s}{\
seq};\n $seq=uc($seq);\n        $L=length($seq);\n      @list=\
split //, $seq;\n       \n      #Original Profile Sequence\n    \
$pseq=$p{$s}{seq};\n    $pseq=uc($pseq);\n      $PL=length\
($pseq);\n      @plist=split //, $pseq;\n       \n      for ($c=0,\
$b=0; $b<$PL; $b++)\n     {\n       my $r=$plist[$b];\\
n           if($r ne \"-\" && $r ne \"X\")\n          {\n               \
$r=$plist[$b]=$list[$c++];\n          }\n         }\n   \n      if\
 ($c!=$L)\n       {\n       print \"ERROR: Could Not Thr\
ead the Prediction Back [FATAL:tc_generic_method.p\
l]\\n\";\n          myexit ($EXIT_FAILURE);\n     }\n   for\
 ($b=0;$b<$PL; $b++)\n    {\n       my $r=$plist[$b];\
\n          if ( $r ne \"-\" && $r ne \"X\")\n        {\\
n               $R{$b}{$r}++;\n      }\n          }\n      }\n    $L=l\
ength ($p{0}{seq});\n    open (R2, \">$outfile\");\
\n    print R2 \">$name\\n\";\n    \n    for ($a=0\
; $a<$L; $a++)\n      {\n       \n      my ($v,$v_max,$r,$r_m\
ax, @rl);\n     \n      $v=$v_max=0;\n  @rl=keys (%{$R{$a}})\
;\n     foreach $r (@rl)\n        {\n\n     $v=$R{$a}{$r};\\
n           if ($v>=$v_max)\n         {\n               $v_max=$v;\n            $\
r_max=$r;\n           }\n         }\n   print R2 \"$r_max\";\n\
      }\n    print R2 \"\\n\";\n    close (R2);\n \
   return;\n  }\nsub seq2msa_gor_prediction \n  {\\
n    my ($name, $seq,$infile, $outfile, $gor_seq, \
$gor_obs)=(@_);\n    my (%p,%gseq,%R, $blast_outpu\
t, %s, $l);\n    \n    \n    $blast_output=&run_bl\
ast ($name,\"blastp\", \"uniprot\", $infile, \"out\
file\");\n    %p=blast_xml2profile($name,$seq,$max\
id, $minid,$mincov,$blast_output);\n    \n    open\
 (F, \">gor_input\");\n    for ($a=0; $a<$p{n}; $a\
++)\n      {\n  my $s;\n        \n      $s=$p{$a}{seq};\n       $s=~s\
/\\-//g;\n      $s=~s/X//g;\n   \n      $s=uc($s);\n    print F \\
">$p{$a}{name}\\n$s\\n\";\n      }\n    close (F);\
\n    print \"\\tPSIGOR: kept  $p{n} Homologues fo\
r Sequence $p{0}{name}\\n\";\n    \n    `gorIV -pr\
d gor_input -seq $gor_seq -obs $gor_obs > gor_tmp`\
;\n    unlink (\"gor_input\");\n    \n    open (GR\
, \">gor_output\");\n    open (OG, \"gor_tmp\");\n\
    \n    while (<OG>)\n      {\n       \n      my $l;\n        $l=$\
_;\n    \n      if ($l=~/\\>/){print GR \"$l\";}\n      elsif (\
 $l=~/Predicted Sec. Struct./)\n          {\n       $l=~s/P\
redicted Sec. Struct\\.//;\n        print GR \"$l\";\\
n         }\n      }\n    close (GR);\n    close (OG);\n\
    \n\n    %gs=read_fasta_seq(\"gor_output\");\n \
    foreach $s (keys(%gs))\n      {\n   my (@list, $\
seq, @plist, @pseq, $L, $PL);\n \n      \n      #Prediction\\
n       $seq=$gs{$s}{seq};\n    $seq=uc($seq);\n        $L=length(\
$seq);\n        @list=split //, $seq;\n \n      #Original Prof\
ile Sequence\n  $pseq=$p{$s}{seq};\n    $pseq=uc($pseq\
);\n    $PL=length($pseq);\n    @plist=split //, $pseq;\\
n       \n      $tseq=\"\";\n   for ($c=0,$b=0; $b<$PL; $b++)\n\
          {\n       my $r=$plist[$b];\n     if($r ne \"-\" \
&& $r ne \"X\")\n             {\n               $r=$plist[$b]=$list[$\
c++];\n       }\n           $tseq.=$r;\n          }\n   \n      if ($c\
!=$L)\n   {\n       print \"ERROR: Could Not Thread \
the Prediction Back [FATAL:tc_generic_method.pl]\\\
n\";\n      print \"SEQ:$seq\\nPSEQ:$pseq\\nTSEQ:$t\
seq\";\n            \n      myexit ($EXIT_FAILURE);\n     }\\
n       for ($b=0;$b<$PL; $b++)\n         {\n       my $r=$plist\
[$b];\n     if ( $r ne \"-\" && $r ne \"X\")\n     \
   {\n          $R{$b}{$r}++;\n      }\n          }\n      }\n   \
\n    $L=length ($p{0}{seq});\n    open (R2, \">$o\
utfile\");\n    print R2 \">$name\\n\";\n    \n   \
 for ($a=0; $a<$L; $a++)\n      {\n     \n      my ($v,$v_m\
ax,$r,$r_max, @rl);\n   \n      $v=$v_max=0;\n  @rl=keys (\
%{$R{$a}});\n   foreach $r (@rl)\n        {\n\n     $v=$R\
{$a}{$r};\n         if ($v>=$v_max)\n         {\n               $v_ma\
x=$v;\n         $r_max=$r;\n          }\n         }\n   print R2 \"$\
r_max\";\n      }\n    print R2 \"\\n\";\n    clos\
e (R2);\n    return;\n  }\n\nsub run_blast\n  {\n \
   my ($name, $method, $db,$infile, $outfile, $run\
)=(@_);\n    if (!$run){$run=1;}\n    \n    \n    \
if (&cache_file(\"GET\",$infile,$name,$method,$db,\
$outfile,$SERVER)){return $outfile;}\n    else\n  \
    {\n \n      if ( $SERVER eq \"EBI\")\n        {\n       $c\
l_method=$method;\n         if ($cl_method =~/wu/)\n     \
     {\n                $cl_method=~s/wu//;\n           if ( $cl_method e\
q \"psiblast\")\n                 {\n               print STDERR \"\\n**\
*************WARNING: PSI BLAST cannot be used wit\
h the NCBI BLAST Client. Use server=EBI Or server=\
LOCAL. blastp will be used instead***********\\n\"\
;\n                 $cl_method=\"blastp\";\n              }\n           \n              $com\
mand=\"t_coffee -other_pg wublast.pl --email $EMAI\
L $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 $outfi\
le.xml $outfile`;}\n          }\n           else\n            {\\
n               if ($cl_method eq \"psiblast\"){$cl_method =\"b\
lastp -j5\";}\n         \n              $command=\"t_coffee -other_pg\
 blastpgp.pl --email $EMAIL $infile -d $db --outfi\
le $outfile -p $cl_method --mode PSI-Blast>/dev/nu\
ll 2>/dev/null\";\n             &safe_system ( $command);\n             \
\n              if (-e \"$outfile.xml\") {`mv $outfile.xml $ou\
tfile`;}\n            }\n         }\n   elsif ($SERVER eq \"NCB\
I\")\n    {\n       if ($db eq \"uniprot\"){$cl_db=\"\
nr\";}\n            else {$cl_db=$db;}\n            \n      if ( \
$method eq \"psiblast\")\n            {\n               print STDERR\
 \"\\n***************WARNING: PSI BLAST cannot be \
used with the NCBI BLAST Client. Use server=EBI Or\
 server=LOCAL. blastp will be used instead********\
***\\n\";\n             $cl_method=\"blastp\";\n              }\n         \
  else\n              {\n               $cl_method=$method;\n         }\\
n           $command=\"blastcl3 -p $cl_method -d $cl_db \
-i $infile -o $outfile -m 7\";\n            &mysystem ($c\
ommand);\n        }\n   elsif ($SERVER =~/CLIENT_(.*)/)\n\
          {\n       my $client=$1;\n        $command=\"$client\
 -p $method -d $db -i $infile -o $outfile -m 7\";\\
n           &mysystem ($command);\n       }\n   elsif ( $SERVE\
R eq \"LOCAL_blastall\")\n        {\n       if ($method e\
q \"blastp\")\n       {\n               $command=\"blastall -d \
$db -i $infile -o $outfile -m7 -p blastp\";\n       \
  }\n       &mysystem ($command);\n       }\n   elsif ( $S\
ERVER eq \"LOCAL\")\n     {\n\n     if ($ENV{\"BLAST\
_DB_DIR\"})\n         {\n               $x=$ENV{\"BLAST_DB_DIR\"}\
;\n             $cl_db=\"$x$db\";\n           }\n           else\n          \
  {\n           $cl_db=$db;\n         }\n           \n      if ($met\
hod eq \"blastp\")\n          {\n               $command=\"blastpg\
p -d $cl_db -i $infile -o $outfile -m7 -j1\";\n   \
    }\n     elsif ($method eq \"psiblast\")\n       \
  {\n           $command=\"blastpgp -d $cl_db -i $infile -o\
 $outfile -m7 -j5\";\n        }\n               elsif ($method e\
q \"blastn\")\n         {\n                     $command=\"blastall -p blas\
tn -d $cl_db -i $infile -o $outfile -m7 -W6\";\n                \
}       \n          &mysystem ($command);\n       }\n   else\n    {\\
n           print (\"*************** ERROR: $SERVER is a\
n Unknown Server***********\");\n         }\n   \n      if ( !-\
e $outfile)\n     {\n       \n      if ( $run==$BLAST_M\
AX_NRUNS)\n           {\n               print STDERR \"COM: $comman\
d\\n\";\n               print STDERR (\"BLAST failed against $n\
ame [FATAL:$mode/$method/$program]\\n\");\n             if  (\
 $SERVER eq \"EBI\" && !($method=~/wu/))\n                {\n   \
            print STDERR (\"Try WuBlast instead\");\n             \
  return run_blast ($name,\"wublastp\", $db,$infil\
e, $outfile);\n           }\n         }\n           else\n            \
{\n             print STDERR \"(Blast for $name failed  [$com\
mand][Attempt $run/$BLAST_MAX_NRUNS] [Try again]\\\
n\";\n          return run_blast ($name, $method, $db,$inf\
ile, $outfile, $run+1);\n             }\n         }\n\n &cache\
_file(\"SET\",$infile,$name,$method,$db,$outfile,$\
SERVER);\n      return $outfile;\n      }\n  }\nsub mys\
ystem \n  {\n    my $command=@_[0];\n    my $count\
=0;\n    my $r;\n    \n    while (($r=&safe_system\
($command))!=$EXIT_SUCCESS && $count<5)\n      {\n\
        print \"\\nCOMMAND $command Failed. Will try agai\
n\\n\";\n       $count++;\n      }\n    return $r;\n  }\\
nsub cache_file\n  {\n    my ($cache_mode,$infile,\
$name,$method,$db, $outfile,$server)=(@_);\n    my\
 $cache_file;\n    #Protect names so that they can\
 be turned into legal filenames\n    $name=&clean_\
file_name ($name);\n\n    if ($db=~/\\//)\n      {\
\n      $db=~/([^\\/]+)$/;\n    $db=$1;\n      }\n    $cac\
he_file_sh=\"$name.$method.$db.$server.tmp\";\n   \
 $cache_file=\"$CACHE/$name.$method.$db.$server.tm\
p\";\n    \n    if ($infile ne \"\")\n      {\n $c\
ache_file_infile_sh=\"$name.$method.$db.$server.in\
file.tmp\";\n   $cache_file_infile=\"$CACHE/$name.$m\
ethod.$db.$server.infile.tmp\";\n      }\n    \n  \
  if ($cache_mode eq \"GET\")\n      {\n        if ($CACH\
E eq \"\" || $CACHE eq \"no\" || $CACHE eq \"ignor\
e\"  || $CACHE eq \"local\" || $CACHE eq \"update\\
"){return 0;}\n elsif ( !-d $CACHE)\n     {\n       pr\
int STDERR \"ERROR: Cache Dir: $CACHE Does not Exi\
st\";\n     return 0;\n   }\n   else\n    {\n       if \
( -e $cache_file && &fasta_file1_eq_fasta_file2($i\
nfile,$cache_file_infile)==1)\n       {\n               `cp $ca\
che_file $outfile`;\n           $CACHE_STATUS=\"READ CACHE\\
";\n            return 1;\n           }\n         }\n      }\n    elsi\
f ($cache_mode eq \"SET\")\n      {\n   if ($CACHE e\
q \"\" || $CACHE eq \"no\" || $CACHE eq \"ignore\"\
  || $CACHE 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 ($cac\
he_file_infile ne \"\"){ `cp $infile $cache_file_i\
nfile`;}\n\n        #functions for updating the cache\
\n          #`t_coffee -other_pg clean_cache.pl -file $\
cache_file_sh -dir $CACHE`;\n       #`t_coffee -othe\
r_pg clean_cache.pl -file $cache_file_infile_sh -d\
ir $CACHE`;\n       return 1;\n   }\n      }\n    $C\
ACHE_STATUS=\"COMPUTE CACHE\";\n    return 0;\n  }\
\nsub file1_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    elsif ( !-e $f2){return 0;}\n    elsif ($f\
1 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    $n\
ame=~s/[^A-Za-z1-9.-]/_/g;\n    return $name;\n  }\
\nsub url2file\n  {\n    my ($address, $out)=(@_);\
\n    \n    if (&pg_is_installed (\"wget\"))\n  {\n\
          return &safe_system (\"wget $address -O$out >/d\
ev/null 2>/dev/null\");\n       }\n    elsif (&pg_is_ins\
talled (\"curl\"))\n      {\n   return &safe_system \
(\"curl $address -o$out >/dev/null 2>/dev/null\");\
\n      }\n    else\n      {\n  print stderr \"ERRO\
R: neither curl nor wget are installed. Imnpossibl\
e to fectch remote file [FATAL]\\n\";\n exit ($EXI\
T_FAILURE);\n      }\n  }\nsub fasta_file1_eq_fast\
a_file2\n  {\n    my ($f1, $f2)=@_;\n    my (%s1, \
%s2);\n    my @names;\n    %s1=read_fasta_seq (%f1\
);\n    %s2=read_fasta_seq (%f2);\n\n    @names=(k\
eys (%s1));\n    \n    foreach $n (keys(%s1))\n   \
   {\n  if ($s1{$n}{seq} ne $s2{$n}{seq}){return 0;\
}\n      } \n    \n    foreach $n (keys(%s2))\n   \
   {\n  if ($s1{$n}{seq} ne $s2{$n}{seq}){return 0;\
}\n      }\n    return 1;\n  }\n        \nsub safe_system\
 \n{\n  my $com=@_[0];\n  my $pid;\n  my $status;\\
n  if ($com eq \"\"){return 1;}\n\n\n  if (($pid =\
 fork ()) < 0){return (-1);}\n  if ($pid == 0)\n  \
  {\n      exec ($com);\n    }\n  else\n      {\n       \
$PIDCHILD=$pid;\n      }\n  \n  waitpid ($pid,WTER\
MSIG);\n  return $?; #contains the status of the e\
xit\n}\nEND {\n  kill ($PIDCHILD);\n}\n\n\nsub rea\
d_template_file\n{\n    my $pdb_templates = @_[0];\n    \
open (TEMP, \"<$pdb_templates\");\n     my %temp_h;\n   \
while (<TEMP>)\n{\n             $line = $_;\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.pep\");\n        \n      %pdb_template_\
h = &read_template_file($pdbfile);\n    my $pdb_chain\
;\n     open (R, \">result.aln\");\n\n\n        #print stdout\
 \"\\n\";\n     foreach $seq (keys(%s))\n       {\n             if ($pd\
b_template_h{$seq} eq \"\")\n           {\n                     next;\n         }\n     \
        open (F, \">seqfile\");\n               print (F \">$s{$seq}{n\
ame}\\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          safe_system (\"t_coffee -other_pg \
RNAplfold2tclib.pl -in=seqfile -out=$lib_name\");\\
n               \n              safe_system (\"secondary_struc.py seqfile \
$CACHE$pdb_chain  $lib_name\");\n               \n              if ( !-e $l\
ib_name)\n              {\n                     print STDERR (\"RNAplfold failed\
 to compute the secondary structure of $s{$seq}{na\
me} [FATAL:$mode/$method/$program]\\n\");\n                     myex\
it ($EXIT_FAILURE);\n           }\n             else\n          {\n                     print st\
dout \"\\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}\n\
\n\n\nsub seq2rna_pair{\n       my ($mode, $pdbfile1, $p\
dbfile2, $method, $param, $outfile)=@_;\n\n     if ($m\
ethod eq \"runsara.py\")\n      {\n             open(TMP,\"<$pdbfi\
le1\");\n               my $count = 0;\n                my $line;\n             while (<\
TMP>)\n         {\n                     $line = $_;\n                   if ($count ==1)\n               \
        {\n                             last;\n                 }\n                     $count += 1;\n          }\n     \n              my\
 $y = length($line);\n\n                $chain1 = substr($line,l\
ength($line)-3,1);\n            close TMP;\n            open(TMP,\"<$p\
dbfile2\");\n           my $count = 0;\n                while (<TMP>)\n         \
{\n                     $line = $_;\n                   if ($count ==1)\n                       {\n                             l\
ast;\n                  }\n                     $count += 1;\n          }\n             $chain2 = subs\
tr($line,length($line)-3,1);\n          close TMP;\n            \n              \
\n              system(\"runsara.py $pdbfile1 $chain1 $pdbfile\
2 $chain2 -s -o tmp >/dev/null 2>/dev/null\");\n                \
open(TMP,\"<tmp\") or die \"cannot open the sara t\
mp file:$!\\n\";\n              open(OUT,\">$outfile\") or die\
 \"cannot open the $outfile file:$!\\n\";\n\n           my \
$switch = 0;\n          my $seqNum = 0;\n               foreach my $lin\
e (<TMP>)\n             {\n                     next unless ($line=~/SARAALI/);\
\n                      if ($line=~/>/)\n                       {\n                             $switch =0;\n                           p\
rint OUT \">seq$seqNum\\n\";\n                          $seqNum++;                              \n\
                        }\n                     if ($switch < 2){\n                             $switch++;\n                            ne\
xt;\n                   }\n     \n                      if ($line =~/REMARK\\s+SARAALI\\s\
+([^\\*]+)\\*/)\n                       {\n                             my $string = $1;\n                              p\
rint OUT \"$string\\n\";\n                      }\n             }\n             close TMP; \
\n              close OUT;\n    }\n}$program=\"T-COFFEE (Version_\
8.07)\";\\n\n","*TC_METHOD_FORMAT_01\n************\
******generic_method.tc_method*************\n*\n* \
      Incorporating new methods in T-Coffee\n*    \
   Cedric Notredame 26/08/08\n*\n*****************\
**************************************\n*This file\
 is a method file\n*Copy it and adapt it to your n\
eed so that the method \n*you want to use can be i\
ncorporated within T-Coffee\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 using the following\n*call\
:\n*<EXECUTABLE><PARAM1><IN_FLAG><seq_file><PARAM2\
><OUT_FLAG><outname><PARAM>\n*\n*Conventions:\n*<F\
LAG_NAME>       <TYPE>          <VALUE>\n*<VALUE>:      no_name         <=>\
 Replaced with a space\n*<VALUE>:       &nbsp   <=> Replac\
ed with a space\n*\n******************************\
*************************\n*                  ALN_\
MODE                           *\n****************\
***************************************\n*pairwise\
   ->all Vs all (no self )[(n2-n)/2aln]\n*m_pairwi\
se ->all Vs all (no self)[n^2-n]^2\n*s_pairwise ->\
all Vs all (self): [n^2-n]/2 + n\n*multiple   ->Al\
l the sequences in one go\n*\nALN_MODE          pairwise\n\
*\n***********************************************\
********\n*                  OUT_MODE             \
              *\n*********************************\
**********************\n* mode for the output:\n*E\
xternal methods: \n* aln -> alignmnent File (Fasta\
 or ClustalW Format)\n* lib-> Lib file (TC_LIB_FOR\
MAT_01)\n*Internal Methods:\n* fL -> Internal Func\
tion returning a List (Librairie)\n* fA -> Interna\
l Function returning an Alignmnent\n*\nOUT_MODE         a\
ln\n**********************************************\
*********\n*                  SEQ_TYPE            \
               *\n********************************\
***********************\n*G: Genomic, S: Sequence,\
 P: PDB, R: Profile\n*Examples:\n*SEQTYPE       S       sequen\
ces against sequences (default)\n*SEQTYPE       S_P     sequ\
ence against structure\n*SEQTYPE        P_P     structure aga\
inst structure\n*SEQTYPE        PS      mix of sequences and s\
tructure        \n*\nSEQ_TYPE   S\n*\n\n*******************\
************************************\n*           \
     COMMAND LINE                         *\n*EXEC\
UTABLE PARAM1 IN_FLAG OUT_FLAG PARAM             *\
\n************************************************\
*******\n*****************************************\
**************\n*                  EXECUTABLE     \
                    *\n***************************\
****************************\n*name of the executa\
ble\n*passed to the shell: executable\n*        \nEXECUTA\
BLE     tc_generic_method.pl\n*\n*********************\
**********************************\n*             \
     IN_FLAG                             *\n******\
*************************************************\\
n*IN_FLAG\n*flag indicating the name of the in com\
ing sequences\n*IN_FLAG S no_name ->no flag\n*IN_F\
LAG S &bnsp-in&bnsp -> \" -in \"\n*\nIN_FLAG            -inf\
ile=\n*\n*****************************************\
**************\n*                  OUT_FLAG       \
                    *\n***************************\
****************************\n*OUT_FLAG\n*flag ind\
icating the name of the out-coming data\n*same con\
ventions as IN_FLAG\n*OUT_FLAG  S no_name ->no flag\
\n*if you want to redirect, pass the parameters vi\
a PARAM1\n*set OUT_FLAG to >\n*\nOUT_FLAG               -outfil\
e=\n*\n*******************************************\
************\n*                  PARAM_1          \
                    *\n***************************\
****************************\n*<EXECUTABLE><PARAM1\
><IN_FLAG><seq_file><PARAM2><OUT_FLAG><outname><PA\
RAM>\n*Parameters sent to the EXECUTABLE and speci\
fied *before* IN_FLAG \n*If there is more than 1 P\
ARAM line, the lines are\n*concatenated\n*Command_\
line: @EP@PARAM@-gapopen%e10%s-gapext%e20\n*    %s wh\
ite space\n*    %e equal sign\n*\n*PARAM1       \n*\n*\n*\n\
**************************************************\
*****\n*                  PARAM_2                 \
             *\n**********************************\
*********************\n*<EXECUTABLE><PARAM1><IN_FL\
AG><seq_file><PARAM2><OUT_FLAG><outname><PARAM>\n*\
Parameters sent to the EXECUTABLE and specified \n\
*after* IN_FLAG and *before* OUT_FLAG\n*If there i\
s more than 1 PARAM line, the lines are\n*concaten\
ated\n*\n*PARAM1        \n*\n*\n*************************\
******************************\n*                 \
 PARAM                              *\n***********\
********************************************\n*<EX\
ECUTABLE><PARAM1><IN_FLAG><seq_file><PARAM2><OUT_F\
LAG><outname><PARAM>\n*Parameters sent to the EXEC\
UTABLE and specified *after* OUT_FLAG\n*If there i\
s more than 1 PARAM line, the lines are\n*concaten\
ated\n*\nPARAM  -mode=seq_msa -method=clustalw\nPAR\
AM   -OUTORDER=INPUT -NEWTREE=core -align -gapopen\
=-15\n*\n*****************************************\
**************\n*                  END            \
                    *\n***************************\
****************************\n","*TC_METHOD_FORMAT\
_01\n***************clustalw_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","$VersionTa\
g =                                               \
                                                  \
                                  2.43;\n$SILENT=\\
" >/dev/null 2>/dev/null\";\n$EXIT_SUCCESS=0;\n$EX\
IT_FAILURE=1;\n$INTERNET=-1;\n\n\n\n\n\nuse FileHa\
ndle;\nuse Env qw(HOME);\n\nmy %onelett_prot=&fill\
_onelett_prot();\nmy %threelett_prot=&fill_threele\
tt_prot();\nmy %onelett_RNA=&fill_onelett_RNA();\n\
my %threelett_RNA=&fill_threelett_RNA();\nmy %onel\
ett_DNA=&fill_onelett_DNA();\nmy %threelett_DNA=&f\
ill_threelett_DNA();\n\n\n\n\n\nmy %onelett = (\n'\
P' => \\%onelett_prot,\n'D' => \\%onelett_DNA,\n'R\
' => \\%onelett_RNA\n);\n\n\nmy %threelett = (\n'P\
' => \\%threelett_prot,\n'D' => \\%threelett_DNA,\\
n'R' => \\%threelett_RNA\n);\n\n\n\n\n\n\n\nif($AR\
GV[0]=~/help/ ||$ARGV[0]=~/man/ || $ARGV[0]=~/HELP\
/ || $ARGV[0]=~/Man/ || $ARGV[0] eq \"-h\"  || $AR\
GV[0] eq \"-H\"  )\n{die \"SYNTAX: extract_from_pd\
b Version $VersionTag   \n      Minimum:             [ext\
ract_from_pdb file] \n                     OR \n                             [... | ex\
tract_from_pdb]\n       Flags (Default setting on the f\
irst line)\n       -version...................[Return\
s the Version Number]\n           -force..........\
...........[Forces the file to be treated like a P\
DB file]\n                                      [R\
egenerates the header and SEQRES fields]\n        \
   -force_name................[Forces the file 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 compressed 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 wget]\n \
                                     [wget or curl\
 must be installed]\n                             \
         [ftp://ftp.gnu.org/pub/gnu/wget/]\n      \
                                [http://curl.haxx.\
se/]\n                                      [Must \
also be used to retrieve the file from a local pdb\
 copy (cf netaddress)]\n           -netaddress....\
............[Address used for the retrieving the n\
etfile]\n                                      [ht\
tp://www.rcsb.org/pdb/cgi/export.cgi/%%.pdb.gz?for\
mat=PDB&pdbId=%%&compression=gz]\n                \
                      [http://www.expasy.ch/cgi-bi\
n/get-pdb-entry.pl?%%]\n                          \
            [local -> will get the file from pdb_d\
ir (see pdb_dir)]\n           -netcompression.....\
.......[Extension if the netfile comes compressed]\
\n                                      [gz]\n    \
       -pdb_dir...................[address of the \
repertory where the pdb is installed]\n           \
                           [Supports standard ftp \
style installation OR every stru in DIR]\n        \
                              [Give the ..../pdb/s\
tructure/ dir]\n                                  \
    [If value omitted, the pg gets it from the env\
 variable PDB_DIR]\n           -netcompression_pg.\
........[gunzip]\n           -is_pdb_name........n\
ame...[Returns 1 if the name is a PDB ID, 0 otherw\
ise]\n           -get_pdb_chains.....name...[Retur\
ns the list of chains corresponding to the entry]\\
n           -get_pdb_id.........name...[Returns th\
e PDB id within the provided pdb file]\n          \
 -get_fugue_name.....name...[Turns a name into a n\
ame valid for fugue]\n                            \
          [Uses the netaddress to do so]\n         -cha\
in......FIRST..........[Extract the first chain on\
ly]\n                  A B C..........[Extract Several chai\
ns if needed]\n                ALL............[Extract al\
l the chains]   \n           -ligand.....ALL........\
....[Extract the ligands in the chain (HETATM)]\n \
                      <name1>,<name2>[Extract All \
the named lignds]\n        -ligand_only...............\
[Extract only the ligands]\n           -ligand_lis\
t...............[Extract the list of ligands]\n   \
 -coor.......<start>..<end>.[Coordinates of the fr\
agment to extract]\n                                  [Omit end to \
include the Cter]\n           -num........absolute\
.......[absolute: relative to the seq] \n         \
              file...........[file: relative to fi\
le]\n           -num_out....new............[new: s\
tart 1->L]\n                       old............\
[old: keep the file coordinates]\n           -dele\
te.....<start>..<end>.[Delete from residue start t\
o residue end]\n           -atom.......CA.............[At\
oms to include, ALL for all of them]\n                 CA \
O N.........[Indicate several atoms if needed]\n         \
  -code.......3..............[Use the 1 letter cod\
e or the 3 letters code]\n         -mode.......raw.....\
.......[Output original pdb file]\n               \
        pdb............[Output something that look\
s like pdb]\n                  fasta..........[Output the s\
equences in fasta format]\n                    simple........\
.[Output a format easy to parse in C ]\n          \
  -seq_field..ATOM...........[Field used to extrac\
t the sequence]\n                      SEQRES.........[Use the \
complete sequence]\n       -seq......................\
.[Equivalent to  -mode fasta]\n    -model......1..\
............[Chosen Model in an NMR file]\n       \
    -nodiagnostic..............[Switches Error Mes\
sages off]\n           -debug.....................\
[Sets the DEBUG ON]\n           -no_remote_pdb_dir\
.........[Do not look for a remote file]\n        \
   -cache_pdb.................[Cache Value, defaul\
t is $HOME/.t_coffee/cache, other values: NO<=> No\
 cache]\n\n      Environement Variables\n         \
  These variables can be set from the environement\
\n           Command line values with the correspo\
nding flag superseed evironement value\n          \
 NO_REMOTE_PDB_DIR..........[Prevents the program \
from searching remote file: faster]\n           PD\
B_DIR....................[Indicates where PDB file\
 must be fetched (localy)]\n\n   PROBLEMS: please c\
ontact cedric.notredame\\@europe.com\\n\";\n     exit\
 ($EXIT_SUCCESS);\n}\n\n$np=0;\n$n_para=$#ARGV;\n$\
model=1;\n$pdb_dir=$ENV{'PDB_DIR'};if ($pdb_dir){$\
pdb_dir.=\"/\";}\n$debug=$ENV{'DEBUG_EXTRACT_FROM_\
PDB'};\n\n$no_remote_pdb_dir=$ENV{NO_REMOTE_PDB_DI\
R};\n$HOME=$ENV{'HOME'};\nif ( $ENV{CACHE_4_TCOFFE\
E})\n{$cache=$ENV{CACHE_4_TCOFFEE};}\nelse\n{\n   \
 $cache=\"$HOME/.t_coffee/cache/\";\n}\n\n   \n$ne\
taddress=\"http://www.rcsb.org/pdb/files/%%.pdb.gz\
\";\n$netcompression_pg=\"gunzip\";\n$netcompressi\
on=\"gz\";\n\n  foreach ($np=0; $np<=$n_para; $np+\
+)\n{        \n    $value=$ARGV[$np];\n    \n    i\
f  ($np==0 && !($value=~/^-.*/))\n{ \n       $pdb_\
file= $ARGV[$np];\n}\n    elsif ( !($value=~/^-.*/\
))\n{\n print \"@ARGV\";\n      die;\n} \n    \n    els\
if ($value eq \"-nodiagnostic\"){$nodiagnostic=1;}\
\n    elsif ($value eq \"-force\")\n{\n $force_pdb\
=1;\n}\n    elsif ($value eq \"-force_name\")\n{\n\
        $force_name=$ARGV[++$np];\n     $force_pdb=1;\n}\n   \
 \n    elsif ($value eq \"-is_pdb_name\")\n{\n  $pd\
b_file= $ARGV[++$np];\n \n      $is_pdb_name=1;\n       \n} \\
n    elsif ($value eq \"-debug\")\n{\n  $debug=1;\n\
}\n    elsif ($value eq \"-get_pdb_chains\")\n{\n       \
$pdb_file= $ARGV[++$np];\n      $get_pdb_chains=1;\n}\n\
    elsif ($value eq \"-get_pdb_ligands\")\n{\n $g\
et_pdb_ligands=1;\n}\n    \n    elsif ($value eq \\
"-get_pdb_id\")\n{\n    $pdb_file= $ARGV[++$np];\n      $g\
et_pdb_id=1;\n  \n}\n    \n    elsif ( $value eq \"\
-get_fugue_name\")\n{\n $pdb_file= $ARGV[++$np];\n\
        $get_fugue_name=1;\n}\n    elsif ( $value eq \"-i\
nfile\")\n{\n       $pdb_file= $ARGV[++$np];\n} \n\
    elsif ($value eq \"-netfile\")\n{\n $netfile=1\
;\n     if ( !($ARGV[$np+1]=~/^-.*/)){$pdb_file= $ARGV\
[++$np];}\n}\n    elsif (  $value eq \"-num\")\n{\\
n       $numbering= $ARGV[++$np];\n}\n    elsif ( \
 $value eq \"-num_out\")\n{\n       $numbering_out\
= $ARGV[++$np];\n}\n    elsif ( $value eq \"-netad\
dress\")\n{\n   $netadress=$ARGV[++$np];\n}\n     \n\
    elsif ( $value eq \"-netcompression\")\n{\n  $\
netcompression=$ARGV[++$np];\n}\n    elsif ( $valu\
e eq \"-pdb_dir\")\n{\n  if ( !($ARGV[$np+1]=~/^-.\
*/)){$pdb_dir= \"$ARGV[++$np]/\";}\n}\n     elsif \
( $value eq \"-no_remote_pdb_dir\")\n{\n        $no_remot\
e_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=$ARGV[++$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[++$n\
p];\n}   \n    elsif ($value eq \"-coor\" )\n{\n  \
     $start= $ARGV[++$np];\n  \n       if (($ARGV[\
$np+1] eq \"\") ||($ARGV[$np+1]=~/^-.*/)){$end=\"*\
\";} \n       else {$end=   $ARGV[++$np];}     \n \
      $coor_set=1;\n}\n    elsif ($value eq \"-del\
ete\" )\n{\n       $delete_start= $ARGV[++$np];\n \
      $delete_end= $ARGV[++$np];\n       $delete_s\
et=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 \"\") && !($A\
RGV[$np+1]=~/^-.*/))\n{\n             ++$np;\n        $at\
om[$n_atom++]=  $ARGV[$np];\n         $atom_list{$AR\
GV[$np]}=1;           \n} \n       \n}\n    elsif ( $v\
alue eq \"-unfold\")\n{\n       $unfold=1;\n}\n    elsif\
 ($value eq \"-seq\" ||$value eq \"-fasta\" )\n{\n\
       $MODE=\"fasta\";\n}\n    elsif ( $value eq \
\"-version\")\n{\n      print STDERR  \"\\nextract_from\
_pdb: Version $VersionTag\\n\";\n       &myexit ($EXIT_S\
UCCESS);\n}\n    elsif ( $value eq \"-ligand\")\n{\
\n      while (!($ARGV[$np+1] eq \"\") && !($ARGV[$np+1\
]=~/^-.*/))\n{\n            ++$np;\n        $ligand=1;\n           \
 $ligand_list{$ARGV[$np]}=1;          \n} \n    $hc_chai\
n{'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_pdb] PDB_DIR\
: $pdb_dir\\n\";\n}\n\nif ( $is_pdb_name)\n{\n    \
if (remote_is_pdb_name($pdb_file, $netaddress))\n{\
\n      print \"1\";\n}\n    else\n{\n  print \"0\";\n}\\
n    exit ($EXIT_SUCCESS);\n}\n    \n\nif (!$force\
_name)\n{\n    $pdb_file=~/([^\\/]*)$/;\n    $forc\
e_name=$1;\n}\n\n$local_pdb_file=$pdb_file;\n\nif \
( $debug){print STDERR \"\\n[DEBUG: extract_from_p\
db] Scan For $local_pdb_file\\n\";}\n\n$mem=$no_re\
mote_pdb_dir;\n$no_remote_pdb_dir=1;\n$tmp_pdb_fil\
e=get_pdb_file ($local_pdb_file);\n\nif ( !-e $tmp\
_pdb_file || $tmp_pdb_file eq \"\")\n{\n    $local\
_pdb_file=$pdb_file;\n    ($local_pdb_file, $suffi\
x_chain)=&pdb_name2name_and_chain($local_pdb_file)\
;\n\n    if ($local_pdb_file)\n{\n      if ( $debug){pr\
int STDERR \"\\nSplit $pdb_file into $local_pdb_fi\
le and $suffix_chain \\n\";}\n  $tmp_pdb_file=get_p\
db_file ($local_pdb_file);\n    if ( $tmp_pdb_file ne\
 \"\")\n{\n         @c_chain=();\n          @c_chain=($suff\
ix_chain);\n        %hc_chain=();\n         $hc_chain{$su\
ffix_chain}=1;\n}\n}\n}\n\n$no_remote_pdb_dir=$mem\
;\nif ($no_remote_pdb_dir==0)\n{\n    if ( !-e $tm\
p_pdb_file || $tmp_pdb_file eq \"\")\n{\n       \n      $loca\
l_pdb_file=$pdb_file;\n ($local_pdb_file, $suffix_\
chain)=&pdb_name2name_and_chain($local_pdb_file);\\
n       if ($local_pdb_file)\n{\n           if ( $debug){print\
 STDERR \"\\nSplit $pdb_file into $local_pdb_file \
and $suffix_chain \\n\";}\n         $tmp_pdb_file=get_\
pdb_file ($local_pdb_file);    \n           if ( $tmp_pd\
b_file ne \"\")\n{\n            @c_chain=();\n          @c_chain=($s\
uffix_chain);\n         %hc_chain=();\n         $hc_chain{$suffi\
x_chain}=1;\n}\n}\n}\n}\n\nif ( $debug){print STDE\
RR \"\\n$pdb_file copied into ##$tmp_pdb_file##\\n\
\";}\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_f\
ile [FATAL:EXTRACT_FROM_PDB Version $VersionTag]\\\
n\";\n      &myexit ($EXIT_FAILURE);    \n}\n}\n\n\n\n\
\n%molecule_type=&pdbfile2chaintype($tmp_pdb_file)\
;\n\n$pdb_id=&get_pdb_id ($tmp_pdb_file);\n\nif ( \
$pdb_id eq \"\"){$pdb_id=$force_name;}\n\n@f_chain\
=&get_chain_list ($tmp_pdb_file);\n\n\n\nif ( $get\
_pdb_chains)\n{\n    print \"@f_chain\\n\";\n    &\
myexit ($EXIT_SUCCESS);\n}\nif ( $get_pdb_ligands)\
\n{\n    %complete_ligand_list=&get_ligand_list ($\
tmp_pdb_file);\n    print $complete_ligand_list{\"\
result\"};\n    &myexit ($EXIT_SUCCESS);\n}\n\nels\
if ( $get_pdb_id ||$get_fugue_name )\n{\n    if   \
 (@c_chain && $c_chain[0] eq \"FIRST\"){$pdb_id=$p\
db_id.$f_chain[0];}\n    elsif (@c_chain && $c_cha\
in[0] ne \" \"){$pdb_id=$pdb_id.$c_chain[0];}\n   \
 \n    print \"$pdb_id\\n\";\n    &myexit ($EXIT_S\
UCCESS);\n    \n}\nelsif ( $is_pdb_name)\n{\n    p\
rintf \"1\\n\";\n    &myexit ($EXIT_SUCCESS);\n}\n\
  \n\n$structure_file=vtmpnam();\n\n\n$INFILE=vfop\
en (\"$tmp_pdb_file\", \"r\"); \n$TMP=vfopen (\"$s\
tructure_file\", \"w\");\n\n$print_model=1;\n$in_m\
odel=0;\nwhile ( <$INFILE>)\n{\n  $line=$_;\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          $pr\
int_model=0;\n}\n       elsif ( $in_model==1)\n{\n          l\
ast;\n}\n}\n  if ($print_model){print $TMP $line;}\
  \n\n}\nclose ($TMP);\nclose ($INFILE);\n\n    \n\n \
 if ($numbering eq \"\"){$numbering=\"absolute\";}\
\n  if ($numbering_out eq \"\"){$numbering_out=\"n\
ew\";}\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++]=\"A\
LL\";$atom_list{$atom_list[0]}=1;}\n  if ( $seq_fi\
eld eq \"\"){$seq_field=\"ATOM\";}\n  \n  if ( $MO\
DE 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_cha\
in{' '}=1;$c_chain[0]=\" \";}\nelsif (!@c_chain){$\
hc_chain{FIRST}=1;$c_chain[0]=\"FIRST\";}#make sur\
e the first chain is taken by default\n\nif    ($h\
c_chain{ALL}) \n{\n      @c_chain=@f_chain;\n     \
 foreach $e (@c_chain){$hc_chain{$e}=1;}\n}\nelsif\
($hc_chain{FIRST})\n{\n @c_chain=($f_chain[0]);\n       \
$hc_chain{$f_chain[0]}=1;\n}\n\n\n$MAIN_HOM_CODE=&\
get_main_hom_code ($structure_file);\n$INFILE=vfop\
en ($structure_file, \"r\");\n\n\nif ( $MODE eq \"\
raw_pdb\" || $MODE eq \"raw\")\n{\n    while (<$IN\
FILE>)\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= subst\
r($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_SUC\
CESS);\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    U\
NKNOWN                                 00-JAN-00  \
 $force_name\\n\";\n}\n\n    $INFILE=vfopen ($stru\
cture_file, \"r\");\n    \n    print \"COMPND   1 \
CHAIN:\";\n    $last=pop(@c_chain);\n    foreach $\
c ( @c_chain){ print \" $c,\";}\n    if ( $last eq\
 \" \"){print \" NULL;\\n\";}\n    else \n{\n     \
 print \" $last;\\n\";\n}\n    @c_chain=(@c_chain,\
 $last);\n    \n    print \"REMARK Output of the p\
rogram extract_from_pdb (Version $VersionTag)\\n\"\
;\n    print \"REMARK Legal PDB format not Guarant\
eed\\n\";\n    print \"REMARK This format is not m\
eant to be used in place of the PDB format\\n\";\n\
    print \"REMARK The header refers to the origin\
al entry\\n\";\n    print \"REMARK The sequence fr\
om 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 an\
d Cedric Notredame\\n\";   \n    if ( $coor_set)\n\
{\n       print \"REMARK Partial chain: Start $sta\
rt 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 \"R\
EMARK Contains Coordinates of: \";\n       foreach\
 $a (@atom){print \"$a \";}\n       print \"\\n\";\
\n}  \n}\n\n\n\n\nmy $residue_index = -999;\nmy $o\
ld_c = \"TemporaryChain\";\n\nwhile (<$INFILE>) \n\
{\n     $line=$_;\n\n\n if ($line =~ /^SEQRES/)\n{\n\n\
                @field=/(\\S*)\\s*/g;\n \n      \n              $c= substr($_,11,\
1);\n\n         \n              $l=$#field;\n           for ($a=4; $a<$#field \
;)\n{\n                 if (!$onelett{$molecule_type{$c}}->{$fie\
ld[$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\
_chain_len [$n_pdb_chains]=$len;\n                      $in_chain=$c;\
\n                      $n_pdb_chains++;\n}\n   \n              for ( $a=4; $a<$#fi\
eld;$a++)\n{\n                  @{$complete_seq{$c}}->[$complete_\
seq_len{$c}++]=$field[$a];\n}\n}\n    elsif ( $lin\
e=~/^ATOM/ || ($line=~/^HETATM/ && &is_aa(substr($\
line,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,2\
1,1));\n        $CHAIN=substr($line,21,1);\n\n    $RES_NO\
=substr($line,22,4);\n  $HOM_CODE=substr ($line, 26\
, 1);\n $TEMP=substr($line,60,6);\n     \n      $TEMP=~s/\\\
s//g;\n        $AT_ID=~s/\\s//g;\n      $RES_ID=~s/\\s/\
/g;\n        $RES_NO=~s/\\s//g;\n               \n      if ( $HOM_CO\
DE ne $MAIN_HOM_CODE){next;}\n  elsif ( $already_re\
ad2{$CHAIN}{$RES_ID}{$AT_ID}{$RES_NO}){next;}\n el\
se{$already_read2{$CHAIN}{$RES_ID}{$AT_ID}{$RES_NO\
}=1;}\n \n      \n      if ($coor_set && $numbering eq \"fil\
e\" && $residue_index ne $RES_NO)\n{\n      \n      \
if ( $RES_NO<=$start){$real_start{$CHAIN}++;}\n   \
  if ( $RES_NO<=$end){$real_end{$CHAIN}++;}\n}\n        e\
lsif ($numbering eq \"absolute\")\n{\n      $real_s\
tart{$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_l\
ist[$n_pdb_atom_chains]=$c;\n     $pdb_atom_chain_le\
n [$n_pdb_atom_chains]=$len;\n    $in_atom_chain=$c\
;\n       $n_pdb_atom_chains++;\n}\n    \n      if ( $residue_\
index ne $RES_NO)\n{\n       $residue_index = $RES_\
NO;\n        @{$atom_seq{$CHAIN}}->[$atom_seq_len{$C\
HAIN}++]=$RES_ID;;\n}\n}\n\n}\nclose ($INFILE);\n\\
n\n\n\n\n\n$INFILE=vfopen ($structure_file, \"r\")\
;\nforeach $c (@c_chain)\n{\n   if    ( $seq_field e\
q \"SEQRES\"){@pdb_seq=@{$complete_seq{$c}};}\n el\
sif ( $seq_field eq \"ATOM\")  {@pdb_seq=@{$atom_s\
eq{$c}};}\n     \n\n    $full_length=$l=$#pdb_seq+1;\n          \\
n       if ( $real_end{$c}==\"*\"){$real_end{$c}=$full_l\
ength;}\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_se\
q, $delete_start, $delete_end-$delete_start+1;\n         \
  $l=$#pdb_seq;\n}\n    \n      $new_fasta_name=\"$pdb_id$\
c\";\n  if ( $coor_set)\n{\n       if ( $n_pdb_chains=\
=0){$new_fasta_name=\"$new_fasta_name$c\";}\n      $\
new_fasta_name= $new_fasta_name.\"\\_$start\\_$end\
\";\n}\n           \n   if ( $MODE eq \"pdb\")\n{\n        $nl=\
1;\n       $n=0;\n         \n      foreach $res ( @pdb_seq)\\
n               {\n             if ( !$n)\n             {\n             \n               printf \"SEQRES  %2\
d %1s %4d  \", $nl,$c, $l;\n             $nl++;\n       }\n          $\
res=~s/\\s//g;\n             \n      if ($code==1){ print\
f \"%3s \",$onelett{$molecule_type{$c}}->{$res};}\\
n            elsif  ($code==3){ printf \"%3s \",$res};\n\
             \n      $n++;                \n         if ( $n==13){$n=0;p\
rint \"\\n\";}\n}\n       if ( $n!=0){print \"\\n\"; $\
n=0;}\n}\n      elsif ( $MODE eq \"simple\")\n{\n         pri\
nt \"# SIMPLE_PDB_FORMAT\\n\";\n          if ( $new_fasta\
_name eq \" \"){$new_fasta_name=\"dummy_name\";}\n\
          print \">$new_fasta_name\\n\";\n\n      foreach $r\
es ( @pdb_seq)\n{\n           print \"$onelett{$molecu\
le_type{$c}}->{$res}\";\n}\n      print \"\\n\";\n}\n\
        elsif ( $MODE eq \"fasta\")\n{\n          $n=0;\n         prin\
t \">$new_fasta_name\\n\";\n      \n      foreach $res (\
 @pdb_seq)\n{\n\n             print \"$onelett{$molecule\
_type{$c}}->{$res}\";\n              $n++;\n         \
 if ( $n==60){print \"\\n\"; $n=0;}\n}\n          print \\
"\\n\"; \n}\n}\n\nif ( $MODE eq \"fasta\")\n{\n   \
  &myexit($EXIT_SUCCESS);\n  \n}\n\n  \n  $charcou\
nt=0;\n  $inchain=\"BEGIN\";\n  $n=0;\n  while (<$\
INFILE>) \n{\n    $line=$_;\n     \n    if ($line \
=~/^ATOM/  ||  ($line=~/^HETATM/))\n{\n $line_head\
er=\"UNKNWN\";\n        $RES_ID=substr($line,17,3);\n   $ch\
ain = substr($line,21,1);\n\n   if ($line =~/^ATOM/)\
\n{\n       $line_header=\"ATOM\";\n        $RES_ID=(&i\
s_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_I\
D,$chain)))\n{\n            $line_header=\"HETATM\";\n}\n\
        elsif ($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=$A\
T_ID=substr($line,12,4);\n      $CHAIN=substr($line,21,\
1);\n   $RES_NO=substr($line,22,4);\n   $HOM_CODE=subs\
tr ($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}{$RE\
S_ID}{$AT_ID}{$RES_NO}=1;}\n    \n      $KEY=\"ALL\";\n\n \
        if ( $RES_NO ==0){$start_at_zero=1;}\n\n        $RE\
S_NO+=$start_at_zero;    \n     \n      if ( $current_chain\
 ne $CHAIN)\n{\n            $current_chain=$CHAIN;\n        \
$pos=$current_residue=0;\n          $offset=($coor_set)\
?($real_start{$CHAIN}-1):0;\n       if    ( $seq_fie\
ld eq \"SEQRES\"){@ref_seq=@{$complete_seq{$CHAIN}\
};}\n       elsif ( $seq_field eq \"ATOM\")  {@ref_s\
eq=@{$atom_seq{$CHAIN}};}\n}\n  \n      if ($current_res\
idue != $RES_NO)\n{\n       $current_residue=$RES_NO\
;\n         if    ( $seq_field eq \"SEQRES\"){$pos=$cu\
rrent_residue;}\n           elsif ( $seq_field eq \"ATOM\
\"){$pos++;}\n}\n       \n      \n      if ($n_atom==0 || $atom_li\
st{$AT_ID}==1 || $atom_list{$KEY}==1)\n{        \n          \\
n           $do_it=(!@c_chain || $hc_chain{$CHAIN} ||$hc\
_chain{'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 ||$p\
os>$delete_end );\n         if ($ligand==0 && $line_he\
ader eq \"HETATM\" ){$do_it=0;}\n           if ($ligand_\
only==1 && $line_header eq \"ATOM\" ){$do_it=0;}\n\
            if ($ligand==1 && $line_header eq \"HETATM\" \
&& $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 ( \
$delete_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 ( $\
numbering_out eq \"old\"){$out_pos=$RES_NO;}\n     \
    \n       \n        \n              if ( $code==1){$R\
ES_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                 prin\
tf \"%-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\
_ID eq \"\"){$RES_ID=\"X\";}\n            printf \"%-6s %5\
s %s %2s %4d    %8.3f %8.3f %8.3f\\n\",$line_heade\
r, $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\n\
if ( $error ne \"\") \n{$error=$error.\"\\nDiagnos\
tic:    SEQRES and the residues in ATOM are probab\
ly Incompatible\\n\";\n    $error=$error.  \"Recom\
endation: Rerun with '-fix 1' in order to ignore t\
he SEQRES sequences\\n\";\n}\nif (!$nodiagnostic){\
print STDERR $error;}\n&myexit ( $EXIT_SUCCESS);\n\
\nsub remote_is_pdb_name \n{\n    my $in=@_[0];\n \
   my $netaddress=@_[1];\n    my $ref_file, $pdb;\\
n    my $value;\n\n    if ( $in=~/[^\\w\\d\\:\\_]/\
){return 0;}\n    \n    \n    $ref_file=\"$cache/p\
db_entry_type.txt\";\n    \n    if ( !-e $ref_file\
 || (-M $ref_file)>2 || -z $ref_file)\n{\n      &url2fi\
le(\"ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_\
entry_type.txt\", $ref_file);\n}\n \n    $pdb=subs\
tr ($in,0, 4);\n    \n    \n    $value=`grep -c $p\
db $ref_file`;\n    return $value;\n}\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 (/^HEADER/)\n{\\
n           close $F;\n     return 1;\n}\n      elsif ( /^SEQ\
RES/)\n{\n          close $F;\n     return 1;\n}\n      elsi\
f ( /^ATOM/)\n{\n           close $F;\n     return 1;\n}\
\n}\n    return 0;\n}\nsub get_pdb_id\n{\n    my $\
header_file=@_[0];\n    my $id;\n    \n\n    $F=vf\
open (\"$header_file\", \"r\");\n\n    while ( <$F\
>)\n{\n \n      if ( /HEADER/)\n{\n         $id=substr($_,6\
2,4 );\n            return $id;\n}\n}\n    close ($F);\n \
   \n    return \"\";\n}\n\nsub get_ligand_list\n{\
\n    my $pdb_file=@_[0];\n    my $chain;\n    my \
$ligand;\n    my %complete_ligand_list;\n    \n\n \
   $F=vfopen ($pdb_file, \"r\");\n    while ( <$F>\
)\n{\n  if ( /^HETATM/)\n{\n        $line=$_;\n     $c\
hain=substr($line,21,1);\n          $ligand=substr($lin\
e,17,3);\n          \n      if (!$complete_ligand_list{$\
chain}{$ligand})\n{\n           \n              $complete_ligand_list{\\
"result\"}.=\"CHAIN $chain LIGAND $ligand\\n\";\n       \
        $complete_ligand_list{$chain}{$ligand}=1;\n}\n}\n\
}\n    close ($F);\n    return %complete_ligand_li\
st;\n}\n\nsub get_chain_list \n{\n    my $header_f\
ile;\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       \n\
            \n      if ($chain && !$hasch{$chain}){$hasch{\
$chain}=1;push @chain_list, $chain;}\n}\n       if (/^AT\
OM/ || /^HETATM/)\n{\n      $chain = substr($_,21,1\
); $chain=~s/\\s//g;if ( $chain eq \"\"){$chain=\"\
 \";}\n     if ($chain && !$hasch{$chain}){$hasch{\
$chain}=1;push @chain_list, $chain;}\n}\n}\n    \n\
   \n    close ($F);\n    if (!@chain_list)\n{\n        @\
chain_list=(\"A\");\n}\n    return @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]){return $a;}\n}\n}\
\n\nsub pdb_name2name_and_chain \n{\n    my $pdb_f\
ile=@_[0];\n    my $pdb_file_in;\n    my @array;\n\
    my $chain;\n    my $c;\n\n    $pdb_file_in=$pd\
b_file;\n\n    $pdb_file=~/^(.{4})/;$pdb_id=$1;\n \
   @array=($pdb_file=~/([\\w])/g);\n  \n  \n    $c\
hain=uc ($array[4]);\n    $chain=($chain eq \"\")?\
\"FIRST\":$chain;\n    \n    return ( $pdb_id, $ch\
ain);\n\n    if ( $#array==3){return ($pdb_id, \"F\
IRST\");}\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 %hom, $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    $pdb_file=($pdb_fi\
le_in=~/\\S+_S_(\\S+)/)?$1:$pdb_file_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_remot\
e_pdb_dir=0;\n  if ( $result){return $result;}\n        el\
se\n{\n     \n      lc ($pdb_file);\n       $result=g\
et_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 $p\
db_file_in=@_[0];\n    my $result;\n    my @letter\
;\n    my @chain;\n    my $lcfile;\n    my $ucfile\
;\n    my $pdb_file=$pdb_file_in;\n    \n    $lcfi\
le=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 $result\
;}\n    if ($ucfile ne $pdb_file && ($result=get_p\
db_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 ( ($resul\
t=get_pdb_file1 ($pdb_file))){$return_value=$resul\
t;}\n    elsif ( !($pdb_file=~/\\.pdb/) && !($pdb_\
file=~/\\.PDB/))\n{\n   if ( ($result=get_pdb_file1 \
(\"$pdb_file.pdb\"))){$return_value=$result;}\n el\
sif ( ($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_pdb\
_file1 (\"PDB$pdb_file.pdb\"))){$return_value=$res\
ult;}\n \n      \n      elsif ( ($result=get_pdb_file1 (\"$p\
db_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=$resu\
lt;}\n\n        elsif ( ($result=get_pdb_file1 (\"$pdb_fi\
le.ENT\"))){$return_value=$result;}\n   elsif ( ($re\
sult=get_pdb_file1 (\"pdb$pdb_file.ENT\"))){$retur\
n_value=$result;}\n     elsif ( ($result=get_pdb_file1\
 (\"PDB$pdb_file.ENT\"))){$return_value=$result;}\\
n       \n      \n      \n}\n    return $return_value;\n}\n    \ns\
ub 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_p\
db_file0 (\"$pdb_file.Z\"))){$return_value=$result\
;}\n    elsif ( ($result=get_pdb_file0 (\"$pdb_fil\
e.gz\"))){$return_value=$result;}\n    elsif ( ($r\
esult=get_pdb_file0 (\"$pdb_file.GZ\"))){$return_v\
alue=$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_fil\
e;    \n    my $return_value;\n\n    if ( !$attemp\
t){$attempt=1;}\n    \n    $local_pdb_file=\"$pdb_\
file\";\n    if ( $local_pdb_file eq \"\")\n{\n $t\
mp_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 ( $l\
ocal_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_file4compress\
ion ($local_pdb_file);\n    if ( -e $local_pdb_fil\
e && (&is_pdb_file ($local_pdb_file) || $force_pdb\
))\n{\n &debug_print ( \"\\n\\tIs in Current Dir\"\
);\n    $tmp_pdb_file=vtmpnam();\n      `cp $local_pdb_fil\
e $tmp_pdb_file`;\n     return $tmp_pdb_file;\n}\n    \
else\n{\n       &debug_print (\"\\n\\tFile Not in Curren\
t Dir\");\n}\n\n    if ($pdb_file=~/^pdb/||$pdb_fi\
le=~/^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_f\
ile\";\n    $local_pdb_file=&check_pdb_file4compre\
ssion ( $local_pdb_file);\n    &debug_print (\"\\n\
Try 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_print ( \"\\n\
\\tIs in Local PDB DIR\");\n    $tmp_pdb_file=vtmpnam\
();\n   `cp $local_pdb_file $tmp_pdb_file`;\n   return\
 $tmp_pdb_file;\n}\n\n    $local_pdb_file=\"$pdb_d\
ir/$pdb_file\";\n    $local_pdb_file=&check_pdb_fi\
le4compression ( $local_pdb_file);\n    &debug_pri\
nt (\"\\nTry access file From PDB_DIR: local_pdb_f\
ile\");\n    if ($pdb_dir && -e $local_pdb_file &&\
 &is_pdb_file ($local_pdb_file))\n{\n   &debug_print\
 ( \"\\n\\tIs in Local PDB DIR\");\n    $tmp_pdb_file\
=vtmpnam();\n   `cp $local_pdb_file $tmp_pdb_file`;\\
n       return $tmp_pdb_file;\n}\n\n    $local_pdb_file=\
\"$pdb_dir$pdb_file\";\n    $local_pdb_file=&check\
_pdb_file4compression ( $local_pdb_file);\n    &de\
bug_print (\"\\nTry access file From PDB_DIR: $loc\
al_pdb_file\");\n    if ($pdb_dir && -e $local_pdb\
_file && &is_pdb_file ($local_pdb_file))\n{\n   &deb\
ug_print ( \"\\n\\tIs in Local PDB DIR\");\n    $tmp_\
pdb_file=vtmpnam();\n   `cp $local_pdb_file $tmp_pdb\
_file`;\n       return $tmp_pdb_file;\n}\n    else\n{&de\
bug_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_p\
db_file=&check_pdb_file4compression ( $local_pdb_f\
ile);\n &debug_print(\"\\nTry access file From Cac\
he: $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          $tm\
p_pdb_file=vtmpnam();\n     `cp $local_pdb_file $t\
mp_pdb_file`;\n     return $tmp_pdb_file;\n}\n  els\
e{&debug_print ( \"\\n\\tNot in Cache Dir\");}\n}\\
n\n    if (!$no_remote_pdb_dir) \n{\n\n my $return\
_value=\"\";\n  if ( &remote_is_pdb_name ($pdb_file\
, $netaddress)==1)\n{\n     &debug_print (\"\\n***\
**************************************************\
**\\nTry Remote Access for $pdb_file\");\n          $tm\
p_pdb_file=vtmpnam();\n     $netcommand=$netaddres\
s;\n        $netcommand=~s/%%/$pdb_file/g;\n        &url\
2file(\"$netcommand\", \"$tmp_pdb_file.$netcompres\
sion\");\n          &debug_print(\"\\nREMOTE: $netcomma\
nd\\n\");\n        \n       $compressed_tmp_file_name=\"\
$tmp_pdb_file.$netcompression\";\n          \n      if (\
$netcompression && -B $compressed_tmp_file_name)\n\
{\n             my $r;\n                &debug_print (\"\\n\\tFile Found Re\
motely\");\n            if (($r=safe_system ( \"$netcompress\
ion_pg $compressed_tmp_file_name\")!=$EXIT_SUCCESS\
) && $attempts<5)\n{\n              &debug_print (\"\\n\\t\
Proper Download Failed Try again\");\n              unlink\
 $compressed_tmp_file_name;\n               print \"\\nFail\
ed to Download $compressed_tmp_file_name. New Atte\
mpt $attempt/5\\n\";\n              return &get_pdb_file0(\
$pdb_file, $attempt+1);\n}\n            elsif ($r== $EXIT_SU\
CCESS)\n{\n                 &debug_print (\"\\n\\tProper Down\
load Succeeded \");\n               $return_value=$tmp_pdb_\
file;\n}\n              else\n{\n                   &debug_print (\"\\n\\tP\
roper Download Failed \");\n                &debug_print (\"\
\\nFile Not Found Remotely\");\n                    unlink $comp\
ressed_tmp_file_name;\n}\n}\n       else\n{\n           &debu\
g_print (\"\\nFile Not Found Remotely\");\n             unlin\
k $compressed_tmp_file_name;\n}\n           if ($cache n\
e \"no\" && $cache ne \"update\" && -e $return_val\
ue)\n{\n                `cp $return_value $cache/$pdb_file.pdb`;\
\n}\n}\n        &debug_print (\"\\nRemote Download Finish\
ed\");\n        return $return_value;\n}\n    return \"\"\
;\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 $t\
mp`;`gunzip $tmp.Z $SILENT`;$r=$tmp;}\n    elsif (\
-B $file && ($file=~/\\.gz/)){`cp $file $tmp.gz`;`\
gunzip $tmp.gz $SILENT`;return $r=$tmp;}\n    elsi\
f (-B $file ){`cp $file $tmp.gz`;`gunzip $tmp.gz $\
SILENT`;$r=$tmp;}\n    elsif ( -e $file ) {$r= $fi\
le;}\n    elsif ( -e \"$file.gz\" ){ `cp $file.gz \
$tmp.gz`;`gunzip     $tmp.gz $SILENT`;$r=$tmp;}   \
 \n    elsif ( -e \"$file.Z\") {`cp $file.Z  $tmp.\
Z`; `gunzip $tmp.Z $SILENT`;$r=$tmp;}\n    else  {\
$r= $file;}\n\n    if ( -e \"$tmp.Z\"){unlink \"$t\
mp.Z\";}\n    if ( -e \"$tmp.gz\"){unlink \"$tmp.g\
z\";}\n    \n    return $r;\n    \n}\n\nsub vtmpna\
m\n{\n    my $tmp_file_name;\n    $tmp_name_counte\
r++;\n    $tmp_file_name=\"tmp_file_for_extract_fr\
om_pdb$$.$tmp_name_counter\";\n    $tmp_file_list[\
$ntmp_file++]=$tmp_file_name;\n    if ( -e $tmp_fi\
le_name) {return &vtmpnam ();}\n    else {return $\
tmp_file_name;}\n}\n\n\n\n    \n\n\nsub safe_syste\
m \n{\n  my $com=@_[0];\n  my $pid;\n  my $status;\
\n  if ($com eq \"\"){return 1;}\n  if (($pid = fo\
rk ()) < 0){return (-1);}\n  if ($pid == 0)\n{\n  \
    exec ($com);\n}\n  else\n{\n        $PIDCHILD=$pid;\n\
}\n  \n  waitpid ($pid,WTERMSIG);\n  return $?; #c\
ontains the status of the exit\n}\nEND {\n  kill (\
$PIDCHILD);\n  clean(@tmp_file_list);\n}\nsub myex\
it\n{\n    my $exit_status=@_[0];\n    \n    &clea\
n(@tmp_file_list);\n    exit ( $exit_status);\n}\n\
\nsub clean\n{\n  my @fl=@_;\n  my $file;\n  \n\n \
  if ( $debug){print STDERR \"remove $#fl files\\n\
\";}\n\n  foreach $file ( @fl)\n{\n      if (-e $f\
ile)\n{\n         if ( $debug){print STDERR \"\\n$file [\
NOT DELETED]\";}\n        else{unlink ($file);} \n}\n}\\
n}\nsub vfopen \n{\n    my $file=@_[0];\n    my $m\
ode=@_[1];\n    my $tmp;\n    my $F = new FileHand\
le;\n    \n    \n    $tmp=$file;\n      \n    \n    if \
( $mode eq \"r\" && !-e $file){ die \"Cannot open \
file $file [FATAL: EXTRACT_FROM_PDB]\\n\";}\n    e\
lsif ($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 - $message [DEBUG:extract_from_pdb]\";}\n    r\
eturn;\n}\nsub is_aa \n{\n    my ($aa, $chain) =@_\
;\n\n    my $one;\n    my $trhee;\n    \n    if ( \
$onelett{$molecule_type{$chain}}->{$aa} eq 'X' || \
!$onelett{$molecule_type{$chain}}->{$aa} ){return \
'';}\n    else\n{\n     $one=$onelett{$molecule_type{$\
chain}}->{$aa};\n\n     $three=$threelett{$molecule_ty\
pe{$chain}}->{$one};\n  \n\n    return $three;\n}\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    $r=`which $p 2>/dev/null`;\n    \
if ($r eq \"\"){return 0;}\n    else {return 1;}\n\
}\nsub check_pg_is_installed\n{\n    my @ml=@_;\n \
   my $r=&pg_is_installed (@ml);\n    if (!$r)\n{\\
n       print STDERR \"\\nProgram $p Supported but Not I\
nstalled on your system [FATAL:tc_generic_method]\\
\n\";\n myexit ($EXIT_FAILURE);\n}\n    else\n{\n       \
return 1;\n}\n}\n\nsub url2file\n{\n    my ($addre\
ss, $out, $wget_arg, $curl_arg)=(@_);\n    my ($pg\
, $flag, $r, $arg, $count);\n    \n    if ( $INTER\
NET==-1)\n{\n   $INTERNET=1;\n  $INTERNET=&check_inte\
rnet_connection();\n}\n    if ($INTERNET==0){exit(\
$EXIT_FAILURE);}\n   \n    if (&pg_is_installed (\\
"wget\"))   {$pg=\"wget\"; $flag=\"-O\";$arg=$wget\
_arg;}\n    elsif (&pg_is_installed (\"curl\")){$p\
g=\"curl\"; $flag=\"-o\";$arg=$curl_arg;}\n    els\
e\n{\n  print stderr \"ERROR: neither curl nor wget\
 are installed. Imnpossible to tectch remote file \
[FATAL]\\n\";\n exit ($EXIT_FAILURE);\n}\n   \n   \
 $r=safe_system (\"$pg $flag$out $address >/dev/nu\
ll 2>/dev/null\");\n    if ($r!=$EXIT_SUCCESS)\n{\\
n       unlink $file;\n}\n    return $r;\n}\n\n\n\nsub c\
heck_internet_connection\n{\n    my $internet;\n  \
  \n    if ( -e \"x\"){unlink (\"x\");}\n    url2f\
ile(\"www.google.com\", \"x\");\n    \n    if ( !-\
e \"x\" || -s \"x\" < 10){$internet=0;}\n    else \
{$internet=1;}\n    if (-e \"x\"){unlink \"x\";}\n\
    return $internet;\n}\n\n\n\nsub pdbfile2chaint\
ype\n  {\n    my $file=@_[0];\n    my %ct;\n    my\
 $F;\n    \n    $F=vfopen ($file, \"r\");\n    whi\
le (<$F>)\n      {\n    my $line=$_;\n  if ($line =~/^\
ATOM/)\n          {\n       my $C=substr($line,21,1);\n    \
 if (!$ct{$C})\n              { \n              my $r=substr($line,17\
,3);\n          $r=~s/\\s+//;\n         if (length ($r)==1){$ct{$\
C}=\"R\";}\n            elsif (length ($r)==2){$ct{$C}=\"D\"\
;}\n            elsif (length ($r)==3){$ct{$C}=\"P\";}\n                el\
se \n             {\n               print \"ERROR: Could not read RE\
S_ID field in file $file [FATAL:extract_from_pdb]\\
\n\";die;\n               }\n         }\n         }\n      }\n    clo\
se ($F);\n    return %ct;\n  }\n   \n    \n\n\n\ns\
ub fill_threelett_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      re\
turn %threelett;\n\n}\n\n\nsub fill_onelett_RNA\n{\
\n      my   %onelett=(\n       '  A' => 'A',\n '  T' => 'T',\
\n      '  U' => 'U',\n '  C' => 'C',\n '  G' => 'G',\n\
        'CSL' => 'X',\n 'UMS' => 'X',\n '  I' => 'I',\n '\
A' => 'A',\n    'T' => 'T',\n   'U' => 'U',\n   'C' => 'C\
',\n    'G' => 'G',\n   'I' => 'I',\n   );\n\n  return %on\
elett;\n\n}\n\n\nsub fill_onelett_DNA\n{\n      my   %o\
nelett=(\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 f\
ill_threelett_prot\n{  \n  my %threelett;\n\n  %th\
reelett=(\n'A', 'ALA',\n'C', 'CYS',\n'D', 'ASP',\n\
'E', 'GLU',\n'F', 'PHE',\n'G', 'GLY',\n'H', 'HIS',\
\n'I', 'ILE',\n'K', 'LYS',\n'L', 'LEU',\n'N', 'ASN\
',\n'M', 'MET',\n'P', 'PRO',\n'Q', 'GLN',\n'R', 'A\
RG',\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'1GL', 'X',\n'1GN', 'X',\n'1IN', 'X',\n'1L\
U', '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'26P', 'X',\n'2AB', 'X',\n'2AM', 'X',\n'2AN\
', 'X',\n'2AP', 'X',\n'2AR', 'X',\n'2AS', 'D',\n'2\
BL', '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'2MD', 'X',\n'2ME', 'X',\n'2MG', 'X',\n'2M\
L', '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'35G', 'X',\n'3AA', 'X',\n'3AD', 'X',\n'3AH\
', 'H',\n'3AN', 'X',\n'3AP', 'X',\n'3AT', 'X',\n'3\
BT', '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'3MF', 'X',\n'3MP', 'X',\n'3MT', 'X',\n'3O\
L', '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'4NC', 'X',\n'4NP', 'X',\n'4OX', 'X',\n'4PB\
', 'X',\n'4PN', 'X',\n'4PP', 'X',\n'4SC', 'X',\n'4\
SU', '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'5PV', 'X',\n'6AB', 'X',\n'6CT', 'X',\n'6H\
A', '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'8IN', 'X',\n'8OG', 'X',\n'95A', 'X',\n'9AD\
', 'X',\n'9AM', 'X',\n'9AP', 'X',\n'9DG', 'X',\n'9\
DI', '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'A80', 'X',\n'A85', 'X',\n'A88', 'X',\n'A9\
A', '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'ABH', 'X',\n'ABI', 'X',\n'ABK', 'X',\n'ABM\
', 'X',\n'ABN', 'X',\n'ABP', 'X',\n'ABR', 'X',\n'A\
BS', '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'ACV', 'V',\n'ACX', 'X',\n'ACY', 'X',\n'AD\
2', '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'AEI', 'D',\n'AEN', 'X',\n'AET', 'T',\n'AF1\
', 'X',\n'AF3', 'X',\n'AFA', 'D',\n'AFP', 'X',\n'A\
G7', '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'AHS', 'X',\n'AHT', 'Y',\n'AHU', 'X',\n'AH\
X', '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'AL8', 'X',\n'AL9', 'X',\n'ALA', 'A',\n'ALB\
', 'X',\n'ALC', 'X',\n'ALD', 'L',\n'ALE', 'X',\n'A\
LF', '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'AML', 'X',\n'AMN', 'X',\n'AMO', 'X',\n'AM\
P', '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'AOE', 'X',\n'AOP', 'X',\n'AP1', 'X',\n'AP2\
', 'X',\n'AP3', 'X',\n'AP4', 'X',\n'AP5', 'X',\n'A\
P6', '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'APZ', 'X',\n'AQS', 'X',\n'AR1', 'X',\n'AR\
2', 'X',\n'ARA', 'X',\n'ARB', 'X',\n'ARC', 'X',\n'\
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,\n'TPP', 'X',\n'TPQ', 'A',\n'TPR', 'P',\n'TPS', '\
X',\n'TPT', 'X',\n'TPV', 'X',\n'TPX', 'X',\n'TPY',\
 'X',\n'TQ3', 'X',\n'TQ4', 'X',\n'TQ5', 'X',\n'TQ6\
', 'X',\n'TR1', 'X',\n'TRA', 'X',\n'TRB', 'X',\n'T\
RC', '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'TSA', 'X',\n'TSB', 'X',\n'TSI', 'X',\n'TS\
M', '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'TYS', 'Y',\n'TYV', 'X',\n'TYY', 'A',\n'TZB\
', 'X',\n'TZC', 'X',\n'TZE', 'X',\n'TZL', 'X',\n'T\
ZO', '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'UAP', 'X',\n'UAR', 'X',\n'UC1', 'X',\n'UC\
2', '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'UNK', 'X',\n'UNN', 'X',\n'UNX', 'X',\n'UP5\
', 'X',\n'UP6', 'X',\n'UPA', 'X',\n'UPF', 'X',\n'U\
PG', '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'VAD', 'V',\n'VAF', 'V',\n'VAG', 'X',\n'VA\
L', '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'W03', 'X',\n'W11', 'X',\n'W33', 'X',\n'W35\
', 'X',\n'W42', 'X',\n'W43', 'X',\n'W54', 'X',\n'W\
56', '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'XBP', 'X',\n'XDN', 'X',\n'XDP', 'X',\n'XI\
F', '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'Z34', 'G',\n'Z5A', 'X',\n'ZAF', 'X',\n'ZAP\
', 'X',\n'ZEB', 'X',\n'ZEN', 'X',\n'ZES', 'X',\n'Z\
ID', '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\n\n","use Cwd;\nuse File::Path;\nuse FileHand\
le;\nuse strict;\n\n\nour (%MODE, %PG, %ENV_SET, %\
SUPPORTED_OS);\n\n\nour $EXIT_SUCCESS=0;\nour $EXI\
T_FAILURE=1;\nour $INTERNET=0;\n\nour $CP=\"cp \";\
 #was causing a crash on MacOSX\nour $SILENT=\">/d\
ev/null 2>/dev/null\";\nour $WEB_BASE=\"http://www\
.tcoffee.org\";\nour $TCLINKDB_ADDRESS=\"$WEB_BASE\
/Resources/tclinkdb.txt\";\nour $OS=get_os();\nour\
 $ROOT=&get_root();\nour $CD=cwd();\nour $CDIR=$CD\
;\nour $HOME=$ENV{'HOME'};\nour $CXX=\"g++\";\nour\
 $CXXFLAGS=\"\";\n\nour $CPP=\"g++\";\nour $CPPFLA\
GS=\"\";\n\nour $CC=\"gcc\";\nour $CFLAGS=\"\";\n\\
nour $FC=\"f77\";\nour $FFLAGS=\"\";\n\nmy $instal\
l=\"all\";\nmy $default_update_action=\"no_update\\
";\nmy @required_applications=(\"wget_OR_curl\");\\
nmy @smode=(\"all\", \"clean\", \"install\");\n\n&\
initialize_PG();\n\nmy $cl=join( \" \", @ARGV);\ni\
f ($#ARGV==-1 || ($cl=~/-h/) ||($cl=~/-H/) )\n  {\\
n     print \"\\n!!!!!!! ./install  t_coffee      \
       --> installs t_coffee only\";\n     print \\
"\\n!!!!!!! ./install  all                  --> in\
stalls all the modes [mcoffee, expresso, psicoffee\
,rcoffee..]\";\n     print \"\\n!!!!!!! ./install \
 [mcoffee|rcoffee|..] --> installs the specified m\
ode\";\n     print \"\\n!!!!!!! ./install  -h     \
              --> print usage\\n\\n\";\n     if ( \
$#ARGV==-1){exit ($EXIT_FAILURE);}\n   }\n     \ni\
f (($cl=~/-h/) ||($cl=~/-H/) )\n  {\n    my $m;\n \
   print \"\\n\\n!!!!!!! advanced mode\\n\";\n    \
foreach $m ((keys (%MODE)),@smode)\n      {\n   prin\
t \"!!!!!!!       ./install $m\\n\";\n      }\n   \
 \n    print \"!!!!!!! ./install [target:package|m\
ode|] [-update|-force|-exec=dir|-dis=dir|-root|-tc\
linkdb=file|-] [CC=|FCC=|CXX=|CFLAGS=|CXXFLAGS=]\\\
n\";\n    print \"!!!!!!! ./install clean    [remo\
ves all executables]\\n\";\n    print \"!!!!!!! ./\
install [optional:target] -update               [u\
pdates package already installed]\\n\";\n    print\
 \"!!!!!!! ./install [optional:target] -force     \
           [Forces recompilation over everything]\\
\n\";\n    \n    print \"!!!!!!! ./install [option\
al:target] -root                 [You are running \
as root]\\n\";\n    print \"!!!!!!! ./install [opt\
ional:target] -exec=/foo/bar/       [address for t\
he T-Coffee executable]\\n\";\n    print \"!!!!!!!\
 ./install [optional:target] -dis=/foo/bar/       \
 [Address where distributions should be stored]\\n\
\";\n    print \"!!!!!!! ./install [optional:targe\
t] -tclinkdb=foo|update  [file containing all the \
packages to be installed]\\n\";\n    print \"!!!!!\
!! ./install [optional:target] -tclinkdb=foo|updat\
e  [file containing all the packages to be install\
ed]\\n\";\n    print \"!!!!!!! ./install [optional\
:target] -clean                [clean everything]\\
\n\";\n    print \"!!!!!!! ./install [optional:tar\
get] -plugins              [plugins directory]\\n\\
";\n    print \"!!!!!!! mode:\";\n    foreach $m (\
keys(%MODE)){print \"$m \";}\n    print \"\\n\";\n\
    print \"!!!!!!! Packages:\";\n    foreach $m (\
keys (%PG)){print \"$m \";}\n    print \"\\n\";\n \
   \n    print \"\\n\\n\";\n    exit ($EXIT_FAILUR\
E);\n  }\n\n\n\nmy (@argl)=($cl=~/(\\S+=[^=]+)\\s\\
\w+=/g);\npush (@argl, ($cl=~/(\\S+=[^=]+\\S)\\s*$\
/g));\n\nforeach $a (@argl)\n  {\n    if ( ($cl=~/\
CXX=(.*)/)){$CXX=$1;}\n    if ( ($cl=~/-CC=(.*)/  \
  )){$CC=$1;}\n    if ( ($cl=~/-FC=(.*)/    )){$FC\
=$1;}\n    if ( ($cl=~/-CFLAGS=(.*)/)){$CFLAGS=$1;\
}\n    if ( ($cl=~/-CXXFLAGS=(.*)/)){$CXXFLAGS=$1;\
}\n  }\nour ($ROOT_INSTALL, $NO_QUESTION, $default\
_update_action,$BINARIES_ONLY,$force, $default_upd\
ate_action, $INSTALL_DIR, $PLUGINS_DIR, $DISTRIBUT\
IONS,$tclinkdb, $proxy, $clean);\nif ( ($cl=~/-roo\
t/)){$ROOT_INSTALL=1;}\nif ( ($cl=~/-no_question/)\
){$NO_QUESTION=1;}\nif ( ($cl=~/-update/)){$defaul\
t_update_action=\"update\";}\nif ( ($cl=~/-binarie\
s/)){$BINARIES_ONLY=1;}\nif ( ($cl=~/-force/)){$fo\
rce=1;$default_update_action=\"update\"}\nif ( ($c\
l=~/-exec=\\s*(\\S+)/)){$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=$1;}\ni\
f ( ($cl=~/-clean/)){$clean=1;}\nif ($tclinkdb){&u\
pdate_tclinkdb ($tclinkdb);}\n\nour $TCDIR=$ENV{DI\
R_4_TCOFFEE};\nour $TCCACHE=$ENV{CACHE_4_TCOFFEE};\
\nour $TCTMP=$ENV{CACHE_4_TCOFFEE};\nour $TCM=$ENV\
{MCOFFEE_4_TCOFFEE};\nour $TCMETHODS=$ENV{METHODS_\
4_TCOFFEE};\nour $TCPLUGINS=$ENV{PLUGINS_4_TCOFFEE\
};\nour $PLUGINS_DIR=\"\";\nour $INSTALL_DIR=\"\";\
\n\n&add_dir ($TCDIR=\"$HOME/.t_coffee\");\n&add_d\
ir ($TCCACHE=\"$TCDIR/cache\");\n&add_dir ($TCTMP=\
\"$CDIR/tmp\");\n&add_dir ($TCM=\"$TCDIR/mcoffee\"\
);\n&add_dir ($TCMETHODS=\"$TCDIR/methods\");\n&ad\
d_dir ($TCPLUGINS=\"$TCDIR/plugins/$OS\");\n\n\nou\
r $BASE=\"$CD/bin\";\nour $BIN=\"$BASE/binaries/$O\
S\";\nour $DOWNLOAD_DIR=\"$BASE/download\";\nour $\
DOWNLOAD_FILE=\"$DOWNLOAD_DIR/files\";\nour $TMP=\\
"$BASE/tmp\";\n\n&add_dir($BASE);\n&add_dir($BIN);\
\n&add_dir($DOWNLOAD_DIR);\n&add_dir($DOWNLOAD_FIL\
E);\nif (!$DISTRIBUTIONS){$DISTRIBUTIONS=\"$DOWNLO\
AD_DIR/distributions\";}\n&add_dir ($DISTRIBUTIONS\
);\n&add_dir ($TMP);\n\n\nif    (!$PLUGINS_DIR && \
!$ROOT_INSTALL){$PLUGINS_DIR=$TCPLUGINS;}\nelsif (\
!$PLUGINS_DIR &&  $ROOT_INSTALL){$PLUGINS_DIR=\"/u\
sr/local/bin/\";}\n\nif    (!$INSTALL_DIR && !$ROO\
T_INSTALL){$INSTALL_DIR=\"$HOME/bin/\";mkpath ($IN\
STALL_DIR);}\nelsif (!$INSTALL_DIR &&  $ROOT_INSTA\
LL){$INSTALL_DIR=\"/usr/local/bin/\";}\n\nif (-d \\
"mcoffee\"){`cp mcoffee/* $TCM`;}\n\n\nour $ENV_FI\
LE=\"$TCDIR/t_coffee_env\";\n&env_file2putenv ($EN\
V_FILE);\n&set_proxy($proxy);\nmy ($target, $p, $r\
);\n$target=$p;\n\nforeach $p (  ((keys (%PG)),(ke\
ys(%MODE)),(@smode)) )\n  {\n    if ($ARGV[0] eq $\
p && $target eq \"\"){$target=$p;}\n  }\nif ($targ\
et eq \"\"){exit ($EXIT_FAILURE);}\n\n\nforeach $r\
 (@required_applications)\n  {\n    my @app_list;\\
n    my $i;\n    $i=0;\n    \n    @app_list=split \
(/_OR_/, $r);\n    foreach my $pg (@app_list)\n   \
   {\n  $i+=&pg_is_installed ($pg);\n      }\n    i\
f ($i==0)\n      {\n      print \"One of the follo\
wing packages must be installed to proceed: \";\n \
     foreach my $pg (@app_list)\n       {\n       print (\"$\
pg \");\n       }\n      die;\n    }\n  }\n\n\n\n\n\n\n&\
sign_license_ni();\n\n\n$PG{C}{compiler}=get_C_com\
piler($CC);\n$PG{Fortran}{compiler}=get_F_compiler\
($FC);\n$PG{CXX}{compiler}=$PG{CPP}{compiler}=$PG{\
GPP}{compiler}=get_CXX_compiler($CXX);\nif ($CXXFL\
AGS){$PG{CPP}{options}=$PG{GPP}{options}=$PG{CXX}{\
options}=$CXXFLAGS;}\nif ($CFLAGS){$PG{C}{options}\
=$CFLAGS;}\nforeach my $c (keys(%PG))\n  {\n    my\
 $arguments;\n    if ($PG{$c}{compiler})\n      {\\
n       $arguments=\"$PG{$c}{compiler_flag}=$PG{$c}{comp\
iler} \";\n     if ($PG{$c}{options})\n   {\n       $arg\
uments.=\"$PG{$c}{options_flag}=$PG{$c}{options} \\
";\n      }\n   $PG{$c}{arguments}=$arguments;\n      }\
\n  }\n\nif ($PG{$target}){$PG{$target}{install}=1\
;}\nelse\n  {\n    foreach my $pg (keys(%PG))\n   \
   {\n  if ( $target eq \"all\" || ($PG{$pg}{mode}=\
~/$target/))\n    {\n       $PG{$pg} {install}=1;\n      \
 }\n      }\n  }\n\nforeach my $pg (keys(%PG))\n  \
{\n    if (!$PG{$pg}{update_action}){$PG{$pg}{upda\
te_action}=$default_update_action;}\n    elsif ($P\
G{$pg}{update_action} eq \"never\"){$PG{$pg}{insta\
ll}=0;}\n    if ( $force && $PG{$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\nforeach my $m (keys(%MODE))\n  {\n\
    if ( $target eq \"all\" || $target eq $m)\n   \
   {\n  print \"\\n------- The installer will now i\
nstall the $m components $MODE{$m}{description}\\n\
\";\n   foreach my $pg (keys(%PG))\n      {\n       if ( \
$PG{$pg}{mode} =~/$m/ && $PG{$pg}{install})\n       \
  {\n           if ($PG{$pg}{touched}){print \"------- $PG{\
$pg}{dname}: already processed\\n\";}\n         else {$PG\
{$pg}{success}=&install_pg($pg);$PG{$pg}{touched}=\
1;}\n         }\n         }\n      }\n  }\n\nif ( $PG{$tar\
get}){print \"------- Installing Individual Packag\
e\\n\";}\nforeach my $pg (keys (%PG))\n  {\n    \n\
    if ( $PG{$pg}{install} && !$PG{$pg}{touched})\\
n      {\n      print \"\\n------- Install $pg\\n\";\n  \
$PG{$pg}{success}=&install_pg($pg);$PG{$pg}{touche\
d}=1;\n      }\n  }\nprint \"------- Finishing The\
 installation\\n\";\nmy $final_report=&install ($I\
NSTALL_DIR);\n\nprint \"\\n\";\nprint \"**********\
**************************************************\
*********\\n\";\nprint \"********              INS\
TALLATION SUMMARY          *****************\\n\";\
\nprint \"****************************************\
*****************************\\n\";\nprint \"-----\
-- SUMMARY package Installation:\\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}:\
 installed $bin_status\\n\"; $PG{$pg}{status}=1;}\\
n       elsif  ( $PG{$pg}{new} &&  $PG{$pg}{old})       \
              {print \"*------        $PG{$pg}{dna\
me}: updated $bin_status\\n\"  ; $PG{$pg}{status}=\
1;} \n  elsif  (!$PG{$pg}{new} &&  $PG{$pg}{old} &&\
 !$PG{$pg}{update}){print \"*------        $PG{$pg\
}{dname}: previous\\n\" ; $PG{$pg}{status}=1;}\n        e\
lsif  (!$PG{$pg}{new} &&  $PG{$pg}{old} &&  $PG{$p\
g}{update}){print \"*------        $PG{$pg}{dname}\
: failed update (previous installation available)\\
\n\";$PG{$pg}{status}=0;}\n     else                  \
                                        {print \"*\
------        $PG{$pg}{dname}: failed installation\
\";$PG{$pg}{status}=0;}\n      }\n  }\n\nif ( !$PG\
{$target}){print \"*------ SUMMARY mode Installati\
on:\\n\";}\nforeach my $m (keys(%MODE))\n  {\n    \
if ( $target eq \"all\" || $target eq $m)\n      {\
\n      my $succesful=1;\n      foreach my $pg (keys(%PG))\n\
          {\n       if (($PG{$pg}{mode}=~/$m/) && $PG{$pg}{\
install} && $PG{$pg}{status}==0)\n            {\n               $suc\
cesful=0;\n             print \"*!!!!!!       $PG{$pg}{dname}\
: Missing\\n\";\n             }\n         }\n   if ( $succesful)\
\n        {\n       $MODE{$m}{status}=1;\n          print \"*-\
-----       MODE $MODE{$m}{dname} SUCCESFULY insta\
lled\\n\";\n      }\n   else\n    {\n       $MODE{$m}{stat\
us}=0;\n            print \"*!!!!!!       MODE $MODE{$m}{\
dname} UNSUCCESFULY installed\\n\";\n     }\n      }\
\n  }\n\nif ($clean==1 && ($BASE=~/install4tcoffee\
/) ){print \"*------ Clean Installation Directory:\
 $BASE\\n\";`rm -rf $BASE`;}\nforeach my $pg (keys\
(%PG)){if ($PG{$pg}{install} && $PG{$pg}{status}==\
0){exit ($EXIT_FAILURE);}}\nexit ($EXIT_SUCCESS); \
 \n\nsub get_CXX_compiler\n  {\n    my $c=@_[0];\n\
    my (@clist)=(\"g++\");\n    \n    return get_c\
ompil ($c, @clist);\n }\nsub get_C_compiler\n  {\n\
    my $c=@_[0];\n    my (@clist)=(\"gcc\", \"cc\"\
, \"icc\");\n    \n    return get_compil ($c, @cli\
st);\n }\n\nsub get_F_compiler\n  {\n    my ($c)=@\
_[0];\n    my @clist=(\"f77\", \"g77\", \"gfortran\
\", \"ifort\");\n    return get_compil ($c, @clist\
);\n  } \n       \nsub get_compil\n  {\n    my ($f\
av,@clist)=(@_);\n    \n    #return the first comp\
iler found installed in the system. Check first th\
e favorite\n    foreach my $c ($fav,@clist)\n     \
 {\n    if  (&pg_is_installed ($c)){return $c;}\n    \
  }\n    return \"\";\n  }\nsub exit_if_pg_not_ins\
talled\n  {\n    my (@arg)=(@_);\n    \n    foreac\
h my $p (@arg)\n      {\n       if ( !&pg_is_installed (\
$p))\n    {\n       print \"!!!!!!!! The $p utility m\
ust be installed for this installation to proceed \
[FATAL]\\n\";\n     die;\n        }\n      }\n    retur\
n 1;\n  }\nsub set_proxy\n  {\n    my ($proxy)=(@_\
);\n    my (@list,$p);\n    \n    @list= (\"HTTP_p\
roxy\", \"http_proxy\", \"HTTP_PROXY\", \"ALL_prox\
y\", \"all_proxy\",\"HTTP_proxy_4_TCOFFEE\",\"http\
_proxy_4_TCOFFEE\");\n    \n    if (!$proxy)\n    \
  {\n   foreach my $p (@list)\n   {\n       if ( ($ENV\
_SET{$p}) || $ENV{$p}){$proxy=$ENV{$p};}\n        }\n  \
    }\n    foreach my $p(@list){$ENV{$p}=$proxy;}\\
n  }\n  \nsub check_internet_connection\n  {\n    m\
y $internet;\n    \n    if ( -e \"x\"){unlink (\"x\
\");}\n    if     (&pg_is_installed    (\"wget\"))\
{`wget www.google.com -Ox >/dev/null 2>/dev/null`;\
}\n    elsif  (&pg_is_installed    (\"curl\")){`cu\
rl www.google.com -ox >/dev/null 2>/dev/null`;}\n \
   else\n      {\n      printf stderr \"\\nERROR: No pg\
 for remote file fetching [wget or curl][FATAL]\\n\
\";\n   exit ($EXIT_FAILURE);\n      }\n    \n    if\
 ( !-e \"x\" || -s \"x\" < 10){$internet=0;}\n    \
else {$internet=1;}\n    if (-e \"x\"){unlink \"x\\
";}\n    return $internet;\n  }\nsub url2file\n  {\
\n    my ($cmd, $file,$wget_arg, $curl_arg)=(@_);\\
n    my ($exit,$flag, $pg, $arg);\n    \n    if ($\
INTERNET || check_internet_connection ()){$INTERNE\
T=1;}\n    else\n      {\n      print STDERR \"ERROR: N\
o Internet Connection [FATAL:install.pl]\\n\";\n        e\
xit ($EXIT_FAILURE);\n      }\n    \n    if     (&\
pg_is_installed    (\"wget\")){$pg=\"wget\"; $flag\
=\"-O\";$arg=$wget_arg;}\n    elsif  (&pg_is_insta\
lled    (\"curl\")){$pg=\"curl\"; $flag=\"-o\";$ar\
g=$curl_arg;}\n    else\n      {\n      printf stderr \\
"\\nERROR: No pg for remote file fetching [wget or\
 curl][FATAL]\\n\";\n   exit ($EXIT_FAILURE);\n     \
 }\n    \n    \n    if (-e $file){unlink($file);}\\
n    $exit=system \"$pg $cmd $flag$file $arg\";\n \
   return $exit;\n  }\n\nsub pg_is_installed\n  {\\
n    my ($p, $dir)=(@_);\n    my ($r,$m);\n    my \
($supported, $language, $compil);\n    \n    if ( \
$PG{$p})\n      {\n     $language=$PG{$p}{language2};\\
n       $compil=$PG{$language}{compiler};\n      }\n    \
\n    if ( $compil eq \"CPAN\")\n      {\n      if ( sy\
stem (\"perl -M$p -e 1\")==$EXIT_SUCCESS){return 1\
;}\n    else {return 0;}\n      }\n    elsif ($dir)\n\
      {\n       if (-e \"$dir/$p\" || -e \"$dir/$p\\.exe\
\"){return 1;}\n        else {return 0;}\n      }\n    el\
sif (-e \"$PLUGINS_DIR/$p\" || -e \"$PLUGINS_DIR/$\
p.exe\"){return 1;}\n    else\n      {\n        $r=`which\
 $p 2>/dev/null`;\n     if ($r eq \"\"){return 0;}\n    e\
lse {return 1;}\n      }\n    return 0;\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    if ($pg eq \"t_coffee\")  {re\
turn   &install_t_coffee ($pg);}\n    elsif ($pg e\
q \"TMalign\"){return   &install_TMalign ($pg);}\n\
    \n    chdir $DISTRIBUTIONS;\n    \n    $downlo\
ad=$PG{$pg}{source};\n    \n    if (($download =~/\
tgz/))\n      {\n       ($address,$name,$ext)=($download\
=~/(.+\\/)([^\\/]+)(\\.tgz)/);\n      }\n    elsif\
 (($download=~/tar\\.gz/))\n      {\n   ($address,$n\
ame,$ext)=($download=~/(.+\\/)([^\\/]+)(\\.tar\\.g\
z)/);\n      }\n    elsif (($download=~/tar/))\n  \
    {\n ($address,$name,$ext)=($download=~/(.+\\/)\
([^\\/]+)(\\.tar)/);\n      }\n    else\n      {\n\
        ($address,$name)=($download=~/(.+\\/)([^\\/]+)/);\
\n      $ext=\"\";\n      }\n    $distrib=\"$name$ext\"\
;\n    \n    if ( !-d $pg){mkdir $pg;}\n    chdir \
$pg;\n   \n    #get the distribution if available\\
n    if ( -e \"$DOWNLOAD_DIR/$distrib\")\n      {\\
n       `$CP $DOWNLOAD_DIR/$distrib .`;\n      }\n    #U\
NTAR and Prepare everything\n    if (!-e \"$name.t\
ar\" && !-e \"$name\")\n      {\n       &check_rm ($wget\
_tmp);\n        print \"\\n------- Downloading/Installing\
 $pg\\n\";\n    if (!-e $distrib && &url2file (\"$dow\
nload\", \"$wget_tmp\")==$EXIT_SUCCESS)\n         {\n     \
  \n        `mv $wget_tmp $distrib`;\n      `$CP $dist\
rib $DOWNLOAD_DIR/`;\n    }\n\n if (!-e $distrib)\n\
          {\n       print \"!!!!!!! Download of $pg distrib\
ution failed\\n\";\n        print \"!!!!!!! Check Add\
ress: $PG{$pg}{source}\\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_com\
mand(\"tar -xvf $name.tar\");\n   }\n      }\n    \
#Guess and enter the distribution directory\n    @\
fl=ls($p);\n    foreach my $f (@fl)\n      {\n  if \
(-d $f)\n         {\n       $main_dir=$f;\n       }\n      }\n\
    if (-d $main_dir)\n   {chdir $main_dir;}\n    \
\n    print \"\\n------- Compiling/Installing $pg\\
\n\";\n    `make clean $SILENT`;\n    #sap\n    if\
 ($pg eq \"sap\")\n      {\n    `rm *.o sap  sap.exe \
./util/aa/*.o  ./util/wt/.o $SILENT`;\n &flush_com\
mand (\"make $arguments sap\");\n       &check_cp ($pg, \
\"$BIN\");\n      }\n    elsif ($pg eq \"clustalw2\
\")\n      {\n  &flush_command(\"./configure\");\n      \
&flush_command(\"make $arguments\");\n  &check_cp (\
\"./src/$pg\", \"$BIN\");\n     \n      }\n    elsif (\
$pg eq \"clustalw\")\n      {\n &flush_command(\"m\
ake $arguments clustalw\");\n   `$CP $pg $BIN $SILEN\
T`;\n      }\n    \n    elsif ($pg eq \"mafft\")\n\
      {\n       my $base=cwd();\n       my $c;\n        \n      #compile c\
ore\n   mkpath (\"./mafft/bin\");\n     mkpath (\"./maff\
t/lib\");\n     chdir \"$base/core\";\n `make clean $S\
ILENT`;\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 $arguments\");\n &flus\
h_command (\"make install LIBDIR=../mafft/lib BIND\
IR=../mafft/bin\");\n   \n      #put everything in mafft \
and copy the coompiled stuff in bin\n   chdir \"$bas\
e\";\n  if ($ROOT_INSTALL)\n      {\n       &root_run (\\
"You Must be Roor to Install MAFFT\\n\", \"mkdir /\
usr/local/mafft/;$CP mafft/lib/* /usr/local/mafft;\
$CP mafft/lib/mafft* /usr/local/bin ;$CP mafft/bin\
/mafft /usr/local/bin/; \");\n    }\n   else\n    {\n   \
    `$CP mafft/lib/*  $BIN`;\n      `$CP mafft/bin/\
mafft  $BIN`;\n   }\n   `tar -cvf mafft.tar mafft`;\\
n       `gzip mafft.tar`;\n     `mv mafft.tar.gz $BIN`;\n   \
   }\n    elsif ( $pg eq \"dialign-tx\")\n      {\\
n       my $f;\n        my $base=cwd();\n\n     chdir \"./source\";\
\n      &flush_command (\" make CPPFLAGS='-O3 -funroll-\
loops' all\");\n        \n      chdir \"..\";\n &check_cp (\".\
/source/$pg\", \"$BIN\");\n     &check_cp (\"./source/\
$pg\", \"$BIN/dialign-t\");\n      }\n    elsif ($\
pg eq \"poa\")\n      {\n       &flush_command (\"make $\
arguments poa\");\n     &check_cp (\"$pg\", \"$BIN\");\
\n      }\n    elsif ( $pg eq \"probcons\")\n     \
 {\n    `rm *.exe $SILENT`;\n   &flush_command (\"make \
$arguments probcons\");\n       &check_cp(\"$pg\", \"$BI\
N/$pg\");\n      }\n    elsif ( $pg eq \"probcons\\
" || $pg eq \"probconsRNA\")\n      {\n `rm *.exe \
$SILENT`;\n     &flush_command (\"make $arguments prob\
cons\");\n      &check_cp(\"probcons\", \"$BIN/$pg\");\\
n      }\n\n    elsif (  $pg eq \"muscle\")\n     \
 {\n    `rm *.o muscle muscle.exe $SILENT`;\n   &flush_\
command (\"make $arguments all\");\n    &check_cp(\"$\
pg\", \"$BIN\");\n      }\n    elsif ( $pg eq \"pc\
ma\")\n      {\n        &flush_command (\"make $arguments\
 pcma\");\n     &check_cp(\"$pg\", \"$BIN\");\n      }\
\n    elsif ($pg eq \"kalign\")\n      {\n      &flush_\
command (\"./configure\");\n    &flush_command(\"make\
 $arguments\");\n       &check_cp (\"$pg\",$BIN);\n     \
 }\n    elsif ( $pg eq \"amap\")\n      {\n     chdir \
\"align\";\n    `make clean $SILENT`;\n &flush_comman\
d (\"make $arguments all\");\n  &check_cp (\"$pg\",\
 $BIN);\n      }\n    elsif ( $pg eq \"proda\")\n \
     {\n        &flush_command (\"make $arguments all\");\
\n      &check_cp (\"$pg\", $BIN);\n      }\n    elsif \
( $pg eq \"prank\")\n      {\n  &flush_command (\"m\
ake $arguments all\");\n        &check_cp (\"$pg\", $BIN)\
;\n      }\n    elsif ( $pg eq \"mustang\")\n     \
 {\n    &flush_command (\"make $arguments all\");\n     i\
f ( $OS=~/windows/){&check_cp(\"./bin/MUSTANG_v.3\\
", \"$BIN/mustang.exe\");}\n    else {&check_cp(\"./b\
in/MUSTANG_v.3\", \"$BIN/mustang\");}\n      }\n  \
  elsif ( $pg eq \"RNAplfold\")\n      {\n      &flush_\
command(\"./configure\");\n     &flush_command (\"make\
 $arguments all\");\n   &check_cp(\"./Progs/RNAplfol\
d\", \"$BIN\");\n      }\n    chdir $CDIR;\n    re\
turn &pg_is_installed ($pg, $BIN);\n  }\n\nsub ins\
tall_t_coffee\n  {\n    my ($pg)=(@_);\n    my ($r\
eport,$cflags, $arguments, $language, $compiler) ;\
\n    #1-Install T-Coffee\n    chdir \"t_coffee_so\
urce\";\n    &flush_command (\"make clean\");\n   \
 print \"\\n------- Compiling T-Coffee\\n\";\n    \
$language=$PG{$pg} {language2};\n    $arguments=$P\
G{$language}{arguments};\n    if (!($arguments =~/\
CFLAGS/)){$arguments .= \" CFLAGS=-O2 \";}\n\n    \
if ( $CC ne \"\"){&flush_command (\"make -i $argum\
ents t_coffee\");}\n    &check_cp ($pg, $BIN);\n  \
  \n    chdir $CDIR;\n    return &pg_is_installed \
($pg, $BIN);\n  }\nsub install_TMalign\n  {\n    m\
y ($pg)=(@_);\n    my $report;\n    chdir \"t_coff\
ee_source\";\n    print \"\\n------- Compiling TMa\
lign\\n\";\n    `rm TMalign TMalign.exe $SILENT`;\\
n    if ( $FC ne \"\"){&flush_command (\"make -i $\
PG{Fortran}{arguments} TMalign\");}\n    &check_cp\
 ($pg, $BIN);\n    if ( !-e \"$BIN/$pg\" && pg_has\
_binary_distrib ($pg))\n      {\n       print \"!!!!!!! \
Compilation of $pg impossible. Will try to install\
 from binary\\n\";\n    return &install_binary_packag\
e ($pg);\n      }\n    chdir $CDIR;\n    return &p\
g_is_installed ($pg, $BIN);\n  }\n\nsub pg_has_bin\
ary_distrib\n  {\n    my ($pg)=(@_);\n    if ($PG{\
$pg}{windows}){return 1;}\n    elsif ($PG{$pg}{osx\
}){return 1;}\n    elsif ($PG{$pg}{linux}){return \
1;}\n    return 0;\n  }\nsub install_binary_packag\
e\n  {\n    my ($pg)=(@_);\n    my ($base,$report,\
$name, $download, $arguments, $language, $dir);\n \
   my $isdir;\n    &input_os();\n    \n    if (!&s\
upported_os($OS)){return 0;}\n    if ( $PG{$pg}{bi\
nary}){$name=$PG{$pg}{binary};}\n    else \n      \
{\n     $name=$pg;\n    if ( $OS eq \"windows\"){$name.=\\
".exe\";}\n      }\n    \n    $download=\"$WEB_BAS\
E/Packages/Binaries/$OS/$name\";\n    \n    $base=\
cwd();\n    chdir $TMP;\n    \n    if (!-e $name)\\
n      {\n      `rm x $SILENT`;\n       if ( url2file(\"$down\
load\",\"x\")==$EXIT_SUCCESS)\n   {\n       `mv x $n\
ame`;\n   }\n      }\n    \n    if (!-e $name)\n  \
    {\n print \"!!!!!!! $PG{$pg}{dname}: Download \
of $pg binary failed\\n\";\n    print \"!!!!!!! $PG{$\
pg}{dname}: Check Address: $download\\n\";\n    retur\
n 0;\n      }\n    print \"\\n------- Installing $\
pg\\n\";\n    \n    if ($name =~/tar\\.gz/)\n     \
 {\n    `gunzip  $name`;\n      `tar -xvf $pg.tar`;\n   chdi\
r $pg;\n        if ( $pg eq \"mafft\")\n          {\n       if ($R\
OOT_INSTALL)\n        {\n               &root_run (\"You Must be\
 Roor to Install MAFFT\\n\", \"$CP mafft/bin/* /us\
r/local/mafft;mkdir /usr/local/mafft/; $CP mafft/l\
ib/* /usr/local/bin/\");\n            }\n           else\n        \
    {\n         `$CP $TMP/$pg/bin/* $BIN $SILENT`;\n            `$C\
P $TMP/$pg/lib/* $BIN $SILENT`;\n             }\n         }\n   \
else\n    {\n       if (-e \"$TMP/$pg/data\"){`$CP $T\
MP/$pg/data/* $TCM $SILENT`;}\n     if (!($pg=~/\\\
*/)){`rm -rf $pg`;}\n     }\n      }\n    else\n    \
  {\n   &check_cp (\"$pg\", \"$BIN\");\n        `chmod u+x \
$BIN/$pg`; \n   unlink ($pg);\n      }\n    chdir $b\
ase;\n    $PG{$pg}{from_binary}=1;\n    return &pg\
_is_installed ($pg, $BIN);\n  }\n\nsub add_dir \n \
 {\n    my $dir=@_[0];\n    \n    if (!-e $dir && \
!-d $dir)\n      {\n    return mkpath ($dir);\n      \
}\n    else\n      {\n  return 0;\n      }\n  }\nsu\
b check_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 $from){return 0;}\n        \n    `$CP $from $t\
o`;\n    return 1;\n  }\nsub check_file_list_exist\
s \n  {\n    my ($base, @flist)=(@_);\n    my $f;\\
n\n    foreach $f (@flist)\n      {\n   if ( !-e \"$\
base/$f\"){return 0;}\n      }\n    return 1;\n  }\
\nsub ls\n  {\n    my $f=@_[0];\n    my @fl;\n    \
chomp(@fl=`ls -1 $f`);\n    return @fl;\n  }\nsub \
flush_command\n  {\n    my $command=@_[0];\n    my\
 $F=new FileHandle;\n    open ($F, \"$command|\");\
\n    while (<$F>){print \"    --- $_\";}\n    clo\
se ($F);\n  }    \n\nsub input_installation_direct\
ory\n  {\n    my $dir=@_[0];\n    my $new;\n    \n\
    print \"------- The current installation direc\
tory is: [$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 $new. Is this correct? ([y]/n):\"))\n     {\\
n           print \"???????New installation directory:\"\
;\n         chomp ($new=<stdin>);\n       }\n   $dir=($new e\
q \"\")?$dir:$new;\n    $dir=~s/\\/$//;\n      }\n   \
 \n    if ( -d $dir){return $dir;}\n    elsif (&ro\
ot_run (\"You must be root to create $dir\",\"mkdi\
r $dir\")==$EXIT_SUCCESS){return $dir;}\n    else\\
n      {\n      print \"!!!!!!! $dir could not be creat\
ed\\n\";\n      if ( $NO_QUESTION)\n      {\n       return \\
"\";\n    }\n   elsif ( &input_yes (\"??????? Do you \
want to provide a new directory([y]/n)?:\"))\n    {\
\n          return input_installation_directory ($dir);\
\n        }\n   else\n    {\n       return \"\";\n        }\n    \
  }\n    \n  }\nsub input_yes\n  {\n    my $questi\
on =@_[0];\n    my $answer;\n\n    if ($NO_QUESTIO\
N==1){return 1;}\n    \n    if ($question eq \"\")\
{$question=\"??????? Do you wish to proceed ([y]/n\
)?:\";}\n    print $question;\n    chomp($answer=l\
c(<STDIN>));\n    if (($answer=~/^y/) || $answer e\
q \"\"){return 1;}\n    elsif ( ($answer=~/^n/)){r\
eturn 0;}\n    else\n      {\n  return input_yes($q\
uestion);\n      }\n  }\nsub root_run\n  {\n    my\
 ($txt, $cmd)=(@_);\n    \n    if ( system ($cmd)=\
=$EXIT_SUCCESS){return $EXIT_SUCCESS;}\n    else \\
n      {\n      print \"------- $txt\\n\";\n    if ( $ROOT\
 eq \"sudo\"){return system (\"sudo $cmd\");}\n el\
se {return system (\"su root -c \\\"$cmd\\\"\");}\\
n      }\n  }\nsub get_root\n  {\n    if (&pg_is_i\
nstalled (\"sudo\")){return \"sudo\";}\n    else {\
return \"su\";}\n  }\n\nsub get_os\n  {\n    my $r\
aw_os=`uname`;\n    my $os;\n\n    $raw_os=lc ($ra\
w_os);\n    \n    if ($raw_os =~/cygwin/){$os=\"wi\
ndows\";}\n    elsif ($raw_os =~/linux/){$os=\"lin\
ux\";}\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 $answe\
r;\n    if ($OS) {return $OS;}\n    \n    print \"\
??????? which os do you use: [w]indows, [l]inux, [\
m]acosx:?\";\n    $answer=lc(<STDIN>);\n\n    if (\
($answer=~/^m/)){$OS=\"macosx\";}\n    elsif ( ($a\
nswer=~/^w/)){$OS=\"windows\";}\n    elsif ( ($ans\
wer=~/^linux/)){$OS=\"linux\";}\n    \n    else\n \
     {\n        return &input_os();\n      }\n    return \
$OS;\n  }\n\nsub supported_os\n  {\n    my ($os)=(\
@_[0]);\n    return $SUPPORTED_OS{$os};\n  }\n    \
\n    \n\n\nsub update_tclinkdb \n  {\n    my $fil\
e =@_[0];\n    my $name;\n    my $F=new FileHandle\
;\n    my ($download, $address, $name, $l, $db);\n\
    \n    if ( $file eq \"update\"){$file=$TCLINKD\
B_ADDRESS;}\n    \n    if ( $file =~/http:\\/\\// \
|| $file =~/ftp:\\/\\//)\n      {\n     ($address, $na\
me)=($download=~/(.*)\\/([^\\/]+)$/);\n `rm x $SIL\
ENT`;\n if (&url2file ($file,\"x\")==$EXIT_SUCCESS\
)\n       {\n       print \"------- Susscessful upload o\
f $name\";\n        `mv x $name`;\n         $file=$name;\\
n         }\n      }\n    open ($F, \"$file\");\n    whi\
le (<$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 ($F);\n    &post_process_PG();\n\
    return;\n  }\n\n\n\nsub initialize_PG\n  {\n  \
  \n$PG{\"t_coffee\"}{\"4_TCOFFEE\"}=\"TCOFFEE\";\\
n$PG{\"t_coffee\"}{\"type\"}=\"sequence_multiple_a\
ligner\";\n$PG{\"t_coffee\"}{\"ADDRESS\"}=\"http:/\
/www.tcoffee.org\";\n$PG{\"t_coffee\"}{\"language\\
"}=\"C\";\n$PG{\"t_coffee\"}{\"language2\"}=\"C\";\
\n$PG{\"t_coffee\"}{\"source\"}=\"http://www.tcoff\
ee.org/Packages/T-COFFEE_distribution.tar.gz\";\n$\
PG{\"t_coffee\"}{\"update_action\"}=\"always\";\n$\
PG{\"t_coffee\"}{\"mode\"}=\"tcoffee,mcoffee,rcoff\
ee,expresso,3dcoffee\";\n$PG{\"clustalw2\"}{\"4_TC\
OFFEE\"}=\"CLUSTALW2\";\n$PG{\"clustalw2\"}{\"type\
\"}=\"sequence_multiple_aligner\";\n$PG{\"clustalw\
2\"}{\"ADDRESS\"}=\"http://www.clustal.org\";\n$PG\
{\"clustalw2\"}{\"language\"}=\"C++\";\n$PG{\"clus\
talw2\"}{\"language2\"}=\"CXX\";\n$PG{\"clustalw2\\
"}{\"source\"}=\"http://www.clustal.org/download/2\
.0.10/clustalw-2.0.10-src.tar.gz\";\n$PG{\"clustal\
w2\"}{\"mode\"}=\"mcoffee,rcoffee\";\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\
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mcoffee,rcoffee\";\n$PG{\"dialign-t\"}{\"4_TCOFFEE\
\"}=\"DIALIGNT\";\n$PG{\"dialign-t\"}{\"type\"}=\"\
sequence_multiple_aligner\";\n$PG{\"dialign-t\"}{\\
"ADDRESS\"}=\"http://dialign-tx.gobics.de/\";\n$PG\
{\"dialign-t\"}{\"DIR\"}=\"/usr/share/dialign-tx/\\
";\n$PG{\"dialign-t\"}{\"language\"}=\"C\";\n$PG{\\
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-t\"}{\"source\"}=\"http://dialign-tx.gobics.de/DI\
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e\"}=\"mcoffee\";\n$PG{\"dialign-t\"}{\"binary\"}=\
\"dialign-t\";\n$PG{\"dialign-tx\"}{\"4_TCOFFEE\"}\
=\"DIALIGNTX\";\n$PG{\"dialign-tx\"}{\"type\"}=\"s\
equence_multiple_aligner\";\n$PG{\"dialign-tx\"}{\\
"ADDRESS\"}=\"http://dialign-tx.gobics.de/\";\n$PG\
{\"dialign-tx\"}{\"DIR\"}=\"/usr/share/dialign-tx/\
\";\n$PG{\"dialign-tx\"}{\"language\"}=\"C\";\n$PG\
{\"dialign-tx\"}{\"language2\"}=\"C\";\n$PG{\"dial\
ign-tx\"}{\"source\"}=\"http://dialign-tx.gobics.d\
e/DIALIGN-TX_1.0.1.tar.gz\";\n$PG{\"dialign-tx\"}{\
\"mode\"}=\"mcoffee\";\n$PG{\"dialign-tx\"}{\"bina\
ry\"}=\"dialign-tx\";\n$PG{\"poa\"}{\"4_TCOFFEE\"}\
=\"POA\";\n$PG{\"poa\"}{\"type\"}=\"sequence_multi\
ple_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://downloa\
ds.sourceforge.net/poamsa/poaV2.tar.gz\";\n$PG{\"p\
oa\"}{\"DIR\"}=\"/usr/share/\";\n$PG{\"poa\"}{\"FI\
LE1\"}=\"blosum80.mat\";\n$PG{\"poa\"}{\"mode\"}=\\
"mcoffee\";\n$PG{\"poa\"}{\"binary\"}=\"poa\";\n$P\
G{\"probcons\"}{\"4_TCOFFEE\"}=\"PROBCONS\";\n$PG{\
\"probcons\"}{\"type\"}=\"sequence_multiple_aligne\
r\";\n$PG{\"probcons\"}{\"ADDRESS\"}=\"http://prob\
cons.stanford.edu/\";\n$PG{\"probcons\"}{\"languag\
e2\"}=\"CXX\";\n$PG{\"probcons\"}{\"language\"}=\"\
C++\";\n$PG{\"probcons\"}{\"source\"}=\"http://pro\
bcons.stanford.edu/probcons_v1_12.tar.gz\";\n$PG{\\
"probcons\"}{\"mode\"}=\"mcoffee\";\n$PG{\"probcon\
s\"}{\"binary\"}=\"probcons\";\n$PG{\"mafft\"}{\"4\
_TCOFFEE\"}=\"MAFFT\";\n$PG{\"mafft\"}{\"type\"}=\\
"sequence_multiple_aligner\";\n$PG{\"mafft\"}{\"AD\
DRESS\"}=\"http://align.bmr.kyushu-u.ac.jp/mafft/o\
nline/server/\";\n$PG{\"mafft\"}{\"language\"}=\"C\
\";\n$PG{\"mafft\"}{\"language\"}=\"C\";\n$PG{\"ma\
fft\"}{\"source\"}=\"http://align.bmr.kyushu-u.ac.\
jp/mafft/software/mafft-6.603-with-extensions-src.\
tgz\";\n$PG{\"mafft\"}{\"windows\"}=\"http://align\
.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-min\
gw.tar\";\n$PG{\"mafft\"}{\"mode\"}=\"mcoffee,rcof\
fee\";\n$PG{\"mafft\"}{\"binary\"}=\"mafft.tar.gz\\
";\n$PG{\"muscle\"}{\"4_TCOFFEE\"}=\"MUSCLE\";\n$P\
G{\"muscle\"}{\"type\"}=\"sequence_multiple_aligne\
r\";\n$PG{\"muscle\"}{\"ADDRESS\"}=\"http://www.dr\
ive5.com/muscle/\";\n$PG{\"muscle\"}{\"language\"}\
=\"C++\";\n$PG{\"muscle\"}{\"language2\"}=\"GPP\";\
\n$PG{\"muscle\"}{\"source\"}=\"http://www.drive5.\
com/muscle/downloads3.6/muscle3.6_src.tar.gz\";\n$\
PG{\"muscle\"}{\"windows\"}=\"http://www.drive5.co\
m/muscle/downloads3.6/muscle3.6_win32.zip\";\n$PG{\
\"muscle\"}{\"linux\"}=\"http://www.drive5.com/mus\
cle/downloads3.6/muscle3.6_linux_ia32.tar.gz\";\n$\
PG{\"muscle\"}{\"mode\"}=\"mcoffee,rcoffee\";\n$PG\
{\"pcma\"}{\"4_TCOFFEE\"}=\"PCMA\";\n$PG{\"pcma\"}\
{\"type\"}=\"sequence_multiple_aligner\";\n$PG{\"p\
cma\"}{\"ADDRESS\"}=\"ftp://iole.swmed.edu/pub/PCM\
A/\";\n$PG{\"pcma\"}{\"language\"}=\"C\";\n$PG{\"p\
cma\"}{\"language2\"}=\"C\";\n$PG{\"pcma\"}{\"sour\
ce\"}=\"ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz\\
";\n$PG{\"pcma\"}{\"mode\"}=\"mcoffee\";\n$PG{\"ka\
lign\"}{\"4_TCOFFEE\"}=\"KALIGN\";\n$PG{\"kalign\"\
}{\"type\"}=\"sequence_multiple_aligner\";\n$PG{\"\
kalign\"}{\"ADDRESS\"}=\"http://msa.cgb.ki.se\";\n\
$PG{\"kalign\"}{\"language\"}=\"C\";\n$PG{\"kalign\
\"}{\"language2\"}=\"C\";\n$PG{\"kalign\"}{\"sourc\
e\"}=\"http://msa.cgb.ki.se/downloads/kalign/curre\
nt.tar.gz\";\n$PG{\"kalign\"}{\"mode\"}=\"mcoffee\\
";\n$PG{\"amap\"}{\"4_TCOFFEE\"}=\"AMAP\";\n$PG{\"\
amap\"}{\"type\"}=\"sequence_multiple_aligner\";\n\
$PG{\"amap\"}{\"ADDRESS\"}=\"http://bio.math.berke\
ley.edu/amap/\";\n$PG{\"amap\"}{\"language\"}=\"C+\
+\";\n$PG{\"amap\"}{\"language2\"}=\"CXX\";\n$PG{\\
"amap\"}{\"source\"}=\"http://baboon.math.berkeley\
.edu/amap/download/amap.2.2.tar.gz\";\n$PG{\"amap\\
"}{\"mode\"}=\"mcoffee\";\n$PG{\"proda\"}{\"4_TCOF\
FEE\"}=\"PRODA\";\n$PG{\"proda\"}{\"type\"}=\"sequ\
ence_multiple_aligner\";\n$PG{\"proda\"}{\"ADDRESS\
\"}=\"http://proda.stanford.edu\";\n$PG{\"proda\"}\
{\"language\"}=\"C++\";\n$PG{\"proda\"}{\"language\
2\"}=\"CXX\";\n$PG{\"proda\"}{\"source\"}=\"http:/\
/proda.stanford.edu/proda_1_0.tar.gz\";\n$PG{\"pro\
da\"}{\"mode\"}=\"mcoffee\";\n$PG{\"prank\"}{\"4_T\
COFFEE\"}=\"PRANK\";\n$PG{\"prank\"}{\"type\"}=\"s\
equence_multiple_aligner\";\n$PG{\"prank\"}{\"ADDR\
ESS\"}=\"http://www.ebi.ac.uk/goldman-srv/prank/\"\
;\n$PG{\"prank\"}{\"language\"}=\"C++\";\n$PG{\"pr\
ank\"}{\"language2\"}=\"CXX\";\n$PG{\"prank\"}{\"s\
ource\"}=\"http://www.ebi.ac.uk/goldman-srv/prank/\
src/old/prank.src.081202.tgz\";\n$PG{\"prank\"}{\"\
mode\"}=\"mcoffee\";\n$PG{\"sap\"}{\"4_TCOFFEE\"}=\
\"SAP\";\n$PG{\"sap\"}{\"type\"}=\"structure_pairw\
ise_aligner\";\n$PG{\"sap\"}{\"ADDRESS\"}=\"http:/\
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p\"}{\"language\"}=\"C\";\n$PG{\"sap\"}{\"language\
2\"}=\"C\";\n$PG{\"sap\"}{\"source\"}=\"http://www\
.tcoffee.org/Packages/sap_distribution_TCC_0.6.tar\
.gz\";\n$PG{\"sap\"}{\"mode\"}=\"expresso,3dcoffee\
\";\n$PG{\"TMalign\"}{\"4_TCOFFEE\"}=\"TMALIGN\";\\
n$PG{\"TMalign\"}{\"type\"}=\"structure_pairwise_a\
ligner\";\n$PG{\"TMalign\"}{\"ADDRESS\"}=\"http://\
zhang.bioinformatics.ku.edu/TM-align/TMalign.f\";\\
n$PG{\"TMalign\"}{\"language\"}=\"Fortran\";\n$PG{\
\"TMalign\"}{\"language2\"}=\"Fortran\";\n$PG{\"TM\
align\"}{\"source\"}=\"http://zhang.bioinformatics\
.ku.edu/TM-align/TMalign.f\";\n$PG{\"TMalign\"}{\"\
linux\"}=\"http://zhang.bioinformatics.ku.edu/TM-a\
lign/TMalign_32.gz\";\n$PG{\"TMalign\"}{\"mode\"}=\
\"expresso,3dcoffee\";\n$PG{\"mustang\"}{\"4_TCOFF\
EE\"}=\"MUSTANG\";\n$PG{\"mustang\"}{\"type\"}=\"s\
tructure_pairwise_aligner\";\n$PG{\"mustang\"}{\"A\
DDRESS\"}=\"http://www.cs.mu.oz.au/~arun/mustang\"\
;\n$PG{\"mustang\"}{\"language\"}=\"C++\";\n$PG{\"\
mustang\"}{\"language2\"}=\"CXX\";\n$PG{\"mustang\\
"}{\"source\"}=\"http://www.cs.mu.oz.au/~arun/must\
ang/mustang_v.3.tgz\";\n$PG{\"mustang\"}{\"mode\"}\
=\"expresso,3dcoffee\";\n$PG{\"lsqman\"}{\"4_TCOFF\
EE\"}=\"LSQMAN\";\n$PG{\"lsqman\"}{\"type\"}=\"str\
ucture_pairwise_aligner\";\n$PG{\"lsqman\"}{\"ADDR\
ESS\"}=\"empty\";\n$PG{\"lsqman\"}{\"language\"}=\\
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";\n$PG{\"lsqman\"}{\"source\"}=\"empty\";\n$PG{\"\
lsqman\"}{\"update_action\"}=\"never\";\n$PG{\"lsq\
man\"}{\"mode\"}=\"expresso,3dcoffee\";\n$PG{\"ali\
gn_pdb\"}{\"4_TCOFFEE\"}=\"ALIGN_PDB\";\n$PG{\"ali\
gn_pdb\"}{\"type\"}=\"structure_pairwise_aligner\"\
;\n$PG{\"align_pdb\"}{\"ADDRESS\"}=\"empty\";\n$PG\
{\"align_pdb\"}{\"language\"}=\"empty\";\n$PG{\"al\
ign_pdb\"}{\"language2\"}=\"empty\";\n$PG{\"align_\
pdb\"}{\"source\"}=\"empty\";\n$PG{\"align_pdb\"}{\
\"update_action\"}=\"never\";\n$PG{\"align_pdb\"}{\
\"mode\"}=\"expresso,3dcoffee\";\n$PG{\"fugueali\"\
}{\"4_TCOFFEE\"}=\"FUGUE\";\n$PG{\"fugueali\"}{\"t\
ype\"}=\"structure_pairwise_aligner\";\n$PG{\"fugu\
eali\"}{\"ADDRESS\"}=\"http://www-cryst.bioc.cam.a\
c.uk/fugue/download.html\";\n$PG{\"fugueali\"}{\"l\
anguage\"}=\"empty\";\n$PG{\"fugueali\"}{\"languag\
e2\"}=\"empty\";\n$PG{\"fugueali\"}{\"source\"}=\"\
empty\";\n$PG{\"fugueali\"}{\"update_action\"}=\"n\
ever\";\n$PG{\"fugueali\"}{\"mode\"}=\"expresso,3d\
coffee\";\n$PG{\"dalilite.pl\"}{\"4_TCOFFEE\"}=\"D\
ALILITEc\";\n$PG{\"dalilite.pl\"}{\"type\"}=\"stru\
cture_pairwise_aligner\";\n$PG{\"dalilite.pl\"}{\"\
ADDRESS\"}=\"built_in\";\n$PG{\"dalilite.pl\"}{\"A\
DDRESS2\"}=\"http://www.ebi.ac.uk/Tools/webservice\
s/services/dalilite\";\n$PG{\"dalilite.pl\"}{\"lan\
guage\"}=\"Perl\";\n$PG{\"dalilite.pl\"}{\"languag\
e2\"}=\"Perl\";\n$PG{\"dalilite.pl\"}{\"source\"}=\
\"empty\";\n$PG{\"dalilite.pl\"}{\"update_action\"\
}=\"never\";\n$PG{\"dalilite.pl\"}{\"mode\"}=\"exp\
resso,3dcoffee\";\n$PG{\"probconsRNA\"}{\"4_TCOFFE\
E\"}=\"PROBCONSRNA\";\n$PG{\"probconsRNA\"}{\"type\
\"}=\"RNA_multiple_aligner\";\n$PG{\"probconsRNA\"\
}{\"ADDRESS\"}=\"http://probcons.stanford.edu/\";\\
n$PG{\"probconsRNA\"}{\"language\"}=\"C++\";\n$PG{\
\"probconsRNA\"}{\"language2\"}=\"CXX\";\n$PG{\"pr\
obconsRNA\"}{\"source\"}=\"http://probcons.stanfor\
d.edu/probconsRNA.tar.gz\";\n$PG{\"probconsRNA\"}{\
\"mode\"}=\"mcoffee,rcoffee\";\n$PG{\"sfold\"}{\"4\
_TCOFFEE\"}=\"CONSAN\";\n$PG{\"sfold\"}{\"type\"}=\
\"RNA_pairwise_aligner\";\n$PG{\"sfold\"}{\"ADDRES\
S\"}=\"http://selab.janelia.org/software/consan/\"\
;\n$PG{\"sfold\"}{\"language\"}=\"empty\";\n$PG{\"\
sfold\"}{\"language2\"}=\"empty\";\n$PG{\"sfold\"}\
{\"source\"}=\"empty\";\n$PG{\"sfold\"}{\"update_a\
ction\"}=\"never\";\n$PG{\"sfold\"}{\"mode\"}=\"rc\
offee\";\n$PG{\"RNAplfold\"}{\"4_TCOFFEE\"}=\"RNAP\
LFOLD\";\n$PG{\"RNAplfold\"}{\"type\"}=\"RNA_secon\
darystructure_predictor\";\n$PG{\"RNAplfold\"}{\"A\
DDRESS\"}=\"http://www.tbi.univie.ac.at/~ivo/RNA/\\
";\n$PG{\"RNAplfold\"}{\"language\"}=\"C\";\n$PG{\\
"RNAplfold\"}{\"language2\"}=\"C\";\n$PG{\"RNAplfo\
ld\"}{\"source\"}=\"http://www.tbi.univie.ac.at/~i\
vo/RNA/ViennaRNA-1.7.2.tar.gz\";\n$PG{\"RNAplfold\\
"}{\"mode\"}=\"rcoffee\";\n$PG{\"hmmtop\"}{\"4_TCO\
FFEE\"}=\"HMMTOP\";\n$PG{\"hmmtop\"}{\"type\"}=\"p\
rotein_secondarystructure_predictor\";\n$PG{\"hmmt\
op\"}{\"ADDRESS\"}=\"www.enzim.hu/hmmtop/\";\n$PG{\
\"hmmtop\"}{\"language\"}=\"C\";\n$PG{\"hmmtop\"}{\
\"language2\"}=\"C\";\n$PG{\"hmmtop\"}{\"source\"}\
=\"empty\";\n$PG{\"hmmtop\"}{\"update_action\"}=\"\
never\";\n$PG{\"hmmtop\"}{\"mode\"}=\"tcoffee\";\n\
$PG{\"gorIV\"}{\"4_TCOFFEE\"}=\"GOR4\";\n$PG{\"gor\
IV\"}{\"type\"}=\"protein_secondarystructure_predi\
ctor\";\n$PG{\"gorIV\"}{\"ADDRESS\"}=\"http://mig.\
jouy.inra.fr/logiciels/gorIV/\";\n$PG{\"gorIV\"}{\\
"language\"}=\"C\";\n$PG{\"gorIV\"}{\"language2\"}\
=\"C\";\n$PG{\"gorIV\"}{\"source\"}=\"http://mig.j\
ouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz\";\n$PG{\
\"gorIV\"}{\"update_action\"}=\"never\";\n$PG{\"go\
rIV\"}{\"mode\"}=\"tcoffee\";\n$PG{\"wublast.pl\"}\
{\"4_TCOFFEE\"}=\"EBIWUBLASTc\";\n$PG{\"wublast.pl\
\"}{\"type\"}=\"protein_homology_predictor\";\n$PG\
{\"wublast.pl\"}{\"ADDRESS\"}=\"built_in\";\n$PG{\\
"wublast.pl\"}{\"ADDRESS2\"}=\"http://www.ebi.ac.u\
k/Tools/webservices/services/wublast\";\n$PG{\"wub\
last.pl\"}{\"language\"}=\"Perl\";\n$PG{\"wublast.\
pl\"}{\"language2\"}=\"Perl\";\n$PG{\"wublast.pl\"\
}{\"source\"}=\"empty\";\n$PG{\"wublast.pl\"}{\"up\
date_action\"}=\"never\";\n$PG{\"wublast.pl\"}{\"m\
ode\"}=\"psicoffee,expresso,3dcoffee\";\n$PG{\"bla\
stpgp.pl\"}{\"4_TCOFFEE\"}=\"EBIBLASTPGPc\";\n$PG{\
\"blastpgp.pl\"}{\"type\"}=\"protein_homology_pred\
ictor\";\n$PG{\"blastpgp.pl\"}{\"ADDRESS\"}=\"buil\
t_in\";\n$PG{\"blastpgp.pl\"}{\"ADDRESS2\"}=\"http\
://www.ebi.ac.uk/Tools/webservices/services/blastp\
gp\";\n$PG{\"blastpgp.pl\"}{\"language\"}=\"Perl\"\
;\n$PG{\"blastpgp.pl\"}{\"language2\"}=\"Perl\";\n\
$PG{\"blastpgp.pl\"}{\"source\"}=\"empty\";\n$PG{\\
"blastpgp.pl\"}{\"update_action\"}=\"never\";\n$PG\
{\"blastpgp.pl\"}{\"mode\"}=\"psicoffee,expresso,3\
dcoffee\";\n$PG{\"blastcl3\"}{\"4_TCOFFEE\"}=\"NCB\
IWEBBLAST\";\n$PG{\"blastcl3\"}{\"type\"}=\"protei\
n_homology_predictor\";\n$PG{\"blastcl3\"}{\"ADDRE\
SS\"}=\"ftp://ftp.ncbi.nih.gov/blast/executables/L\
ATEST\";\n$PG{\"blastcl3\"}{\"language\"}=\"C\";\n\
$PG{\"blastcl3\"}{\"language2\"}=\"C\";\n$PG{\"bla\
stcl3\"}{\"source\"}=\"empty\";\n$PG{\"blastcl3\"}\
{\"update_action\"}=\"never\";\n$PG{\"blastcl3\"}{\
\"mode\"}=\"psicoffee,expresso,3dcoffee\";\n$PG{\"\
blastpgp\"}{\"4_TCOFFEE\"}=\"NCBIBLAST\";\n$PG{\"b\
lastpgp\"}{\"type\"}=\"protein_homology_predictor\\
";\n$PG{\"blastpgp\"}{\"ADDRESS\"}=\"ftp://ftp.ncb\
i.nih.gov/blast/executables/LATEST\";\n$PG{\"blast\
pgp\"}{\"language\"}=\"C\";\n$PG{\"blastpgp\"}{\"l\
anguage2\"}=\"C\";\n$PG{\"blastpgp\"}{\"source\"}=\
\"empty\";\n$PG{\"blastpgp\"}{\"update_action\"}=\\
"never\";\n$PG{\"blastpgp\"}{\"mode\"}=\"psicoffee\
,expresso,3dcoffee\";\n$PG{\"SOAP::Lite\"}{\"4_TCO\
FFEE\"}=\"SOAPLITE\";\n$PG{\"SOAP::Lite\"}{\"type\\
"}=\"library\";\n$PG{\"SOAP::Lite\"}{\"ADDRESS\"}=\
\"http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite\
-0.710.08/Makefile.PL\";\n$PG{\"SOAP::Lite\"}{\"la\
nguage\"}=\"Perl\";\n$PG{\"SOAP::Lite\"}{\"languag\
e2\"}=\"Perl\";\n$PG{\"SOAP::Lite\"}{\"source\"}=\\
"empty\";\n$PG{\"SOAP::Lite\"}{\"mode\"}=\"psicoff\
ee,expresso,3dcoffee\";\n$MODE{\"tcoffee\"}{\"name\
\"}=\"tcoffee\";\n$MODE{\"rcoffee\"}{\"name\"}=\"r\
coffee\";\n$MODE{\"3dcoffee\"}{\"name\"}=\"3dcoffe\
e\";\n$MODE{\"mcoffee\"}{\"name\"}=\"mcoffee\";\n$\
MODE{\"expresso\"}{\"name\"}=\"expresso\";\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 $n;\n  }\n\n","use E\
nv;\nuse Cwd;\n@suffix=(\"tmp\", \"temp\", \"cache\
\", \"t_coffee\", \"core\", \"tcoffee\");\n\nif ($\
#ARGV==-1)\n  {\n    print \"clean_cache.pl -file \
<file to add in -dir> -dir=<dir> -size=<value in M\
b>\\n0: unlimited -1 always.\\nWill only clean dir\
ectories matching:[\";\n    foreach $k(@suffix){pr\
int \"*$k* \";}\n    print \"]\\n\";\n    exit (EX\
IT_FAILURE);\n  }\n\n$cl=join (\" \",@ARGV);\nif (\
($cl=~/\\-no_action/))\n  {\n    exit (EXIT_SUCCES\
S);\n  }\n\nif (($cl=~/\\-debug/))\n  {\n    $DEBU\
G=1;\n  }\nelse\n  {\n    $DEBUG=0;\n  }\n\nif (($\
cl=~/\\-dir=(\\S+)/))\n  {\n    $dir=$1;\n  }\nels\
e\n  {\n    $dir=\"./\";\n  }\n\nif ($cl=~/\\-file\
=(\\S+)/)\n  {\n    $file=$1;\n  }\nelse\n  {\n   \
 $file=0;\n  }\n\nif ($cl=~/\\-size=(\\S+)/)\n  {\\
n    $max_size=$1;\n  }\nelse\n  {\n    $max_size=\
0;#unlimited\n  }\nif ($cl=~/\\-force/)\n  {\n    \
$force=1;\n  }\nelse\n  {\n    $force=0;\n  }\n\ni\
f ($cl=~/\\-age=(\\S+)/)\n  {\n    $max_age=$1;\n \
 }\nelse\n  {\n    $max_age=0;#unlimited\n  }\n\n$\
max_size*=1000000;\nif ( ! -d $dir)\n  {\n    prin\
t STDERR \"\\nCannot process $dir: does not exist \
\\n\";\n    exit (EXIT_FAILURE);\n  }\n\nif ( !($d\
ir=~/^\\//))\n  {\n    $base=cwd();\n    $dir=\"$b\
ase/$dir\";\n  }\n\n$proceed=0;\nforeach $s (@suff\
ix)\n  {\n    \n    if (($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 directories whose\
 absolute path name contains the following strings\
:\";\n    foreach $w (@suffix) {print STDERR \"$w \
\";$w=lc($w); print STDERR \"$w \";}\n    print ST\
DERR \"\\nCannot process $dir\\n\";\n    exit (EXI\
T_FAILURE);\n  }\n\n$name_file=\"$dir/name_file.tx\
t\";\n$size_file=\"$dir/size_file.txt\";\nif ( $fo\
rce){&create_ref_file ($dir,$name_file,$size_file)\
;}\nif ($file){&add_file ($dir, $name_file, $size_\
file, $file);}\n&clean_dir ($dir, $name_file, $siz\
e_file, $max_size,$max_age);\nexit (EXIT_SUCCESS);\
\n\nsub clean_dir \n  {\n    my ($dir, $name_file,\
 $size_file, $max_size, $max_age)=@_;\n    my ($to\
t_size, $size, $f, $s);\n\n  \n    $tot_size=&get_\
tot_size ($dir, $name_file, $size_file);\n\n    if\
 ( $tot_size<=$max_size){return ;}\n    else {$max\
_size/=2;}\n    \n    #recreate the name file in c\
ase some temprary files have not been properly reg\
istered\n    &create_ref_file ($dir, $name_file, $\
size_file, $max_age);\n  \n    $new_name_file=&vtm\
pnam();\n    open (R, \"$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        $tot_s\
ize-=$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_fil\
e){`mv $new_name_file $name_file`;}\n    close (F)\
;\n  }\nsub get_tot_size\n  {\n    my ($dir, $name\
_file, $size_file)=@_;\n    my $size;\n    \n    i\
f ( !-d $dir){return 0;}\n    if ( !-e $name_file)\
\n      {\n     \n      &create_ref_file ($dir, $name_file,\
 $size_file);\n      }\n    open (F, \"$size_file\\
");\n    $size=<F>;\n    close (F);\n    chomp ($s\
ize);\n    return $size;\n  }\nsub size \n  {\n   \
 my $f=@_[0];\n\n    if ( !-d $f){return -s($f);}\\
n    else {return &dir2size($f);}\n  }\nsub dir2si\
ze\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+=&dir\
2size (\"$d/$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    debu\
g_print( \"--- $file ---\\n\");\n    if (($file eq\
 \".\") || ($file eq \"..\") || ($file=~/\\*/)){re\
turn EXIT_FAILURE;}\n    elsif ( !-d $file)\n     \
 {\n    debug_print (\"unlink $file\\n\");\n    if (-e $\
file){unlink ($file);}\n      }\n    elsif ( -d $f\
ile)\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 EXIT_SUCCESS;\n \
 }\n\nsub dir2list\n  {\n    my $dir=@_[0];\n    m\
y (@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 \"..\"){@list2=(@list2, $l\
);}\n      }\n    @list3 = sort { (-M \"$dir/$list\
2[$b]\") <=> (-M \"$dir/$list2[$a]\")} @list2;\n  \
  return @list3;\n    \n  }\n\nsub debug_print\n  \
{\n    \n    if ($DEBUG==1){print @_;}\n    \n  }\\
nsub create_ref_file\n  {\n    my ($dir,$name_file\
,$size_file)=@_;\n    my ($f, $s, $tot_size, @l);\\
n    \n    if ( !-d $dir){return;}\n    \n    @l=&\
dir2list ($dir);\n    open (F, \">$name_file\");\n\
    foreach $f (@l)\n      {\n  $s=&size(\"$dir/$f\\
");\n   $tot_size+=$s;\n        print F \"$f $s\\n\";\n    \
  }\n    &myecho ($tot_size, \">$size_file\");\n  \
  close (F);\n  }\nsub add_file \n  {\n    my ($di\
r,$name_file,$size_file,$file)=@_;\n    my ($s, $t\
ot_size);\n    \n    if ( !-d $dir)   {return;}\n \
   if ( !-e \"$dir/$file\" ) {return;}\n    if ( !\
-e $name_file){&create_ref_file ($dir,$name_file,$\
size_file);}\n                                      \n    $s=&size(\"$dir/$file\
\");\n    open (F, \">>$name_file\");\n    print F\
 \"$file\\n\";\n    close (F);\n\n    $tot_size=&g\
et_tot_size ($dir,$name_file,$size_file);\n    $to\
t_size+=$s;\n    &myecho ($tot_size, \">$size_file\
\");\n    \n  }\n       \nsub myecho\n  {\n    my ($stri\
ng, $file)=@_;\n    open (ECHO, $file) || die;\n  \
  print ECHO \"$string\";\n    close (ECHO);\n  }\\
n    \n         \n      \nsub vtmpnam\n  {\n    my $tmp_file_n\
ame;\n    $tmp_name_counter++;\n    $tmp_file_name\
=\"tmp_file_for_clean_cache_pdb$$.$tmp_name_counte\
r\";\n    $tmp_file_list[$ntmp_file++]=$tmp_file_n\
ame;\n    if ( -e $tmp_file_name) {return &vtmpnam\
 ();}\n    else {return $tmp_file_name;}\n  }\n","\
\n$t_coffee=\"t_coffee\";\n\nforeach $value ( @ARG\
V)\n  {\n    $seq_file=$seq_file.\" \".$value;\n  \
}\n\n$name=$ARGV[0];\n$name=~s/\\.[^\\.]*$//;\n$li\
b_name=\"$name.mocca_lib\";\n$type=`t_coffee $seq_\
file -get_type -quiet`;\nchop ($type);\n\nif ( $ty\
pe eq \"PROTEIN\"){$lib_mode=\"lalign_rs_s_pair -l\
align_n_top 20\";}\nelsif ( $type eq\"DNA\"){$lib_\
mode=\"lalign_rs_s_dna_pair -lalign_n_top 40\";}\n\
\nif ( !(-e $lib_name))\n  {\n    \n  $command=\"$t\
_coffee -mocca -seq_weight=no -cosmetic_penalty=0 \
-mocca_interactive -in $lib_mode -out_lib $lib_nam\
e -infile $seq_file\";\n  \n  }\nelsif ( (-e $lib_\
name))\n  {\n  $command=\"$t_coffee -mocca -seq_we\
ight=no -cosmetic_penalty=0 -mocca_interactive -in\
 $lib_name -infile $seq_file\";\n  \n  }\n\nsystem\
 ($command);\n\nexit;\n\n","my $WSDL = 'http://www\
.ebi.ac.uk/Tools/webservices/wsdl/WSDaliLite.wsdl'\
;\n\nuse SOAP::Lite;\nuse Data::Dumper;\nuse Getop\
t::Long qw(:config no_ignore_case bundling);\nuse \
File::Basename;\n\nmy $checkInterval = 5;\n\nmy %p\
arams=(\n           'async' => '1', # Use async mode and\
 simulate sync mode in client\n     );\nGetOptions\
(\n    'pdb1=s'     => \\$params{'sequence1'},\n  \
  'chainid1=s' => \\$params{'chainid1'},\n    'pdb\
2=s'     => \\$params{'sequence2'},\n    'chainid2\
=s' => \\$params{'chainid2'},\n    \"help|h\"    => \
\\$help, # Usage info\n    \"async|a\"   => \\$asyn\
c, # Asynchronous submission\n    \"polljob\"    => \
\\$polljob, # Get results\n    \"status\"        => \\$s\
tatus, # Get status\n    \"jobid|j=s\"  => \\$jobi\
d, # JobId\n    \"email|S=s\"  => \\$params{email}\
, # E-mail address\n    \"trace\"      => \\$trace\
, # SOAP messages\n    \"sequence=s\" => \\$sequen\
ce, # Input PDB\n    );\n\nmy $scriptName = basena\
me($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 exce\
ption for all faults\n        if(ref($res) eq '') \
{\n            die($res);\n        } else {\n     \
       die($res->faultstring);\n        }\n       \
 return new SOAP::SOM;\n    }\n               );\n\
\nif( !($polljob || $status) &&\n    !( defined($p\
arams{'sequence1'}) && defined($params{'sequence2'\
}) )\n    ) {\n    print STDERR 'Error: bad option\
 combination', \"\\n\";\n    &usage();\n    exit(1\
);\n}\nelsif($polljob && defined($jobid)) {\n    p\
rint \"Getting results for job $jobid\\n\";\n    g\
etResults($jobid);\n}\nelsif($status && defined($j\
obid)) {\n    print STDERR \"Getting status for jo\
b $jobid\\n\";\n    my $result = $soap->checkStatu\
s($jobid);\n    print STDOUT \"$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{'sequen\
ce1'}) {\n      $params{'sequence1'} = read_file($param\
s{'sequence1'});\n    }\n    if(-f $params{'sequen\
ce2'}) {\n      $params{'sequence2'} = read_file($param\
s{'sequence2'});\n    }\n\n    my $jobid;\n    my \
$paramsData = SOAP::Data->name('params')->type(map\
=>\\%params);\n    # For SOAP::Lite 0.60 and earli\
er parameters are passed directly\n    if($SOAP::L\
ite::VERSION eq '0.60' || $SOAP::Lite::VERSION =~ \
/0\\.[1-5]/) {\n        $jobid = $soap->runDaliLit\
e($paramsData);\n    }\n    # For SOAP::Lite 0.69 \
and later parameter handling is different, so pass\
\n    # undef's for templated params, and then pas\
s the formatted args.\n    else {\n        $jobid \
= $soap->runDaliLite(undef,\n                                $paramsData)\
;\n    }\n\n    if (defined($async)) {\n        print STD\
OUT $jobid, \"\\n\";\n        print STDERR \"To ch\
eck status: $scriptName --status --jobid $jobid\\n\
\";\n    } else { # Synchronous mode\n        prin\
t STDERR \"JobId: $jobid\\n\";\n        sleep 1;\n\
        getResults($jobid);\n    }\n}\n\nsub clien\
tPoll($) {\n    my $jobid = shift;\n    my $result\
 = 'PENDING';\n    # Check status and wait if not \
finished\n    #print STDERR \"Checking status: $jo\
bid\\n\";\n    while($result eq 'RUNNING' || $resu\
lt eq 'PENDING') {\n        $result = $soap->check\
Status($jobid);\n        print STDERR \"$result\\n\
\";\n        if($result eq 'RUNNING' || $result eq\
 'PENDING') {\n            # Wait before polling a\
gain.\n            sleep $checkInterval;\n        \
}\n    }\n}\n\nsub getResults($) {\n    $jobid = s\
hift;\n    # Check status, and wait if not finishe\
d\n    clientPoll($jobid);\n    # Use JobId if out\
put file name is not defined\n    unless(defined($\
outfile)) {\n        $outfile=$jobid;\n    }\n    \
# Get list of data types\n    my $resultTypes = $s\
oap->getResults($jobid);\n    # Get the data and w\
rite it to a file\n    if(defined($outformat)) { #\
 Specified data type\n        my $selResultType;\n\
        foreach my $resultType (@$resultTypes) {\n\
            if($resultType->{type} eq $outformat) \
{\n                $selResultType = $resultType;\n\
            }\n        }\n        $res=$soap->poll\
($jobid, $selResultType->{type});\n        write_f\
ile($outfile.'.'.$selResultType->{ext}, $res);\n  \
  } else { # Data types available\n        # Write\
 a file for each output type\n        for my $resu\
ltType (@$resultTypes){\n            #print \"Gett\
ing $resultType->{type}\\n\";\n            $res=$s\
oap->poll($jobid, $resultType->{type});\n         \
   write_file($outfile.'.'.$resultType->{ext}, $re\
s);\n        }\n    }\n}\n\nsub read_file($) {\n  \
  my $filename = shift;\n    open(FILE, $filename)\
;\n    my $content;\n    my $buffer;\n    while(sy\
sread(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 <<EOF\nDaliLite\n========\n\n\
Pairwise comparison of protein structures\n\n[Requ\
ired]\n\n  --pdb1                : str  : PDB ID f\
or structure 1\n  --pdb2                : str  : P\
DB ID for structure 2\n\n[Optional]\n\n  --chain1 \
             : str  : Chain identifer in structure\
 1\n  --chain2              : str  : Chain identif\
er in structure 2\n\n[General]\n\n  -h, --help    \
        :      : prints this help text\n  -S, --em\
ail           : str  : user email address\n  -a, -\
-async           :      : asynchronous submission\\
n      --status          :      : poll for the sta\
tus of a job\n      --polljob         :      : pol\
l for the results of a job\n  -j, --jobid         \
  : str  : jobid for an asynchronous job\n  -O, --\
outfile         : str  : file name for results (de\
fault is jobid)\n      --trace          :      : sh\
ow SOAP messages being interchanged \n\nSynchronou\
s job:\n\n  The results/errors are returned as soo\
n as the job is finished.\n  Usage: $scriptName --\
email <your\\@email> [options] pdbFile [--outfile \
string]\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  \
are stored for up to 24 hours. \n  The asynchronou\
s submission mode is recommended when users are su\
bmitting \n  batch jobs or large database searches\
        \n  Usage: $scriptName --email <your\\@email> --a\
sync [options] pdbFile\n  Returns: jobid\n\n  Use \
the jobid to query for the status of the job. \n  \
Usage: $scriptName --status --jobid <jobId>\n  Ret\
urns: string indicating the status of the job:\n  \
  DONE - job has finished\n    RUNNING - job is ru\
nning\n    NOT_FOUND - job cannot be found\n    ER\
ROR - the jobs has encountered an error\n\n  When \
done, use the jobid to retrieve the status of the \
job. \n  Usage: $scriptName --polljob --jobid <job\
Id> [--outfile string]\n\n[Help]\n\n  For more det\
ailed help information refer to\n  http://www.ebi.\
ac.uk/DaliLite/\nEOF\n;\n}\n","my $WSDL = 'http://\
www.ebi.ac.uk/Tools/webservices/wsdl/WSWUBlast.wsd\
l';\n\nuse strict;\nuse SOAP::Lite;\nuse Getopt::L\
ong qw(:config no_ignore_case bundling);\nuse File\
::Basename;\n\nmy $checkInterval = 15;\n\nmy $numO\
pts = scalar(@ARGV);\nmy ($outfile, $outformat, $h\
elp, $async, $polljob, $status, $ids, $jobid, $tra\
ce, $sequence);\nmy %params= ( # Defaults\n           \
'async' => 1, # Force into async mode\n       'exp\
' => 10.0, # E-value threshold\n              'numal' => \
50, # Maximum number of alignments\n          'scores\
' => 100, # Maximum number of scores\n            \
);\nGetOptions( # Map the options into variables\n\
    \"program|p=s\"     => \\$params{program}, # B\
LAST program\n    \"database|D=s\"    => \\$params\
{database}, # Search database\n    \"matrix|m=s\" \
     => \\$params{matrix}, # Scoring matrix\n    \\
"exp|E=f\"         => \\$params{exp}, # E-value th\
reshold\n    \"echofilter|e\"    => \\$params{echo\
filter}, # Display filtered sequence\n    \"filter\
|f=s\"      => \\$params{filter}, # Low complexity\
 filter name\n    \"alignments|b=i\"  => \\$params\
{numal}, # Number of alignments\n    \"scores|s=i\\
"      => \\$params{scores}, # Number of scores\n \
   \"sensitivity|S=s\" => \\$params{sensitivity}, \
# Search sensitivity\n    \"sort|t=s\"        => \\\
$params{sort}, # Sort hits by...\n    \"stats|T=s\\
"       => \\$params{stats}, # Scoring statistic t\
o use\n    \"strand|d=s\"      => \\$params{strand\
}, # Strand to use in DNA vs. DNA search\n    \"to\
pcombon|c=i\"   => \\$params{topcombon}, # Consist\
ent sets of HSPs\n    \"outfile=s\"       => \\$ou\
tfile, # Output file\n    \"outformat|o=s\"   => \\
\$outformat, # Output format\n    \"help|h\"         \
 => \\$help, # Usage info\n    \"async|a\"            =\
> \\$async, # Asynchronous 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    \"em\
ail=s\"         => \\$params{email}, # E-mail addr\
ess\n    \"trace\"           => \\$trace, # SOAP t\
race\n    \"sequence=s\"      => \\$sequence, # Qu\
ery sequence\n    );\n\nmy $scriptName = basename(\
$0, ());\nif($help || $numOpts == 0) {\n    &usage\
();\n    exit(0);\n}\n\nif($trace){\n    print STD\
ERR \"Tracing active\\n\";\n    SOAP::Lite->import\
(+trace => 'debug');\n}\n\nmy $soap = SOAP::Lite\n\
    ->service($WSDL)\n    ->proxy('http://localhos\
t/',\n    #proxy => ['http' => 'http://your.proxy.\
server/'], # HTTP proxy\n    timeout => 600, # HTT\
P connection timeout\n    )\n    ->on_fault(sub { \
# SOAP fault handler\n        my $soap = shift;\n \
       my $res = shift;\n        # Throw an except\
ion for all faults\n        if(ref($res) eq '') {\\
n            die($res);\n        } else {\n       \
     die($res->faultstring);\n        }\n        r\
eturn new SOAP::SOM;\n    }\n               );\n\n\
if( !($polljob || $status || $ids) &&\n    !( defi\
ned($ARGV[0]) || defined($sequence) )\n    ) {\n  \
  print STDERR 'Error: bad option combination', \"\
\\n\";\n    &usage();\n    exit(1);\n}\nelsif($pol\
ljob && defined($jobid)) {\n    print \"Getting re\
sults for job $jobid\\n\";\n    getResults($jobid)\
;\n}\nelsif($status && defined($jobid)) {\n    pri\
nt STDERR \"Getting status for job $jobid\\n\";\n \
   my $result = $soap->checkStatus($jobid);\n    p\
rint STDOUT \"$result\\n\";\n    if($result eq 'DO\
NE') {\n        print STDERR \"To get results: $scriptNam\
e --polljob --jobid $jobid\\n\";\n    }\n}  \nelsi\
f($ids && defined($jobid)) {\n    print STDERR \"G\
etting ids from job $jobid\\n\";\n    getIds($jobi\
d);\n}\nelse {\n    # Prepare input data\n    my $\
content;\n    my (@contents) = ();\n    if(-f $ARG\
V[0] || $ARGV[0] eq '-') {      \n      $content={type=>'seq\
uence',content=>read_file($ARGV[0])};   \n    }\n   \
 if($sequence) {        \n      if(-f $sequence || $sequence e\
q '-') {        \n          $content={type=>'sequence',content\
=>read_file($ARGV[0])}; \n      } else {\n          $content\
={type=>'sequence',content=>$sequence};\n       }\n    }\
\n    push @contents, $content;\n\n    # Submit th\
e job\n    my $paramsData = SOAP::Data->name('para\
ms')->type(map=>\\%params);\n    my $contentData =\
 SOAP::Data->name('content')->value(\\@contents);\\
n    # For SOAP::Lite 0.60 and earlier parameters \
are passed directly\n    if($SOAP::Lite::VERSION e\
q '0.60' || $SOAP::Lite::VERSION =~ /0\\.[1-5]/) {\
\n        $jobid = $soap->runWUBlast($paramsData, \
$contentData);\n    }\n    # For SOAP::Lite 0.69 a\
nd later parameter handling is different, so pass\\
n    # undef's for templated params, and then pass\
 the formatted args.\n    else {\n        $jobid =\
 $soap->runWUBlast(undef, undef,\n                                 $paramsDa\
ta, $contentData);\n    }\n\n    # Asynchronous mo\
de: output jobid and exit.\n    if (defined($async\
)) {\n  print STDOUT $jobid, \"\\n\";\n        prin\
t STDERR \"To check status: $scriptName --status -\
-jobid $jobid\\n\";\n    }\n    # Synchronous mode\
: try to get results\n    else {\n        print ST\
DERR \"JobId: $jobid\\n\";\n        sleep 1;\n    \
    getResults($jobid);\n    }\n}\n\nsub getIds($)\
 {\n    my $jobid = shift;\n    my $results = $soa\
p->getIds($jobid);\n    for my $result (@$results)\
{\n     print \"$result\\n\";\n    }\n}\n\nsub clientP\
oll($) {\n    my $jobid = shift;\n    my $result =\
 'PENDING';\n    # Check status and wait if not fi\
nished\n    while($result eq 'RUNNING' || $result \
eq 'PENDING') {\n        $result = $soap->checkSta\
tus($jobid);\n        print STDERR \"$result\\n\";\
\n        if($result eq 'RUNNING' || $result eq 'P\
ENDING') {\n            # Wait before polling agai\
n.\n            sleep $checkInterval;\n        }\n\
    }\n}\n\nsub getResults($) {\n    my $jobid = s\
hift;\n    my $res;\n    # Check status, and wait \
if not finished\n    clientPoll($jobid);\n    # Us\
e JobId if output file name is not defined\n    un\
less(defined($outfile)) {\n        $outfile=$jobid\
;\n    }\n    # Get list of data types\n    my $re\
sultTypes = $soap->getResults($jobid);\n    # Get \
the data and write it to a file\n    if(defined($o\
utformat)) { # Specified data type\n    if($outformat\
 eq 'xml') {$outformat = 'toolxml';}\n  if($outform\
at eq 'txt') {$outformat = 'tooloutput';}\n       \
 my $selResultType;\n        foreach my $resultTyp\
e (@$resultTypes) {\n            if($resultType->{\
type} eq $outformat) {\n                $selResult\
Type = $resultType;\n            }\n        }\n   \
     $res=$soap->poll($jobid, $selResultType->{typ\
e});\n  if($outfile eq '-') {\n      write_file($ou\
tfile, $res);\n } else {\n          write_file($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 \"Getti\
ng $resultType->{type}\\n\";\n            $res=$so\
ap->poll($jobid, $resultType->{type});\n            if($o\
utfile eq '-') {\n              write_file($outfile, $res);\n   \
    } else {\n          write_file($outfile.'.'.$resultTyp\
e->{ext}, $res);\n          }\n        }\n    }\n}\n\ns\
ub read_file($) {\n    my $filename = shift;\n    \
my ($content, $buffer);\n    if($filename eq '-') \
{\n     while(sysread(STDIN, $buffer, 1024)) {\n            $\
content .= $buffer;\n   }\n    }\n    else { # File\\
n       open(FILE, $filename) or die \"Error: unable to \
open input file\";\n    while(sysread(FILE, $buffer, \
1024)) {\n          $content .= $buffer;\n      }\n     close(FI\
LE);\n    }\n    return $content;\n}\n\nsub write_\
file($$) {\n    my ($filename, $data) = @_;\n    p\
rint STDERR 'Creating result file: ' . $filename .\
 \"\\n\";\n    if($filename eq '-') {\n print STDO\
UT $data;\n    }\n    else {\n  open(FILE, \">$file\
name\") or die \"Error: unable to open output file\
\";\n   syswrite(FILE, $data);\n        close(FILE);\n    }\
\n}\n\nsub usage {\n    print STDERR <<EOF\nWU-BLA\
ST\n========\n\nRapid sequence database search pro\
grams utilizing the BLAST algorithm.\n   \n[Requir\
ed]\n\n      --email       : str  : user email add\
ress \n  -p, --program      : str  : BLAST program \
to use: blastn, blastp, blastx, \n                \
             tblastn or tblastx\n  -D, --database \
   : str  : database to search\n  seqFile         \
  : file : query sequence data file (\"-\" for STD\
IN)\n\n[Optional]\n\n  -m, --matrix         : str  : s\
coring matrix\n  -E, --exp          : real : 0<E<= 1000\
. Statistical significance threshold\n            \
                 for reporting database sequence m\
atches.\n  -e, --echofilter  :      : display the \
filtered query sequence in the output\n  -f, --fil\
ter         : str  : activates filtering of the query \
sequence\n  -b, --alignments  : int  : number of a\
lignments to be reported\n  -s, --scores            : int\
  : number of scores to be reported\n  -S, --sensi\
tivity : str  :\n  -t, --sort       : str  :\n  -T, \
--stats       : str  :\n  -d, --strand      : str \
 : DNA strand to search with in DNA vs. DNA search\
es \n  -c, --topcombon   :      :\n\n[General]  \n\\
n  -h, --help       :      : prints this help text\
\n  -a, --async      :      : forces to make an as\
ynchronous 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 was returned when an async\
hronous job \n                            was subm\
itted.\n  -O, --outfile    : str  : name of the fi\
le results should be written to \n                \
            (default is based on the jobid; \"-\" \
for STDOUT)\n  -o, --outformat  : str  : txt or xm\
l output (no file is written)\n      --trace       : \
     : show SOAP messages being interchanged \n\nS\
ynchronous job:\n\n  The results/errors are return\
ed as soon as the job is finished.\n  Usage: $scri\
ptName --email <your\\@email> [options...] seqFile\
\n  Returns: saves the results to disk\n\nAsynchro\
nous job:\n\n  Use this if you want to retrieve th\
e results at a later time. The results \n  are sto\
red for up to 24 hours. \n  The asynchronous submi\
ssion mode is recommended when users are submittin\
g \n  batch jobs or large database searches     \n  Us\
age: $scriptName --async --email <your\\@email> [o\
ptions...] seqFile\n  Returns : jobid\n\n  Use the\
 jobid to query for the status of the job. \n  Usa\
ge: $scriptName --status --jobid <jobId>\n  Return\
s : string indicating the status of the job:\n    \
DONE - job has finished\n    RUNNING - job is runn\
ing\n    NOT_FOUND - job cannot be found\n    ERRO\
R - the jobs has encountered an error\n\n  When do\
ne, use the jobid to retrieve the status of the jo\
b. \n  Usage: $scriptName --polljob --jobid <jobId\
> [--outfile string]\n  Returns: saves the results\
 to disk\n\n[Help]\n\nFor more detailed help infor\
mation refer to \nhttp://www.ebi.ac.uk/blast2/WU-B\
last2_Help_frame.html\n \nEOF\n;\n}\n","\nmy $WSDL\
 = 'http://www.ebi.ac.uk/Tools/webservices/wsdl/WS\
Blastpgp.wsdl';\n\nuse SOAP::Lite;\nuse Getopt::Lo\
ng qw(:config no_ignore_case bundling);\nuse File:\
:Basename;\n\nmy $checkInterval = 15;\n\nmy %param\
s=(\n       'async' => '1', # Use async mode and sim\
ulate sync mode in client\n         );\nGetOptions(\n \
   \"mode=s\"           => \\$params{mode}, # Sear\
ch mode: PSI-Blast or PHI-Blast\n    \"database|d=\
s\"     => \\$params{database}, # Database to sear\
ch\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{filter}, # Low complexity fi\
lter\n    \"dropoff|X=i\"      => \\$params{dropof\
f}, # Dropoff score\n    \"finaldropoff|Z=i\" => \\
\$params{finaldropoff}, # Final dropoff score\n   \
 \"scores|v=i\"       => \\$params{scores}, # Max \
number of scores\n    \"align=i\"          => \\$p\
arams{align}, # Alignment view\n    \"startregion|\
S=i\"  => \\$params{startregion}, # Start of regio\
n in query\n    \"endregion|H=i\"    => \\$params{\
endregion}, # End of region in query\n    \"maxpas\
ses|j=i\"    => \\$params{maxpasses}, # Number of \
PSI iterations\n    \"opengap|G=i\"      => \\$par\
ams{opengap}, # Gap open penalty\n    \"extendgap|\
E=i\"    => \\$params{extendgap}, # Gap extension \
penalty\n    \"pattern=s\"        => \\$params{pat\
tern}, # PHI-BLAST pattern\n    \"usagemode|p=s\" \
   => \\$params{usagemode}, # PHI-BLAST program\n \
   \"appxml=s\"         => \\$params{appxml}, # Ap\
plication XML\n    \"sequence=s\"       => \\$sequ\
ence, # Query sequence\n    \"help\"           => \\$\
help, # Usage info\n    \"polljob\"            => \\$p\
olljob, # Get results\n    \"status\"          => \\\
$status, # Get status\n    \"ids\"                     =>\
 \\$ids, # Get ids from result\n    \"jobid=s\"   \
       => \\$jobid, # JobId\n    \"outfile=s\"    \
    => \\$outfile, # Output filename\n    \"outfor\
mat|o=s\"    => \\$outformat, # Output file format\
\n    \"async|a\"              => \\$async, # Async subm\
ission\n    \"email=s\"          => \\$params{emai\
l}, # User e-mail address\n    \"trace\"          \
  => \\$trace, # Show SOAP messages\n    );\n\nmy \
$scriptName = basename($0, ());\nif($help) {\n    \
&usage();\n    exit(0);\n}\n\nif ($trace){\n    pr\
int \"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        return new SOAP::SOM;\n    }\\
n               );\n\nif( !($polljob || $status ||\
 $ids) &&\n    !( (defined($ARGV[0]) && -f $ARGV[0\
]) || defined($sequence) )\n    ) {\n    print STD\
ERR 'Error: bad option combination', \"\\n\";\n   \
 &usage();\n    exit(1);\n}\nelsif($polljob && def\
ined($jobid)) {\n    print \"Getting results for j\
ob $jobid\\n\";\n    getResults($jobid);\n}\nelsif\
($status && defined($jobid)) {\n    print STDERR \\
"Getting status for job $jobid\\n\";\n    my $resu\
lt = $soap->checkStatus($jobid);\n    print STDOUT\
 $result, \"\\n\";\n    if($result eq 'DONE') {\n       \
print STDERR \"To get results: $scriptName --pollj\
ob --jobid $jobid\\n\";\n    }\n}  \nelsif($ids &&\
 defined($jobid)) {\n    print STDERR \"Getting id\
s from job $jobid\\n\";\n    getIds($jobid);\n}\ne\
lse {\n    if(-f $ARGV[0]) {    \n      $content={type=>'s\
equence', content=>read_file($ARGV[0])};        \n    }\n\
    if($sequence) {     \n      if(-f $sequence) {\n        $c\
ontent={type=>'sequence', content=>read_file($sequ\
ence)}; \n      } else {\n          $content={type=>'sequenc\
e', content=>$sequence};\n      }\n    }\n    push @con\
tent, $content;\n\n    my $jobid;\n    my $paramsD\
ata = SOAP::Data->name('params')->type(map=>\\%par\
ams);\n    my $contentData = SOAP::Data->name('con\
tent')->value(\\@content);\n    # For SOAP::Lite 0\
.60 and earlier parameters are passed directly\n  \
  if($SOAP::Lite::VERSION eq '0.60' || $SOAP::Lite\
::VERSION =~ /0\\.[1-5]/) {\n        $jobid = $soa\
p->runBlastpgp($paramsData, $contentData);\n    }\\
n    # For SOAP::Lite 0.69 and later parameter han\
dling is different, so pass\n    # undef's for tem\
plated params, and then pass the formatted args.\n\
    else {\n        $jobid = $soap->runBlastpgp(un\
def, undef,\n                               $paramsData, $contentData);\n\
    }\n\n    if (defined($async)) {\n   print STDOUT\
 $jobid, \"\\n\";\n        print STDERR \"To check\
 status: $scriptName --status --jobid $jobid\\n\";\
\n    } else { # Synchronous mode\n        print S\
TDERR \"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        p\
rint \"$result\\n\";\n    }\n}\n\nsub clientPoll($\
) {\n    my $jobid = shift;\n    my $result = 'PEN\
DING';\n    # Check status and wait if not finishe\
d\n    #print STDERR \"Checking status: $jobid\\n\\
";\n    while($result eq 'RUNNING' || $result eq '\
PENDING') {\n        $result = $soap->checkStatus(\
$jobid);\n        print STDERR \"$result\\n\";\n  \
      if($result eq 'RUNNING' || $result eq 'PENDI\
NG') {\n            # Wait before polling again.\n\
            sleep $checkInterval;\n        }\n    \
}\n}\n\nsub getResults($) {\n    $jobid = shift;\n\
    # Check status, and wait if not finished\n    \
clientPoll($jobid);\n    # Use JobId if output fil\
e name is not defined\n    unless(defined($outfile\
)) {\n        $outfile=$jobid;\n    }\n    # Get l\
ist of data types\n    my $resultTypes = $soap->ge\
tResults($jobid);\n    # Get the data and write it\
 to a file\n    if(defined($outformat)) { # Specif\
ied data type\n        my $selResultType;\n       \
 foreach my $resultType (@$resultTypes) {\n       \
     if($resultType->{type} eq $outformat) {\n    \
            $selResultType = $resultType;\n       \
     }\n        }\n        $res=$soap->poll($jobid\
, $selResultType->{type});\n        write_file($ou\
tfile.'.'.$selResultType->{ext}, $res);\n    } els\
e { # Data types available\n        # Write a file\
 for each output type\n        for my $resultType \
(@$resultTypes){\n            #print \"Getting $re\
sultType->{type}\\n\";\n            $res=$soap->po\
ll($jobid, $resultType->{type});\n            writ\
e_file($outfile.'.'.$resultType->{ext}, $res);\n  \
      }\n    }\n}\n\nsub read_file($) {\n    my $f\
ilename = shift;\n    open(FILE, $filename);\n    \
my $content;\n    my $buffer;\n    while(sysread(F\
ILE, $buffer, 1024)) {\n        $content.= $buffer;\n    \
}\n    close(FILE);  \n    return $content;\n}\n\n\
sub write_file($$) {\n    my ($tmp,$entity) = @_;\\
n    print STDERR \"Creating result file: \".$tmp.\
\"\\n\";\n    unless(open (FILE, \">$tmp\")) {\n        r\
eturn 0;\n    }\n    syswrite(FILE, $entity);\n   \
 close (FILE);\n    return 1;\n}\n\nsub usage {\n \
   print STDERR <<EOF\nBlastpgp\n========\n   \nTh\
e blastpgp program implements the PSI-BLAST and PH\
I-BLAST variations\nof NCBI BLAST.\n\nFor more det\
ailed help information refer to\nhttp://www.ebi.ac\
.uk/blastpgp/blastpsi_help_frame.html\n \nBlastpgp\
 specific options:\n\n[Required]\n\n      --mode  \
          : str  : search mode to use: PSI-Blast o\
r PHI-Blast\n  -d, --database        : str  : prot\
ein database to search\n  seqFile               : \
file : query sequence\n\n[Optional]\n\n  -M, --mat\
rix          : str  : scoring matrix\n  -e, --exp \
            : real : Expectation value\n  -h, --ex\
pmulti        : real : threshold (multipass model)\
\n  -F, --filter          : str  : filter query se\
quence with SEG [T,F]\n  -m, --align           : i\
nt  : alignment view option:\n                    \
             0 - pairwise, 1 - M/S identities,\n  \
                               2 - M/S non-identit\
ies, 3 - Flat identities,\n                       \
          4 - Flat non-identities\n  -G, --opengap\
         : int  : cost to open a gap\n  -E, --exte\
ndgap       : int  : cost to extend a gap\n  -g, -\
-gapalign        : str  : Gapped [T,F]\n  -v, --sc\
ores          : int  : number of scores to be repo\
rted\n  -j, --maxpasses       : int  : number of i\
terations\n  -X, --dropoff         : int  : Dropof\
f score\n  -Z, --finaldropoff    : int  : Dropoff \
for final alignment\n  -S, --startregion     : int\
  : Start of required region in query\n  -H, --end\
region       : int  : End of required region in qu\
ery\n  -k, --pattern         : str  : Hit File (PH\
I-BLAST only)\n  -p, --usagemode       : str  : Pr\
ogram option (PHI-BLAST only):\n                  \
               blastpgp, patseedp, seedp\n\n[Gener\
al]\n\n      --help            :      : prints thi\
s help text\n  -a, --async           :      : forc\
es to make an asynchronous 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 identifiers for result \n  -O, --ou\
tfile         : str  : name of the file results sh\
ould be written to\n                              \
   (default is based on the jobid)\n  -o, --outfor\
mat       : str  : txt or xml output (no file is w\
ritten)\n      --trace           :      : show SOA\
P messages being interchanged\n\nSynchronous job:\\
n\n  The results/errors are returned as soon as th\
e job is finished.\n  Usage: blastpgp.pl --email <\
your@email> [options...] seqfile\n  Returns: saves\
 the results to disk\n\nAsynchronous job:\n\n  Use\
 this if you want to retrieve the results at a lat\
er time. The results\n  are stored for up to 24 ho\
urs.\n  The asynchronous submission mode is recomm\
ended when users are submitting\n  batch jobs or l\
arge database searches\n  Usage: blastpgp.pl --ema\
il <your@email> --async [options...] seqFile\n  Re\
turns: jobid\n\n  Use the jobid to query for the s\
tatus of the job.\n  Usage: blastpgp.pl --status -\
-jobid <jobId>\n  Returns: string indicating the s\
tatus of the job\n    DONE - job has finished\n   \
 RUNNING - job is running\n    NOT_FOUND - job can\
not be found\n    ERROR - the jobs has encountered\
 an error\n\n  When done, use the jobid to retriev\
e the results of the job.\n  Usage: blastpgp.pl --\
polljob --jobid <jobId> [--outfile <fileName>]\n  \
Returns: saves the results to disk\nEOF\n;\n}\n","\
\n\n\nmy $PROBTRESH = 0.3;# base pairs below this \
prob threshold will be ignored\nmy $WEIGHT = 100.0\
; # float!!\nmy $NUCALPH = \"ACGTUNRYMKSWHBVD\";\n\
use vars qw($NUCALPH $WEIGHT);\n\nmy $myname = bas\
ename($0);\n\nuse strict;\nuse warnings;\n\nuse Fi\
le::Basename;\nuse Getopt::Long;\nuse File::Glob '\
:glob';\nuse File::Spec;\nuse File::Temp qw/ tempf\
ile tempdir /;\n\n\n\n\nsub tcoffeelib_header($;$)\
\n{\n    my ($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 tcoffeelib_header_adds\
eq($$;$)\n{\n    my ($id, $seq, $fd) = @_;\n    if\
 (! defined($fd)) {\n        $fd = *STDOUT;\n    }\
\n    printf $fd \"%s %d %s\\n\", $id, length($seq\
), $seq;\n}\n\n\nsub tcoffeelib_comment($;$)\n{\n \
   my ($comment, $fd) = @_;\n    if (! defined($fd\
)) {\n        $fd = *STDOUT;\n    }\n    printf $f\
d \"!\" . $comment . \"\\n\";\n}\n\n\nsub tcoffeel\
ib_struct($$$;$)\n{\n    my ($nseq, $len, $bpm, $f\
d) = @_;\n\n    if (! defined($fd)) {\n        $fd\
 = *STDOUT;\n    }\n\n    # output basepair indice\
s with fixed weight\n    printf $fd \"#%d %d\\n\",\
 $nseq, $nseq;\n    # output basepairs (only once)\
 and with unit-offset\n    for (my $i=0; $i<$len; \
$i++) {\n        for (my $j=$i+1; $j<$len; $j++) {\
\n            if (! defined($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][$j] . \"\\n\";\n            }\n  \
      }\n    }\n}\n\n\nsub tcoffeelib_footer(;$)\n\
{\n    my ($fd) = @_;\n    if (! defined($fd)) {\n\
        $fd = *STDOUT;\n    }\n    print $fd \"! S\
EQ_1_TO_N\\n\";\n}\n\n\n    \nsub plfold($$$)\n{  \
  \n    my ($id, $seq, $probtresh) = @_;\n    my (\
@struct);# return\n    my ($templ, $fhtmp, $fnamet\
mp, $cmd, $ctr, $window_size);\n\n    $templ = $my\
name . \".\" . $id . \".pid-\" . $$ . \".XXXXXX\";\
\n    ($fhtmp, $fnametmp) = tempfile($templ, UNLIN\
K => 1); \n    print $fhtmp \">$id\\n$seq\\n\";\n\\
n    # --- init basepair array\n    #\n    for (my\
 $i=0; $i<length($seq); $i++) {\n        for (my $\
j=$i+1; $j<length($seq); $j++) {\n            $str\
uct[$i][$j]=0;\n        }\n    }\n\n\n    # --- ca\
ll rnaplfold and drop a readme\n    #\n    $window\
_size=(length($seq)<70)?length($seq):70;\n    $cmd\
 = \"RNAplfold -W $window_size < $fnametmp >/dev/n\
ull\";\n    system($cmd);\n    \n    if ($? != 0) \
{\n        printf STDERR \"ERROR: RNAplfold ($cmd)\
 exited with error status %d\\n\", $? >> 8;\n     \
   return;\n    }\n    #unlink($fnametmp);\n    my\
 $fps = sprintf(\"%s_dp.ps\", $id); # check long n\
ame\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(\"co\
uldn't find expected file $fps\\n\");\n     return\
;\n       }\n      }\n    }\n\n    \n    # --- read ba\
se pairs from created postscript\n    #\n    open(\
FH, $fps);\n    while (my $line = <FH>) {\n       \
 my ($nti, $ntj, $prob);\n        chomp($line);   \
     \n        # line: bp bp sqrt-prob ubox\n     \
   my @match = ($line =~ m/^([0-9]+) +([0-9]+) +([\
0-9\\.]+) +ubox$/);\n        if (scalar(@match)) {\
\n            $nti=$1;\n            $ntj=$2;\n    \
        $prob=$3*$3;# prob stored as square root\n\
\n            if ($prob>$probtresh) {\n           \
     #printf STDERR \"\\$struct[$nti][$ntj] sqrtpr\
ob=$3 prob=$prob > $probtresh\\n\";\n             \
   $struct[$nti-1][$ntj-1] = $WEIGHT\n            \
}\n            # store with zero-offset\n        }\
\n    }\n    close(FH);\n\n    # remove or gzi pos\
tscript\n    #\n    unlink($fps);\n    #\n    # or\
 gzip\n    #$cmd = \"gzip -qf $fps\";\n    #system\
($cmd);\n    #if ($? != 0) {\n    #    printf STDE\
RR \"ERROR: gzip ($cmd) exited with error status %\
d\\n\", $? >> 8;\n    #}\n\n    return \\@struct;\\
n}\n\n\n\n\n\nsub rnaseqfmt($)\n{\n    my ($seq) =\
 @_;\n    # remove gaps\n    $seq =~ s/-//g;\n    \
# uppercase RNA\n    $seq = uc($seq);\n    # T -> \
U\n    $seq =~ s/T/U/g;\n    # check for invalid c\
haraters\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: $errmsg\\n\";\n    }\n    pr\
int STDERR << \"EOF\";\n$myname:\n Creates a T-Cof\
fee RNA structure library from RNAplfold predictio\
n.\n See FIXME:citation\nUsage:\n $myname -in seq_\
file -out tcoffee_lib\nEOF\n    exit(1);\n}\n\nsub\
 read_fasta_seq \n  {\n    my $f=$_[0];\n    my %h\
seq;\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=($s=~/>(\\S*).*\\n[^>]*/g);\n    \n    @s\
eq =($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   $s=$s\
eq[$a];$s=~s/\\s//g;\n  \n      $hseq{$n}{seq}=$s;\n    $hs\
eq{$n}{com}=$com[$a];\n      }\n    return %hseq;\\
n  }\n\n\n\n\n\n\n\nmy $fmsq = \"\";\nmy $flib = \\
"\";\nmy %OPTS;\nmy %seq;\nmy ($id, $nseq, $i);\nm\
y @nl;\n\nGetOptions(\"in=s\" => \\$fmsq, \"out=s\\
" => \\$flib);\n\nif (! -s $fmsq) {\n    usage(\"e\
mpty or non-existant file \\\"$fmsq\\\"\")\n}\nif \
(length($flib)==0) {\n    usage(\"empty out-filena\
me\")\n}\n\n\n\n\n\n\n%seq=read_fasta_seq($fmsq);\\
n\n\n@nl=keys(%seq);\n\n$nseq=$#nl+1;\nopen FD_LIB\
, \">$flib\" or die \"can't open $flib!\";\ntcoffe\
elib_header($nseq, *FD_LIB);\nforeach $id (keys (%\
seq))\n  {\n    my ($seq, $fmtseq);\n    \n    $se\
q = $seq{$id}{seq};\n    \n    $fmtseq = rnaseqfmt\
($seq);# check here, formatting for folding import\
ant later\n    if (length($seq)!=length($fmtseq)) \
{\n        print STDERR \"ERROR: invalid sequence \
$id is not an RNA sequence. read seq is: $seq\\n\"\
;\n        exit\n      }\n   \n    tcoffeelib_head\
er_addseq($id, uc($seq), *FD_LIB);\n  }\ntcoffeeli\
b_comment(\"generated by $myname on \" . localtime\
(), *FD_LIB);\n\n\n\n$i=0;\nforeach $id (keys (%se\
q))\n  {\n    my ($cleanid, $seq, $bpm);\n    $seq\
=$seq{$id}{seq};\n    $cleanid = $id;\n    $cleani\
d =~ s,[/ ],_,g;# needed for rnaplfold\n    $seq =\
 rnaseqfmt($seq);\n    \n    $bpm = plfold($cleani\
d, rnaseqfmt($seq), $PROBTRESH);       \n    \n   \
 tcoffeelib_struct($i+1, length($seq), $bpm, *FD_L\
IB);\n    $i++;\n}\n\n\ntcoffeelib_footer(*FD_LIB)\
;\nclose FD_LIB;\nexit (0);\n\n","\n\n\n\n\n$cmd=j\
oin ' ', @ARGV;\nif ($cmd=~/-infile=(\\S+)/){ $seq\
file=$1;}\nif ($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    p\
rint (F \">$name _F_ $tclib\\n\");\n    seq2RNAplf\
old2tclib ($name, $s{$name}{seq}, $tclib);\n  }\nc\
lose (F);\nexit (EXIT_SUCCESS);\n\nsub seq2RNAplfo\
ld2tclib\n  {\n    my ($name, $seq, $tclib)=@_;\n \
   my ($tmp);\n    $n++;\n    $tmp=\"tmp4seq2RNApl\
fold_tclib.$$.$n.pep\";\n    open (RF, \">$tmp\");\
\n    print (RF \">$name\\n$seq\\n\");\n    close \
(RF);\n    \n    system \"t_coffee -other_pg RNApl\
fold2tclib.pl -in=$tmp -out=$tclib\";\n    \n    u\
nlink ($tmp);\n    return $tclib;\n  }\n    \n    \
\nsub read_fasta_seq \n  {\n    my $f=@_[0];\n    \
my %hseq;\n    my (@seq, @com, @name);\n    my ($a\
, $s,$nseq);\n\n    open (F, $f);\n    while (<F>)\
\n      {\n     $s.=$_;\n      }\n    close (F);\n\n  \
  \n    @name=($s=~/>(\\S*).*\\n[^>]*/g);\n    \n \
   @seq =($s=~/>.*.*\\n([^>]*)/g);\n    @com =($s=\
~/>\\S*(.*)\\n([^>]*)/g);\n\n    \n    $nseq=$#nam\
e+1;\n    \n    for ($a=0; $a<$nseq; $a++)\n      \
{\n     my $n=$name[$a];\n      $hseq{$n}{name}=$n;\n   $hseq\
{$n}{seq}=$seq[$a];\n   $hseq{$n}{com}=$com[$a];\n  \
    }\n    return %hseq;\n  }\n","use Getopt::Long\
;\nGetOptions(\"-in=s\" => \\$fmsq1, \"-out=s\" =>\
 \\$outfile, \"-arch=s\" => \\$arch,\"-psv=s\" => \
\\$psv, \"-hmmtop_home=s\", \\$hmmtop_home );\nope\
n (O, \">$outfile\");\n\nif (!$hmmtop_home){$hmmto\
p_home=\"/home/notredame/packages/hmmtop/hmmtop_2.\
1\";}\nif ($arch){$ENV{'HMMTOP_ARCH'}=$arch;}\nels\
e {$ENV{'HMMTOP_ARCH'}=\"$hmmtop_home/hmmtop.arch\\
";}\n\nif ($psv){$ENV{'HMMTOP_PSV'}=$psv;}\nelse{$\
ENV{'HMMTOP_PSV'}=\"$hmmtop_home/hmmtop.psv\";}\n\\
n$fmsq=\"seq2convert.$$.tmp\";\nsystem (\"t_coffee\
 -other_pg seq_reformat -in $fmsq1 -output fasta_s\
eq > $fmsq\");\n%seq=read_fasta_seq($fmsq);\n\n$tm\
pfile=\"fasta_seq2hmmtop_fasta.$$.tmp\";\nforeach \
$s (keys (%seq))\n  {\n    \n    open F, \">$tmpfi\
le\";\n    print F \">seq\\n$seq{$s}{seq}\\n\";\n \
   close F;\n\n    $result=`hmmtop -if=$tmpfile -s\
f=FAS -pl 2>/dev/null`;\n    @r=($result=~/(.+)/g)\
;\n    foreach $l (@r)\n      {\n       \n      if ($l=~/pred\
(.*)/)\n          {$p.=$1;}\n      }\n    \n    $p=~s/\\s\
//g;\n    print O \">$seq{$s}{name}\\n$p\\n\";\n  \
  $p=\"\";\n  }\nunlink \"$tmpfile\";\nunlink \"$f\
msq\";\nclose (O);\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=~/>(.*).*\\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<$nse\
q; $a++)\n      {\n     my $n=$name[$a];\n      my $s;\n        $h\
seq{$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\nmy $FM\
ODEL =\"\"; \nmy $TMPDIR = \"/tmp\";\n\n\n\n\nmy $\
NUCALPH = \"ACGTUNRYMKSWHBVD\";\nmy $PRIMNUCALPH =\
 \"ACGTUN\";\nuse vars qw($NUCALPH $PRIMNUCALPH $T\
MPDIR);\n\n\nmy $errmsg;\nuse vars qw($errmsg);\n\\
n\n\nuse Getopt::Long;\nuse Cwd;\nuse File::Basena\
me;\nuse File::Temp qw/ tempfile tempdir /;\nuse F\
ile::Copy;\nuse File::Path;\n\n\n\nsub usage(;$)\n\
{\n    my ($errmsg) = @_;\n    my $myname = basena\
me($0);\n\n    if ($errmsg) {\n        print STDER\
R \"ERROR: $errmsg\\n\";\n    }\n\n    print STDER\
R << \"EOF\";\n    \n$myname: align two sequences \
by means of consan\\'s sfold\nUsage:\n $myname -i \
file -o file -d path\nOptions:\n -i|--in : pairwis\
e 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 ($se\
q, $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    retur\
n %hseq;\n  }\nsub read_fasta_seq \n  {\n    my $f\
=$_[0];\n    my %hseq;\n    my (@seq, @com, @name)\
;\n    my ($a, $s,$nseq);\n\n    open (F, $f);\n  \
  while (<F>)\n      {\n        $s.=$_;\n      }\n    clo\
se (F);\n\n    \n    @name=($s=~/>(.*).*\\n[^>]*/g\
);\n    \n    @seq =($s=~/>.*.*\\n([^>]*)/g);\n   \
 @com =($s=~/>.*(.*)\\n([^>]*)/g);\n\n    \n    $n\
seq=$#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, $foutf\
a) = @_;\n    my %haln;\n    my ($fstk, $cmd, $id)\
;\n    open FOUTFA, \">$foutfa\";\n    \n    $fstk\
 = $frawout . \".stk\";\n    \n    # first line of\
 raw out contains info\n    # remaining stuff is s\
tockholm formatted\n    $cmd = \"sed -e '1d' $fraw\
out\";\n    system(\"$cmd > $fstk\");\n    if ($? \
!= 0) {\n        $errmsg = \"command failed with e\
xit status $?.\";\n        $errmsg .=  \"Command w\
as \\\"$cmd\\\"\";\n        return -1;\n    }\n\n \
   # this gives an error message. just ignore it..\
.\n    %haln=read_stk_aln ( $fstk);\n    foreach $\
i (keys (%haln))\n      {\n     my $s;\n        $s=$haln{$i}{\
'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, $frawout, $ferrlog, $freadme, $ftim\
elog, $fstk);\n\n    # add  basename($fmsqin) (unk\
nown here!)\n    $frawout = \"sfold.log\";\n    $f\
errlog = \"sfold.err\";\n    $ftimelog = \"sfold.t\
ime\";\n    $freadme =  \"sfold.README\";\n    $fs\
tk = \"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 fail\
ed with exit status $?\";\n        $errmsg .= \"co\
mmand was \\\"$cmd\\\". See \" . getcwd . \"\\n\";\
\n        return -1;\n    }\n\n    return sfold_pa\
rseoutput($frawout, $foutfa);\n}\n\n\n\n\n\n\n\nmy\
 ($help, $fmsqin, $fmsaout);\nGetOptions(\"help\" \
 => \\$help,\n           \"in=s\" => \\$fmsqin,\n \
          \"out=s\" => \\$fmsaout,\n       \"data=s\"\
 => \\$ref_dir);\n\n\n\nif ($help) {\n    usage();\
\n    exit(0);\n}\nif (! defined($fmsqin)) {\n    \
usage('missing input filename');\n    exit(1);\n}\\
nif (! defined($fmsaout)) {\n    usage('missing ou\
tput filename');\n    exit(1);\n\n}\nif (scalar(@A\
RGV)) {\n    usage('Unknown remaining args');\n   \
 exit(1);\n}\n\n$FMODEL = \"$ref_dir/mix80.mod\";\\
nif (! -e \"$FMODEL\") {\n    die(\"couldn't find \
sfold grammar model file. Expected $FMODEL\\n\");\\
n}\n\n\nmy %hseq=read_fasta_seq ($fmsqin);\nmy $id\
;\n\nforeach $id (keys(%hseq))\n  {\n    push(@seq\
_array, $hseq{$id});\n  }\n\nif ( scalar(@seq_arra\
y) != 2 ) {\n    die(\"Need *exactly* two sequence\
s as input (pairwise alignment!).\")\n}\n\n\n\nmy \
($sec, $min, $hour, $mday, $mon, $year, $wday, $yd\
ay, $isdst) = localtime(time);\nmy $datei = sprint\
f(\"%4d-%02d-%02d\", $year+1900, $mon+1, $mday);\n\
my $templ = basename($0) . \".\" . $datei . \".pid\
-\" . $$ . \".XXXXXX\";\nmy $wd = tempdir ( $templ\
, DIR => $TMPDIR);\n\ncopy($fmsqin, \"$wd/\" . bas\
ename($fmsqin) . \".org\"); # for reproduction\nco\
py($FMODEL, \"$wd\");\nmy $fmodel = basename($FMOD\
EL);\nmy $orgwd = getcwd;\nchdir $wd;\n\n\n\nmy @s\
epseqfiles;\nforeach $id (keys(%hseq)) {\n    my (\
$seq, $orgseq, $fname, $sout);\n    $seq=$hseq{$id\
}{'seq'};\n    \n    $fname = basename($fmsqin) . \
\"_$id.fa\";\n    # replace funnies in file/id nam\
e (e.g. \"/\" \" \" etc)\n    $fname =~ s,[/ ],_,g\
;\n    open (PF, \">$fname\");\n    print (PF \">$\
id\\n$seq\\n\");\n    close (PF);\n\n    push(@sep\
seqfiles, $fname);\n}\n\nmy ($f1, $f2, $fout);\n$f\
1 = $sepseqfiles[0];\n$f2 = $sepseqfiles[1];\n$fou\
t = $wd . basename($fmsqin) . \".out.fa\";\nif (sf\
old_wrapper($f1, $f2, $fmodel, \"$fout\") != 0) {\\
n    printf STDERR \"ERROR: See logs in $wd\\n\";\\
n    exit(1);\n} else {\n    chdir $orgwd;\n    co\
py($fout, $fmsaout);\n    rmtree($wd);\n   exit(0)\
;\n}\n","\nuse Env qw(HOST);\nuse Env qw(HOME);\nu\
se Env qw(USER);\n\n\n$tmp=clean_cr ($ARGV[0]);\no\
pen (F, $tmp);\n\nwhile ( <F>)\n  {\n    my $l=$_;\
\n    if ( $l=~/^# STOCKHOLM/){$stockholm=1;}\n   \
 elsif ( $stockholm && $l=~/^#/)\n      {\n     $l=~/^\
#(\\S+)\\s+(\\S+)\\s+(\\S*)/g;\n        $l=\"_stockholmha\
sch_$1\\_stockholmspace_$2 $3\\n\";\n      }\n    \
$file.=$l;\n  }\nclose (F);\nunlink($tmp);\n$file1\
=$file;\n\n$file=~s/\\#/_hash_symbol_/g;\n$file=~s\
/\\@/_arobase_symbol_/g;\n\n\n$file=~s/\\n[\\.:*\\\
s]+\\n/\\n\\n/g;\n\n$file=~s/\\n[ \\t\\r\\f]+(\\b)\
/\\n\\1/g;\n\n\n$file=~s/(\\n\\S+)(\\s+)(\\S)/\\1_\
blank_\\3/g;\n\n$file=~s/[ ]//g;\n$file=~s/_blank_\
/ /g;\n\n\n\n$file =~s/\\n\\s*\\n/#/g;\n\n$file.=\\
"#\";\n$file =~s/\\n/@/g;\n\n\n\n\n@blocks=split /\
\\#/, $file;\nshift (@blocks);\n@s=split /\\@/, $b\
locks[0];\n$nseq=$#s+1;\n\n\n\n$file=join '@', @bl\
ocks;\n@lines=split /\\@/,$file;\n\n$c=0;\n\nforea\
ch $l (@lines)\n  {\n    if (!($l=~/\\S/)){next;}\\
n    elsif ($stockholm && ($l=~/^\\/\\// || $l=~/S\
TOCKHOLM/)){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 \"ERR\
OR: $ARGV[0] is NOT an MSA in Clustalw format: mak\
e sure there is no blank line within a block [ERRO\
R]\\n\";\n      exit (EXIT_FAILURE);\n      }\n\nfor ($\
a=0; $a< $nseq; $a++)\n  {\n    $name[$a]=cleanstr\
ing ($name[$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 $s\
ize=@_[1];\n    my @list;\n    my $n,$ns, $symbol;\
\n    \n    @list=split //,$s;\n    $n=0;$ns=\"\";\
\n    foreach $symbol (@list)\n      {\n        if ( $n==\
$size)\n          {\n       $ns.=\"\\n\";\n         $n=0;\n       }\
\n      $ns.=$symbol;\n $n++;\n      }\n    return $ns;\
\n    }\n\nsub clean_cr\n  {\n    my $f=@_[0];\n  \
  my $file;\n    \n    $tmp=\"f$.$$\";\n    \n    \
\n    open (IN, $f);\n    open (OUT, \">$tmp\");\n\
    \n    while ( <IN>)\n      {\n      $file=$_;\n     $fi\
le=~s/\\r\\n/\\n/g;\n   $file=~s/\\n\\r/\\n/g;\n        $fi\
le=~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 Env qw(HOME);\nuse Env qw(USER);\n\\
n\n$query_start=-1;\n$query_end=-1;\n\nwhile (<>)\\
n  {\n    if ( /\\/\\//){$in_aln=1;}\n    elsif ( \
$in_aln && /(\\S+)\\s+(.*)/)\n      {\n\n\n     $name=\
$1;\n   \n\n    $seq=$2;\n      $seq=~s/\\s//g;\n        $se\
q=~s/\\~/\\-/g;\n       $seq=~s/\\./\\-/g;\n    if ( $list{\
$n}{'name'} && $list{$n}{'name'} ne $name)\n      {\n\
            print \"$list{$n}{'name'} Vs $name\";\n         \\
n           exit (EXIT_FAILURE);\n        }\n   else\n    {\n     \
  $list{$n}{'name'}= $name;\n     }\n\n $list{$n}{'s\
eq'}=$list{$n}{'seq'}.$seq;\n   \n      $nseq=++$n;\n   \n \
     }\n    else\n      {$n=0;}\n  }\n\n\nfor ($a=\
0; $a<$nseq; $a++)\n  {\n    print \">$list{$a}{'n\
ame'}\\n$list{$a}{'seq'}\\n\";\n  }\n      \n","\n\
use Env qw(HOST);\nuse Env qw(HOME);\nuse Env qw(U\
SER);\n\n                                         \
               \nuse strict;                      \
                       \nuse warnings;\nuse diagno\
stics;\n\nmy $in_hit_list, my $in_aln=0, my(%name_\
list)=(),my (%list)=(),my $n_seq=0; my $test=0;\nm\
y($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 produc\
ing significant alignments/){$in_hit_list=1;}\n   \
 \n    if ($_=~ /^pdb\\|/i) { $_=~ s/pdb\\|//g; }\\
n    if ($_=~ /^(1_\\d+)\\s+\\d+/) { $_=~ s/$1/QUE\
RY/;}\n      \n    if ( /^(\\S+).+?\\s+[\\d.]+\\s+\
([\\de.-]+)\\s+$/ && $in_hit_list)      \n    {\n       my($i\
d)=$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 $start=$2;\n my $seq=$3;\n   my $end=\
$4;\n           \n      if ($name =~ /QUERY/i) { $lg_query=lengt\
h($seq); }\n\n  unless ($test > $n) #m\n        {\n         my\
(@seqq)= split('',$seq);\n          my($gap_missing)= s\
calar(@seqq);\n     \n      while ($gap_missing != \
$lg_query)  { unshift (@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          $list{$n}{'real_name'}=$name_list{$\
j-1};\n }\n             \n      $list{$n}{'name'}=$name;\n\n    $seq=\
~tr/a-z/A-Z/;\n $list{$n}{'seq'}=$list{$n}{'seq'};\
\n      $list{$n}{'seq'}.=$seq;\n\n     $n++;\n $vu{$name}+\
+;\n    $test++;\n   } \n    \n}\n\nmy @numero=();\n\\
nfor (my $a=0; $a<$n; $a++) #m\n{\n    my $long=le\
ngth($list{0}{'seq'});  \n    my $long1= length($l\
ist{$a}{'seq'});\n  \n    while ($long1 ne $long)\\
n    {\n        $list{$a}{'seq'}.=\"-\";\n      $long1= length\
 ($list{$a}{'seq'});\n    } \n \n    push (@numero\
,\"$list{$a}{'name'} $list{$a}{'real_name'}\\n\");\
\n}\n\nmy %dejavu=();\n\n\nfor (my $i=0; $i<=$#num\
ero; $i++)\n{\n    my $s=\">$list{$i}{'real_name'}\
\\n$list{$i}{'seq'}\\n\";\n    my $k=0;\n    \n   \
 if (exists $dejavu{$numero[$i]}) {next;}\n    els\
e\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_coffee -other_pg seq_reformat -in te\
mpo_aln2cons -action +aln2cons +upper |\") ; \n   \
        while (<COM>)\n {       \n          if (/^>/) { $cons =\">\
$list{$i}{'real_name'}\\n\"; next;}\n       $_=~ s/\\
\n//g;\n            $cons .=$_;\n       }\n     close COM; unlink (\
\"tempo_aln2cons\");\n  print $cons,\"\\n\"; print \
F $cons,\"\\n\";\n    } \n    else  { print $s;  p\
rint 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, $blast);\n&output_profile (%p);\n\n\
\nsub output_profile\n  {\n    my (%profile)=(@_);\
\n    my ($a);\n    for ($a=0; $a<$profile{n}; $a+\
+)\n      {\n   \n      print \">$profile{$a}{name} $prof\
ile{$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           retur\
n 0;\n        }\n           $n++;\n       }\n      }\n    clo\
se (FC);\n    return 0;\n  }\n      \n    \nsub file\
2string\n  {\n    my $f=@_[0];\n    my $string, $l\
;\n    open (F,\"$f\");\n    while (<F>)\n      {\\
n\n     $l=$_;\n        #chomp ($l);\n  $string.=$l;\n      }\\
n    close (F);\n    $string=~s/\\r\\n//g;\n    $s\
tring=~s/\\n//g;\n    return $string;\n  }\n\n\n\n\
sub tag2value \n  {\n    \n    my $tag=(@_[0]);\n \
   my $word=(@_[1]);\n    my $return;\n    \n    $\
tag=~/$word=\"([^\"]+)\"/;\n    $return=$1;\n    r\
eturn $return;\n  }\n      \nsub hit_tag2pdbid\n  \
{\n    my $tag=(@_[0]);\n    my $pdbid;\n       \n\
    $tag=~/id=\"(\\S+)\"/;\n    $pdbid=$1;\n    $p\
dbid=~s/_//;\n    return $pdbid;\n  }\nsub id2pdbi\
d \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 se\
t_blast_type \n  {\n    my $file =@_[0];\n    if (\
&file_contains ($file,\"EBIApplicationResult\",100\
)){$BLAST_TYPE=\"EBI\";}\n    elsif (&file_contain\
s ($file,\"NCBI_BlastOutput\",100)) {$BLAST_TYPE=\\
"NCBI\";}\n    else\n      {\n  $BLAST_TYPE=\"\";\n\
      }\n    return $BLAST_TYPE;\n  }\nsub blast_x\
ml2profile \n  {\n    my ($name,$seq,$maxid, $mini\
d, $mincov, $file)=(@_);\n    my (%p, $a, $string,\
 $n);\n    \n\n\n    if ($BLAST_TYPE eq \"EBI\" ||\
 &file_contains ($file,\"EBIApplicationResult\",10\
0)){%p=ebi_blast_xml2profile(@_);}\n    elsif ($BL\
AST_TYPE eq \"NCBI\" || &file_contains ($file,\"NC\
BI_BlastOutput\",100)){%p=ncbi_blast_xml2profile(@\
_);}\n    else \n      {\n      print \"************ ER\
ROR: Blast Returned an unknown XML Format ********\
**************\";\n     die;\n      }\n    for ($a=0; \
$a<$p{n}; $a++)\n      {\n      my $name=$p{$a}{name};\\
n       $p{$name}{seq}=$p{$a}{seq};\n      }\n    return\
 %p;\n  }\nsub ncbi_blast_xml2profile \n  {\n    m\
y ($name,$seq,$maxid, $minid, $mincov, $string)=(@\
_);\n    my ($L,$l, $a,$b,$c,$d,$nhits,@identifyer\
L);\n    \n    \n    $seq=~s/[^a-zA-Z]//g;\n    $L\
=length ($seq);\n    \n    %hit=&xml2tag_list ($st\
ring, \"Hit\");\n    \n    \n    for ($nhits=0,$a=\
0; $a<$hit{n}; $a++)\n      {\n my ($ldb,$id, $ide\
ntity, $expectation, $start, $end, $coverage, $r);\
\n      my (%ID,%DE,%HSP);\n    \n      $ldb=\"\";\n\n  %ID=&xml\
2tag_list ($hit{$a}{body}, \"Hit_id\");\n       $identif\
yer=$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 (%S\
TART,%END,%E,%I,%Q,%M);\n\n      \n         %START=&xml2ta\
g_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_align-len\");\n     %END=  &xml2ta\
g_list ($HSP{$b}{body}, \"Hsp_query-to\");\n        %\
HEND=  &xml2tag_list ($HSP{$b}{body}, \"Hsp_hit-to\
\");\n      %E=&xml2tag_list     ($HSP{$b}{body}, \\
"Hsp_evalue\");\n           %I=&xml2tag_list     ($HSP{$\
b}{body}, \"Hsp_identity\");\n      %Q=&xml2tag_lis\
t     ($HSP{$b}{body}, \"Hsp_qseq\");\n     %M=&xm\
l2tag_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 ($s\
eq eq\"\"){$seq=$qs;$L=length($seq);}\n         \n              $expe\
ctation=$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          $Hsta\
rt=$HSTART{$e}{body};\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]=$lr2[$c];\n                       $d++;\n               }\n                 \
}\n             $Qseq[$nhits]=$qs;\n            $Hseq[$nhits]=$ms;\n            $\
QstartL[$nhits]=$start;\n               $HstartL[$nhits]=$Hstar\
t;\n            $identityL[$nhits]=$identity;\n         $endL[$nhit\
s]=$end;\n              $definitionL[$nhits]=$definition;\n             $\
identifyerL[$nhits]=$identifyer;\n              $comment[$nhit\
s]=\"$ldb|$identifyer [Eval=$expectation][id=$iden\
tity%][start=$Hstart end=$Hend]\";\n            $nhits++;\n     \
      }\n         }\n      }\n    \n    $profile{n}=0;\n\
    $profile{$profile{n}}{name}=$name;\n    $profi\
le{$profile{n}}{seq}=$seq;\n    $profile {n}++;\n \
   \n    for ($a=0; $a<$nhits; $a++)\n      {\n $n\
=$a+1;\n        \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       $profile{$n}{Hstart}=$Hs\
tartL[$a];\n    $profile{$n}{identity}=$identityL[$a]\
;\n     $profile{$n}{definition}=$definitionL[$a];\n    $\
profile{$n}{identifyer}=$identifyerL[$a];\n     $profi\
le{$n}{comment}=$comment[$a];\n for ($b=0; $b<$L; \
$b++)\n   {\n       if ($p[$a][$b])\n         {\n               $pr\
ofile{$n}{seq}.=$p[$a][$b];\n         }\n           else\n\
              {\n               $profile{$n}{seq}.=\"-\";\n           }\n       \
  }\n      }\n    \n    $profile{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    $se\
q=~s/[^a-zA-Z]//g;\n    $L=length ($seq);\n    %hi\
t=&xml2tag_list ($string, \"hit\");\n    \n    for\
 ($nhits=0,$a=0; $a<$hit{n}; $a++)\n      {\n   my (\
$ldb,$id, $identity, $expectation, $start, $end, $\
coverage, $r);\n        my (%Q,%M,%E,%I);\n     \n      $ldb=&tag2\
value ($hit{$a}{open}, \"database\");\n $identifye\
r=&tag2value ($hit{$a}{open}, \"id\");\n\n      $descri\
ption=&tag2value ($hit{$a}{open}, \"description\")\
;\n     \n      %Q=&xml2tag_list ($hit{$a}{body}, \"querySe\
q\");\n %M=&xml2tag_list ($hit{$a}{body}, \"matchS\
eq\");\n        %E=&xml2tag_list ($hit{$a}{body}, \"expec\
tation\");\n    %I=&xml2tag_list ($hit{$a}{body}, \"i\
dentity\");\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=l\
ength($seq);}\n\n           $expectation=$E{$b}{body};\n\
            $identity=$I{$b}{body};\n       \n              \n  \
    $start=&tag2value ($Q{$b}{open}, \"start\");\n\
            $end=&tag2value ($Q{$b}{open}, \"end\");\n    \
  $startM=&tag2value ($M{$b}{open}, \"start\");\n       \
    $endM=&tag2value ($M{$b}{open}, \"end\");\n   \
  $coverage=(($end-$start)*100)/$L;\n       \n     # \
print \"$id: ID: $identity COV: $coverage [$start \
$end]\\n\";\n       \n      \n      if ($identity>$max\
id || $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[$nhit\
s][$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]=$l\
r2[$c];\n                   $d++;\n               }\n         }\n         \n        \\
n           $identifyerL[$nhits]=$identifyer;\n     $com\
ment[$nhits]=\"$ldb|$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    $pr\
ofile{$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}{identifyer}=\
$identifyerL[$a];\n     \n      $profile{$n}{comment}=$comm\
ent[$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    $pr\
ofile{n}=$nhits+1;\n    \n    return %profile;\n  \
}\n\nsub blast_xml2hit_list\n  {\n    my $string=(\
@_[0]);\n    return &xml2tag_list ($string, \"hit\\
");\n  }\nsub xml2tag_list  \n  {\n    my ($string\
_in,$tag)=@_;\n    my $tag_in, $tag_out;\n    my %\
tag;\n    \n    if (-e $string_in)\n      {\n   $str\
ing=&file2string ($string_in);\n      }\n    else\\
n      {\n      $string=$string_in;\n      }\n    $tag_\
in1=\"<$tag \";\n    $tag_in2=\"<$tag>\";\n    $ta\
g_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    $tag{n}=0;\n    $in=0;$n=-1;\n  \n \\
n\n    foreach $t (@l)\n      {\n\n     $t=~s/<#//;\n   \
$t=~s/#>//;\n   \n      if ( $t=~/$tag_in1/ || $t=~/$tag_\
in2/)\n   {\n    \n         $in=1;\n        $tag{$tag{n}}{o\
pen}=$t;\n          $n++;\n         \n    }\n   elsif ($t=~/$t\
ag_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_$li\
st{$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;\n\
foreach $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    $na\
me=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);\nus\
e Env qw(USER);\n\n$tmp=\"$ARGV[0].$$\";\nopen (IN\
, $ARGV[0]);\nopen (OUT, \">$tmp\");\n\nwhile ( <I\
N>)\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 \"\
$file\";\n  }\nclose (IN);\nclose (OUT);\n\nopen (\
OUT, \">$ARGV[0]\");\nopen (IN, \"$tmp\");\n\nwhil\
e ( <IN>)\n{\n  print OUT \"$_\";\n}\nclose (IN);\\
nclose (OUT);\nunlink ($tmp);\n\n"};
/*********************************COPYRIGHT NOTICE**********************************/
/*© Centro de Regulacio Genomica */
/*and */
/*Cedric Notredame */
/*Tue Oct 27 10:12:26 WEST 2009. */
/*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**********************************/