ProtoGene.pl 57.5 KB
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#!/usr/bin/env perl

########################################################
#                                                      #
# ProtoGene : Bona-Fide Back Translation of Protein    #
#             Multiple Sequence Alignments             #
#                                                      #
########################################################

use strict;
use warnings;
use diagnostics;
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use Carp;

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use File::Which qw(which);                 # Locate external executable programs in the PATH
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use Time::localtime;                       # Use localtime+PID for a pseudo-uniq temp file name
use Getopt::Long;                          # Options specifications
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use File::Copy qw(move);                   # Avoid external 'mv' command usage
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use LWP::Simple;                           # To test gigablaster availability
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use Mail::Send;                            # Send warnings and errors files by e-mail ==> only if the $userEMail variable is defined

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use lib '/mnt/common/share/ProtoGene/';    # Local path for ProtoGene's own perl modules
###use lib '/mnt/local/lib/tcoffee_perl/';
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use Exonerate;                             # Exonerate runner, parser, ...
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use Views;                                 # Non-text outputs, e.g. HTML/CSS
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#use CheckOutput;                         # Check output for cds consistancy with query
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################## CONFIGURATION ##################
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$ENV{'PATH'}        .= ':/mnt/local/bin/:./';                               # Additional path for executables
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my $cachePath        = '/scratch/cluster/monthly/t_coffee/ProtoGene_Cache'; # Cache directory
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$cachePath = '/Users/smoretti/Documents/ProtoGene/TTMMPP'; #FIXME
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my $cacheStorageTime = 15;                                                  # Do not update sequences younger than X days

my $userEMail        = 'moretti.sebastien@gmail.com';                       # To receive e-mails with encountered problems; leave blank to inactive
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### BLAST parameters ###
my $blast_param = { 'evalue'    => 0.05,
                    'matrix'    => 'BLOSUM62',
                    'filter'    => 'Off',
                    'species'   => 'All_organisms',

                    'db1'       => 'refseq_protein', # NCBI RefSeq protein
                    'identity1' => 100,
                    'cover1'    => 100,
                    'db2'       => 'nr', # NCBI nr protein
                    'identity2' =>  95,
                    'cover2'    =>  95,

                    'nbesthits' => 10,
                    'core'      => 1,
                  };
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###################################################
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my $VERSION  = '4.0.0';
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my $webblast_exe  = 'webblast.pl';
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my $blast_exe     = 'blastall';            # Or wu-blastall for Wu-BLAST; for local blast usage
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my $exonerate_exe = 'exonerate-1.0';       # Exonerate 1.0 because current parser only works with this version
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################## Option management
my ($msa, $revtrans, $pep, $hideBOJ, $run_name, $template, $lim, $cache) = ('', 0, 0, 0, '', '', 0, 'update');
my ($debug, $tmp)                                                        = (0, 0);
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my ($db, $species, $local, $giga)                                        = ($blast_param->{'db1'}, $blast_param->{'species'}, 0, 0);
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my %opts = ('msa|in=s'        => \$msa,        # Input sequences
            'revtrans'        => \$revtrans,   # Use to reverse-translate sequences with no match
            'pep'             => \$pep,        # Add the original peptide query beneath the related CDS seq
            'hideBOJ'         => \$hideBOJ,    # Hide BOJ output
            'run_name=s'      => \$run_name,   # Use another name, instead of input seq name, for result files
            'template=s'      => \$template,   # Use a template file
            'lim=i'           => \$lim,        # Limit number of input query sequences
            'cache=s'         => \$cache,      # Cache behavior

            'orgm|species=s'  => \$species,    # Organism(s) to blast against
            'db|database=s'   => \$db,         # Database to blast against
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            'local'           => \$local,      # Use to specify a local db query, defined in $local_db
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            'giga'            => \$giga,       # Use GigaBlaster server

            'version|V'       => sub { print "\n\tPROTOGENE : Bona-Fide Back Translation of Protein Multiple Sequence Alignments\n\tversion   : $VERSION\n\n";
                                       exit 0;
                                 },            # Print version information
            'help|H|?'        => sub { system('perldoc', "$0")==0 || print {*STDERR} "\n\tCannot open the documentation with 'perldoc'\n\n";
                                       exit 0;
                                     },        # Print full help message
            'debug'           => \$debug,      # Verbose output
            'tmp'             => \$tmp,        # To keep traces of fake intermediate files like fake xml from NCBI, fake aln, ...
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           );
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my $test_option_values = Getopt::Long::GetOptions(%opts);

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################## Short help message
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if ( !$test_option_values || ($msa eq '' && $cache ne 'empty' && $cache ne 'old') ){
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    print {*STDERR} "\n\tCannot open the MSA file in FASTA format
\tTry:  $0 --msa=path_of_the_fasta_msa_file [Options]

\tOptions: --orgm=All_organisms, Bacteria, Viruses, Vertebrata,
\t                Eukaryota, Mammalia, Primates, Homo_sapiens,
\t                Gallus_gallus, Bos_taurus, Escherichia_coli,
\t                Arabidopsis_thaliana, Mus_musculus,
\t                Drosophila_Melanogaster, ...
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\t                default is '$blast_param->{'species'}'
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\t         --db=nr, pdb, swissprot, refseq_protein
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\t                default is '$blast_param->{'db1'}'
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\t         --local to execute a local BLAST query with
\t                --db=path_for_a_local_db_blast_formated\n
\t         --template to provide your own nucleotidic sequences
\t                following the cds file format
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\t         --revtrans reverse-translates sequences with no
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\t                blast hit, in IUB (IUPAC) depiction code
\t                They are removed from the alignement by default
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\t         --pep  adds the original peptide query beneath the
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\t                back-translated sequence
\t         --cache=none, update, use, 'own_PATH_directory', old, empty
\t                to select the cache mode
\t                default is 'update'\n
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\t         --debug   prints extra information when running
\t         --version prints version information
\t         --help    prints a full help message\n\n";
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    exit(1);
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}
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################## Check cache directory accessibility
checkCacheAccessibility($cachePath);
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# Cache management
$cache = cacheManagement($cache, $cachePath, 0) || '.';
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# Remove old files from the cache directory everytime ProtoGene is running
cacheManagement('old', $cachePath, 1);
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################## Check external software in the PATH
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checkExternalSoftware($webblast_exe, $exonerate_exe);
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if ( $local ){
    checkExternalSoftware($blast_exe);
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}



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################## Check input files
# Open and check template file
my ($template_NT, $template_AA, $template_SEQ);
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#TODO: template is fasta only now
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($template_NT, $template_AA, $template_SEQ) = checkTemplate($template) if ( $template );

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# Open and Check the input fasta file
my $originalMSA    = $msa;
my $converted      = 0; # Accept only fasta format
#TODO: Do a better file converter and identifier is msa is not fasta
#($msa, $converted) = isFastaFile($msa, $converted);
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my $fasta_checker = -1;
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my (@original_names, @original_seq); #Use 2 lists in parallel : original_names, seq
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open( my $MSA, '<', "$msa" ) or die "\n\tCannot open your MSA file\n\n";
READ_MSA:
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while(<$MSA>){
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    next READ_MSA if ( $_ =~ /^#/ );

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    if ( $_ =~ /^>/ ){
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        $fasta_checker++;
        my $name = $_;
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        $name    =~ s{\r\n}{}g; #Remove return lines from windows OS '^M'
        $name    =~ s{\r}{\n}g;
        $name    =~ s{^>[ \t]+}{>};
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        chomp($name);
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        push @original_names, $name;
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    }
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    elsif ( $_ =~ /[A-Z\-\.]/i ){
        my $sequence = $_;
        $sequence    =~ s{\r\n}{}g;
        $sequence    =~ s{\r}{\n}g;
        $sequence    =~ s{\.}{-}g; #for msa with '.' as gap
        #TODO because exonerate cannot work with selenocystein
        $sequence    =~ s{[BJOUZ]}{X}ig; #U here for selenocystein
        $sequence    =~ s{[^A-Za-z\-\*\n]}{}g; #Remove all the non-gap or non-alphabetic characters from the seq
        chomp($sequence);

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        #fasta sequence on 1 line
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        if ( !exists($original_seq[$fasta_checker]) ){
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            push @original_seq, $sequence;
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        }
        else {
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            $original_seq[$fasta_checker] .= $sequence;
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        }
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    }
}
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close $MSA;
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#Are there FASTA sequences ?
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if ( $fasta_checker == -1 ){
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    failure();
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    print {*STDERR} "\tThe MSA file does NOT seem to be a protein FASTA format
\tSee an example of FASTA format <a href='http://en.wikipedia.org/wiki/FASTA_format' target='_blank'>here</a>\n\n";
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    exit(1);
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}
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elsif ( $lim >0 && $fasta_checker > $lim ){
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    failure();
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    print {*STDERR} "\tThe FASTA file is too large, try with less than $lim sequences\n\tor split your file\n\n";
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    exit(1);
}
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elsif ( exists( $original_seq[0] ) && $original_seq[0] =~ /[acgtu]/i ){
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    my $first_seq = $original_seq[0];
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    #Check if sequences are amino acids and not nucleotides ONLY on the 1st sequence
    my $a         = ($first_seq =~ s{[aA]}{}g)               || 0;
    my $c         = ($first_seq =~ s{[cC]}{}g)               || 0;
    my $g         = ($first_seq =~ s{[gG]}{}g)               || 0;
    my $t         = ($first_seq =~ s{[tTuU]}{}g)             || 0;
    my $non       = ($first_seq =~ s{[^aAcCgGtTuUXxNn-]}{}g) || 0;
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    if ( ($a+$c+$g+$t) >= (($a+$c+$g+$t+$non)*80/100) ){
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        failure();
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        print {*STDERR} "\tYour sequences seem already to be nucleotides
\tthe goal of this program is to turn AMINO ACID alignments into CDS nucleotide alignments\n\n";
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        exit(1);
    }
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}
undef $fasta_checker;


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# Check GigaBlaster status if used
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if ( $giga==1 ){
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    $local = 0;
    $local = 2 if ( head('http://www.igs.cnrs-mrs.fr/Giga2/~database/remoteblast.cgi') );
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}

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# Temporary file extension
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my $date = sprintf("%d-%02d-%02d_%02dh%02d", localtime->year() + 1900, localtime->mon(), localtime->mday(), localtime->hour, localtime->min);
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#Start main program with version # of programs and list original queries
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print "\n\t   Protogene\t$VERSION\t$date\n\n";
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open(my $EXONERATEISHERE, "$exonerate_exe --version |");
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my $IsExonerateHere = <$EXONERATEISHERE>;
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close $EXONERATEISHERE;
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print "\t   $IsExonerateHere\n";
undef $IsExonerateHere;
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undef $VERSION;
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for(my $m=0; $m<=$#original_names; $m++){
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    printf("\t>%-3s  is  %s\n", $m, $original_names[$m]);
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}
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$date .= "_$$"; #Add PID to be more uniq
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# run_name implementation for web server
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$originalMSA = $run_name if ( $run_name ne '' );
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unlink("$originalMSA.cds", "$originalMSA.cdsP", "$originalMSA.cdsP.html",
       "$originalMSA.out", "$originalMSA.boj",  "$originalMSA.log");
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# Build the sequences, from the alignment, to perform blast search
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open(my $LOG, '>', "$date.log") or die "\n\tCannot open LOG file\n\n";
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EACH_SEQ:
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for(my $r=0; $r<=$#original_names; $r++){
    my $fasta_header = $original_names[$r];
    my $short_name   = $original_names[$r];
    $fasta_header    =~ s{^>}{};               # Full FASTA header
    $short_name      =~ s{^([^\s\t]+).*$}{$1}; # Short name without description

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    my @equivalent_blast_hits; #Multiple BLAST hits with the same highest e-value/score
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    if ( exists($template_NT->{$short_name}) && $template_NT->{$short_name} ne '' ){
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        # First try nucleotide template
        push @equivalent_blast_hits, 'My_own_seq';
        print "\n\n$r done\n\nNucleotide template for $r:\t$template_NT->{$short_name}\n\n*******************************************************************\n\n";
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    }
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    elsif ( exists($template_AA->{$short_name}) && $template_AA->{$short_name} ne '' ){
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        # Second try amino acid/BLASTp template
        push @equivalent_blast_hits, $template_AA->{$short_name};
        print "\n\n$r done\n\nBlastP template for $r:\t$template_AA->{$short_name}\n\n*******************************************************************\n\n";
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    }
    else{
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    # else send them to webblast
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        # Prepare sequence $r for BLAST
        open(my $READY2BLAST, '>', "$cache/$date.seq2blast.fas.$r");
        my $noGap = $original_seq[$r];
        $noGap    =~ s{\-}{}g; #remove gaps
        print {$READY2BLAST} ">$r\n$noGap\n";
        close $READY2BLAST;

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        if ($r==0){
            # Show BLAST parameters only for the first BLAST run
            display_blast_param();
        }
        run_BLAST("$cache/$date.seq2blast.fas.$r", $local, $blast_param->{'db1'}, $blast_exe, "$cache/$date.blastp.$r");
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        # Get the BLASTp hit(s)  acc number
        open(my $BLASTP, '<', "$cache/$date.blastp.$r");
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        while(<$BLASTP>){
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            push @equivalent_blast_hits, $1  if ( $_ =~ /^>\s*\d+@?\w?\w?\w?__([^\s\|\.]+).*$/ ); #Warning: double '_'
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        }
        close $BLASTP;
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        unlink("$cache/$date.blastp.$r", "$cache/$date.seq2blast.fas.$r") if ( $tmp == 0 || exists($equivalent_blast_hits[0]) );
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        if ( !exists($equivalent_blast_hits[0]) ){
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            print "\n$r ...\tNo blast result found above thresholds for $fasta_header\n\n";
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            buildFailureOutputFiles($r, 'No_BLASTp_Result', 'Not_searched', '');
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            undef $original_seq[$r];
            undef $original_names[$r];
            next EACH_SEQ;
        }
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    }



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    #When multiple equivalent blast hits  ==> use, and add, every hits
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    my ($resultPOS, $resultBOJ) = ('', '');
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    my @failureStatus = (''); # To always have $failureStatus[0] defined
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    my @intronStatus  = ('');
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    HIT_LINK:
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    for(my $qq=0; $qq<=$#equivalent_blast_hits; $qq++){
        print "\n$fasta_header  -->  [$equivalent_blast_hits[$qq]]\n";
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        my @nt_GIs;
        my $intronStep = 0;
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        # Get Nt sequence from template
        if ( exists($template_NT->{$short_name}) && $template_NT->{$short_name} ne '' ){
            if ( $template_NT->{$short_name} !~ /^My_Seq$/i ){
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                download_seq($cache, '', '', $template_NT->{$short_name});
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                @nt_GIs = $template_NT->{$short_name};
            }
            else {
                open(my $MYSEQ, '>', "$cache/My_Seq-$$.fas");
                print {$MYSEQ} ">My_Seq-$$ for $short_name\n".$template_SEQ->{$short_name}."\n";
                close $MYSEQ;
                @nt_GIs = "My_Seq-$$";
            }
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        }
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        # Get Nt sequence through prot acc -> prot gi -> nt linked gi -> nt acc
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        else{
        #Prot ACC -> PUID
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            my $protGI = blastPAcc2PGI($equivalent_blast_hits[$qq]);
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            if ( $protGI eq '' ){
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                print "\tNo protein (prot GI) link found for $equivalent_blast_hits[$qq] in $fasta_header\n\n";
                @failureStatus = ('PUI_unavailable', $equivalent_blast_hits[$qq]);
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                next HIT_LINK;
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            }
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        #PUID -> nt GIs & GeneID
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            my ($ntGIs, $geneID) = protGI2NTGIs($protGI, $equivalent_blast_hits[$qq]);
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            if ( $ntGIs eq '' && $geneID eq '' ){
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                print "\tNo nucleotide (nt GIs) link found for $equivalent_blast_hits[$qq] in $fasta_header\n\n";
                @failureStatus = ('No_nt_link', $equivalent_blast_hits[$qq]);
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                next HIT_LINK;
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            }
            print " linked with [$ntGIs $geneID]\n";


        #Get transcript and contig seq
            @nt_GIs = split(/,/, $ntGIs);
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            if ( $ntGIs ne '' ){
                downloadSeqFromGIs($cache, '', '', @nt_GIs);
            }
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        #GeneID -> Chr
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            if ( $geneID ne '' ){
                my @geneIDs = split(/,/, $geneID);
                while(<@geneIDs>){
                    my $geneID = $_;
                    my ($chr, $amont, $aval) = geneID2Chr($geneID, $equivalent_blast_hits[$qq]);
                    print "\n\tNo gene locus found for $equivalent_blast_hits[$qq] with $geneID in $fasta_header\n\n" if ($chr eq '' and $geneID ne '');

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                    #Get Chr seq
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                    if ( $chr ne '' ){
                        download_seq($cache, $amont, $aval, $chr);
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                        $intronStep = 1; #FIXME: useful ???
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                        @nt_GIs = ("$chr:$amont-$aval", @nt_GIs);
                    }
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                }
            }
        }


    #Align Nt seq with our protein query seq
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        my ($POS, $BOJ) = runExonerate($exonerate_exe, $cache, $date, $r, $original_seq[$r], $fasta_header, $equivalent_blast_hits[$qq], $r, @nt_GIs);
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        my ($POSresult, $bestNucleotide) = prepareResults4CDS($POS, $equivalent_blast_hits[$qq], $original_seq[$r], $fasta_header);
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        $resultPOS .= $POSresult if ( $bestNucleotide ne '' && $POSresult ne '' && $resultPOS !~ /_G_$bestNucleotide/ );

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        @intronStatus = ($POS->{0}, $equivalent_blast_hits[$qq], '')              if ( $intronStep==1 && exists($POS->{0}) && $POS->{0} ne '' && $POS->{0} =~ /\:/ );
        @intronStatus = ($POS->{0}, $equivalent_blast_hits[$qq], $bestNucleotide) if ( $intronStep==0 && ($bestNucleotide =~ /^N[CTWZG]_/ || $bestNucleotide =~ /^AC_/) );
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        my ($intronLess, $nameLess) = ('', '');
        $intronLess = $POS->{0}       if ( %$BOJ eq 0 && exists($POS->{0}) && $POS->{0} ne '' );
        $nameLess   = $bestNucleotide if ( %$BOJ eq 0 && $intronStep==0 && ($bestNucleotide =~ /^N[CTWZG]_/ || $bestNucleotide =~ /^AC_/) );
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        my ($BOJresult, $bestGenomic) = prepareResults4BOJ($BOJ, $equivalent_blast_hits[$qq], $original_seq[$r], $fasta_header, $intronLess, $nameLess);
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        $resultBOJ .= $BOJresult      if ( $bestGenomic ne '' && $BOJresult ne '' && $resultBOJ !~ /_G_$bestGenomic[ \-]/ );
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#    print " $intronStep $POS->{0} [@intronStatus] {$BOJresult} $bestNucleotide - $bestGenomic \t $BOJ->{0}\n";
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    }


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    if ( $resultPOS eq '' ){
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        if ( $failureStatus[0] ne '' ){
            buildFailureOutputFiles($r, $failureStatus[1],         $failureStatus[0],   '');
        }
        else {
            buildFailureOutputFiles($r, $equivalent_blast_hits[0], 'Alignment_failure', '');
        }
        next HIT_LINK;
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    }
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    elsif ( $resultBOJ eq '' ){
        if ( $failureStatus[0] eq 'PUI_unavailable' || $failureStatus[0] eq 'No_nt_link' ){
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            buildFailureBOJOutputFile($failureStatus[1], $failureStatus[0], $fasta_header, $original_seq[$r]);
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        }
        elsif ( $failureStatus[0] eq '' && $intronStatus[0] ne '' ){
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            buildIntronlessBOJOutputFile($intronStatus[1], $intronStatus[0], $intronStatus[2], $fasta_header, $original_seq[$r]);
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        }
        else{
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            buildFailureBOJOutputFile($equivalent_blast_hits[0], 'Unavailable', $fasta_header, $original_seq[$r]);
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        }
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        createCDSOutputFile($resultPOS, $original_seq[$r], $fasta_header);
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    }
    else {
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        createCDSOutputFile($resultPOS, $original_seq[$r], $fasta_header);
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        createBOJOutputFile($resultBOJ, ${original_seq[$r]});
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    }


    undef $original_seq[$r];
    undef $original_names[$r];
}
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close $LOG;
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unlink "$date.log" if ( -z "$date.log" );
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checkAndCleanStderrFiles("$cache/${date}_ExonerateError") if ( -e "$cache/${date}_ExonerateError" );
checkOutputFiles();
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unlink("$msa") if ( $converted==1 );
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unlink 'blast_result.txt';
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my @tmpFiles = glob($cache."/${date}*");
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if ( exists($tmpFiles[0]) ){
    mkdir("$cache/${date}_TMP");
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    move("$_", "$cache/${date}_TMP") while(<@tmpFiles>);
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}


#Ouput Checker


#STDOUT Log output for our server
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if ( -s "${originalMSA}.cds" || -s "${originalMSA}.out"){
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    print "\n\nTERMINATION STATUS: SUCCESS\n";
    print "OUTPUT RESULTS\n";
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    print "    #### File Type=        MSA Format= fasta_CDS Name= ${originalMSA}.cds\n" 
        if ( -s "${originalMSA}.cds");
    print "    #### File Type=        MSA Format= fasta_CDS+Query Name= ${originalMSA}.cdsP\n" 
        if ( -s "${originalMSA}.cdsP");
    print "    #### File Type=        MSA Format= colored_fasta_CDS Name= ${originalMSA}.cdsP.html\n" 
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        if ( Views::Html("${originalMSA}.cdsP") && -s "${originalMSA}.cdsP.html");
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    print "    #### File Type=        MSA Format= Rejected_seq Name= ${originalMSA}.out\n" 
        if ( -s "${originalMSA}.out");
    print "    #### File Type=        MSA Format= fasta_Exon-Boundaries Name= ${originalMSA}.boj\n" 
        if ( -s "${originalMSA}.boj" && -s "${originalMSA}.cds" && $hideBOJ==0);
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}
else{
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    failure();
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    exit(1);
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}

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exit(0);
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=head1 NAME

ProtoGene.pl - Converts a peptidic alignment to a nucleotidic alignment through database search

=head1 SYNOPSIS

B<ProtoGene.pl> --msa=path_of_the_fasta_msa_file [options]

with these options available:

=over 4

=item I<--orgm>=targeted species in the database search

=item All_organisms [default], Bacteria, Viruses, Vertebrata, Eukaryota, Mammalia, Primates, Homo_sapiens, Gallus_gallus, Bos_taurus, Escherichia_coli, Arabidopsis_thaliana, Mus_musculus, Drosophila_Melanogaster, ...

=item I<--db>=targeted database in the database search

=item nr, pdb, swissprot, refseq_protein [default]

=item I<--local> to execute a local BLAST query with  --db=path_for_a_local_db_blast_formated

=item I<--template> to provide your own nucleotidic sequences following the cds file format

=item I<--revtrans> to reverse-translate sequences with no blast hit, in IUB (IUPAC) depiction code

=item They are removed from the alignement by default

=item I<--pep> to add the original peptide query beneath the back-translated sequence

=item I<--cache>=none, update, use, own_path_directory, old, empty

=item none: no cache usage, none temporary files are stored

=item update: use cache but update old files [default]

=item use: force use cache, whatever the age of files

=item own_path_directory: use my own directory, and its files

=item old: remove the old files in the cache directory

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=item empty: empty completely the cache directory
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=item I<--version> to print version information

=item I<--help> to print this help message

=back

=head1 DESCRIPTION

PROTOGENE : Bona-Fide Back Translation of Protein Multiple Sequence Alignments
It converts a peptidic alignment to a nucleotidic alignment through database search.
Blast queries allow to get nucleotidic sequences from where peptidic sequences come from.
Exonerate aligns nucleotidic and peptidic sequences together.
PROTOGENE re-builds the original alignment with nucleotidic information it has gotten.

=head1 REQUIREMENT

=over 4

=item B<Perl 5.6 or better> is required !

=item Standard Perl modules B<lib>, B<strict>,  B<warnings>,  B<diagnostics>, B<Env> are required

=item and some other current ones : B<Getopt::Long>,  B<File::Which>,  B<File::Copy>, B<Mail::Send>

=item -

=item I<exonerate> from http://www.ebi.ac.uk/~guy/exonerate/

=item I<blast> from http://www.ncbi.nlm.nih.gov/BLAST/download.shtml or http://blast.wustl.edu/

=back

=head1 VERSION

=over 8

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=item version 4.0.0
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=item on Apr 02nd, 2011
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=back

=head1 AUTHORS

=over 8

=item Sebastien MORETTI

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=item moretti.sebastien [AT] gmail.com
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=item Vital-IT computing center
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=item Swiss Institute of Bioinformatics
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=item Lausanne, Switzerland
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=item http://www.vital-it.ch/
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=back

=cut


######################  Management  ######################

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# Failure declaration
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sub failure {
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    print {*STDERR} "\n\nFATAL\n\nTERMINATION STATUS: FAILURE\n\n";
    return;
}
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# Check external programs presence in the PATH
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sub checkExternalSoftware {
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    for my $exe ( @_ ){
        if ( ! which($exe) ){
            failure();
            print {*STDERR} "\t'$exe' program is not reachable\n\tIt could not be in your PATH or not installed\n\n";
            exit(1);
        }
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    }
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    return;
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}

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# Check cache directory accessibility: Test and change rights, if required, of the cache directory
sub checkCacheAccessibility {
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    my ($cacheDir) = @_;
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    if ( -d "$cacheDir/" && -w "$cacheDir/" && -x "$cacheDir/" && -r "$cacheDir/" ){
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        # Good
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    }
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    elsif ( -d "$cacheDir/" ){
        if ( -o "$cacheDir/" ){
            chmod 0754, "$cacheDir/";
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        }
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        else{
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            failure();
            print {*STDERR} "\tPermissions do NOT seem to be valid for the '$cacheDir' cache directory\n\n";
            exit(2);
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        }
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    }
    else{
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        mkdir "$cacheDir/"; # FIXME: mkdir is not recursive !
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        if ( -o "$cacheDir/" ){
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            chmod 0754, "$cacheDir/"; #0754 is in octal, so 754 or '0754' are not good !
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        }
        else{
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            failure();
            print {*STDERR} "\tPermissions do NOT seem to be valid for the '$cacheDir' cache directory\n\n";
            exit(2);
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        }
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    }
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    return;
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}

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# Cache Behavior Management
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sub cacheManagement{
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    my ($cache, $cacheDir, $inScript) = @_;
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    if ( $cache eq 'empty' ){
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        unlink <$cacheDir/*.fas>;
        unlink <$cacheDir/*_ExonerateError>;
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        unlink("$cacheDir/webblast.log", "$cacheDir/web_tempo.result", "$cacheDir/debug.tempo");
        print "\n\tcache directory [$cacheDir] is empty\n\n";
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        exit 0;
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    }
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    elsif ( $cache eq 'old' ){
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        unlink    grep { -M $_ > $cacheStorageTime }    glob($cacheDir.'/*.fas'); # Grep list only with $cacheStorageTime days old files

        if ( $inScript==0 ){
            print "\n\tcache directory [$cacheDir] is empty of its old files\n\n";
            exit 0;
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        }
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    }
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    elsif ( $cache eq 'update' || $cache eq 'use' ){
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        # DEFAULT: Limit cached files to less than $cacheStorageTime days old ones for 'update'
        $cache = $cacheDir;
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    }
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    elsif ( $cache eq 'none' ){
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        # Do not use cache
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    }
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    elsif ( -d $cache ){
        die "\n\tProtoGene cannot access to your directory\n\n"  if ( ! -x $cache );
        die "\n\tProtoGene cannot write into your directory\n\n" if ( ! -w $cache );
        die "\n\tProtoGene cannot read into your directory\n\n"  if ( ! -r $cache );
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    }
    else {
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        failure();
        print {*STDERR} "\n\tWrong cache argument, or your cache folder '$cacheDir' doesn't seem to exist\n\n";
        exit(3);
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    }

    return($cache);
}

##########################################################


######################    Fasta    ######################

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# Check input aln format
sub isFastaFile{
    my ($msa, $converted) = @_;

    if ( -s "$msa" ){ # Check is the file exists and is not empty
        # Is FASTA format ?
        my $firstLine = `head $msa`;
        return($msa, 0) if ( $firstLine =~ /^>/ );

        # Convert no fasta format to fasta with readseq
        my $reformat = which('readseq') || '';
        if ( $reformat ne '' ){
            system("$reformat -a -f8 $msa > $msa.007")==0 or do {failure(); print {*STDERR} "\n\tEnable to convert your file to fasta format\n\n";};
            $msa      .= '.007';
            $converted = 1;
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        }
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    }
    else {
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        failure();
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        print {*STDERR} "\tThe file \'$msa\' doesn't not seem to be reachable\n\n";
        exit(1);
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    }

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    return($msa, $converted);
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}

#Prepare Fasta Header of the query name to incorporate our annotations
sub fastaHeaders4ProtoGene{
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    my ($QueryName) = @_;
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    $QueryName =~ s/  +/ /g;
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    my ($acc, $desc) = ($QueryName, $QueryName);
    $acc  =~ s/^ *([^ ]*) .*$/$1/;
    $acc  =~ s/\s+$//g;
    $acc  =  $acc.'_G_@@';

    $desc =~ s/^ *[^ ]* *(.*)$/$1/;
    $desc =~ s/^[\| \.]+//;
    $desc =~ s/[\|\. ]+$//;

    return($acc.$desc);
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}

#Prepare Fasta Header to put it on the fasta header of the result outputs
sub getFastaHeaderAnnot{
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    my ($bestTarget) = @_;
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    #Get annotation from nucleotide file header
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    open(my $BEST, '<', "$cache/${bestTarget}.fas");
    my $annot=<$BEST> || '';
    close $BEST;
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    chomp($annot);
    $annot =~ s/^ *[^ ]* //;
    $annot =~ s/[\. ]*$//;
    $annot =~ s/^ *//;
    $annot =~ s/  +/ /g;

    return($annot);
}

#########################################################


###################### Translation ######################

#Direct Reverse translation
sub reverse_trad{
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    my ($aa) = @_;
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    my %reverse_code = ('A' => 'GCN', 'F' => 'TTy', 'K' => 'AAr', 'P' => 'CCN', 'T' => 'ACN',
                        'C' => 'TGy', 'G' => 'GGN', 'L' => 'yTN', 'Q' => 'CAr', 'V' => 'GTN',
                        'D' => 'GAy', 'H' => 'CAy', 'M' => 'ATG', 'R' => 'mGN', 'W' => 'TGG',
                        'E' => 'GAr', 'I' => 'ATh', 'N' => 'AAy', 'S' => 'wsN', 'Y' => 'TAy',
                        'X' => 'NNN', '-' => '---', '*' => 'Trr',
                       ); # '*' is for stop codon
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    my $triplet = 'nnn';
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    while( my ($x, $y) =each(%reverse_code) ){
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        if ( uc($aa) eq $x ){
            $triplet = $y;
            last;
        }
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    }

    return($triplet);
}

#########################################################


####################### webblast #######################
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sub display_blast_param {
    print "
             Program :                   BLASTp
             Evalue threshold :          $blast_param->{'evalue'}
             Matrix :                    $blast_param->{'matrix'}
             Filter :                    $blast_param->{'filter'}
             Equivalent best hits used : $blast_param->{'nbesthits'}

             Database:                   NCBI $blast_param->{'db1'}
             Blast_identity_threshold :  $blast_param->{'identity1'}
             Cover threshold :           $blast_param->{'cover1'}
          if no match
             Database:                   NCBI $blast_param->{'db2'}
             Blast_identity_threshold :   $blast_param->{'identity2'}
             Cover threshold :            $blast_param->{'cover2'}
\n";
    return;
}

sub run_BLAST{
    my ($infile, $whatBlast, $db, $blast_exe, $outfile) = @_;

    my $blast_at = $whatBlast==2  ? '-gigablast=yes'
                 : $whatBlast==1  ? "-blast_dir=$blast_exe"
                 :                  '';

    # BLAST run 1
    system("$webblast_exe -program=blastp -database=$db $blast_at -infile=$infile -matrix=$blast_param->{'matrix'} -evalue=$blast_param->{'evalue'} -method=geneid -filter=$blast_param->{'filter'} -organism=$species -identity=$blast_param->{'identity1'} -cover=$blast_param->{'cover1'} -hits=$blast_param->{'nbesthits'} -quiet=on -outfile=$outfile");


    if ( -z "$outfile" ){
    # BLAST run 2 if no hit with 100% identity and coverage: refseq100 -> nr95  OR  nr100 -> nr95
        print "run BLAST.. against $blast_param->{'db2'} because there was no acceptable hit against $blast_param->{'db1'}"
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            if ( $whatBlast != 1 && $db ne 'nr' );
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        print "run BLAST.. again, with decreased thresholds, because there was no acceptable hit against $db"
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            if ( $whatBlast == 1 || $db eq 'nr' );
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        system("$webblast_exe -program=blastp -database=$blast_param->{'db2'} $blast_at -infile=$infile -matrix=$blast_param->{'matrix'} -evalue=$blast_param->{'evalue'} -method=geneid -filter=$blast_param->{'filter'} -organism=$species -identity=$blast_param->{'identity2'} -cover=$blast_param->{'cover2'} -hits=$blast_param->{'nbesthits'} -quiet=on -outfile=$outfile");
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    }

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    move('webblast.log',     "$cache"); #Move temporary webblast.pl files
    move('web_tempo.result', "$cache");
    move('debug.tempo',      "$cache");

    unlink("$cache/webblast.log")     if ( -z "$cache/webblast.log" );
    unlink("$cache/web_tempo.result") if ( -z "$cache/web_tempo.result" );
    unlink("$cache/debug.tempo")      if ( -z "$cache/debug.tempo" );
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    return;
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}


########################################################


##################### NCBI requests #####################
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sub fetch {
    my ($url) = @_;

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    XML:
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    for (my $tries=0; $tries <20; $tries++ ){
        my $content = get($url);
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        print "[$content]\n\n" if ($debug);
        if ( defined $content ){
            next XML if ( $content =~ /<ERROR>/i );
            return $content;
        }
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    }
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    print {*STDERR} "Problem with NCBI eutils, please try again later\n";
    exit(40);
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}
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sub fetch_fasta {
    my ($url, $outfile) = @_;

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    return 1 if ( -s "$outfile" && $cache eq 'update' && -M "$outfile" <= $cacheStorageTime );
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    GET_FASTA:
    for (my $tries=0; $tries <20; $tries++ ){
        my $HTTP_status = getstore($url, $outfile);
        if ( is_error($HTTP_status) ){
            next GET_FASTA;
        }
        else {
            open(my $FASTA, '<', "$outfile");
            my $counter = 0;
            my $lines   = 0;
            while(<$FASTA>){
                $lines++              if ( $_ !~ /^>/ );
                $counter = $counter+2 if ( $counter==1 && $_ !~ /^\w/ && $lines==1 && $_ !~ /^>/ );
                $counter++            if ( $_ =~ /^>/ );
                $counter = $counter+2 if ( $_ !~ /^>/ && ($_ =~ /Error:/ || $_ =~ /[<>]/) );
            }
            close $FASTA;
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            return 1 if ( $counter == 1 );
        }
    }
    unlink("$outfile");
    print {*STDERR} "Problem with NCBI eutils, please try again later.\n";
    exit(45);
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}

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#Prot ACC -> PUID
sub blastPAcc2PGI{
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    my ($blastHit) = @_;
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    my $protGI = '';
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    #FIXME: should be ${blastHit}[pacc] but something is broken at NCBI
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    my $content = fetch("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=$blastHit&retmode=xml&tool=ProtoGene&email=smoretti\@unil.ch");
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    if ( $content =~ /<Id>(\d+)<\/Id>/ ){
        $protGI = $1;
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    }

    return($protGI);
}

#PUID -> nt GIs
sub protGI2NTGIs{
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    my ($protGI, $blastHit) = @_;
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    my $ntGIs  = '';
    my $geneID = '';
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    my $content = fetch("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=nuccore,nucleotide,gene&id=$protGI&retmode=xml&tool=ProtoGene&email=smoretti\@unil.ch");

    my @xml  = split("\n", $content);
    my $flag = 0;
    for my $line (@xml){
        if (    $line =~ /<LinkName>protein_nuc[a-z]+<\/LinkName>/ ){ #for nuccleotide and nuccore
            $flag = 1;
        }
        elsif ( $line =~ /<LinkName>protein_gene<\/LinkName>/ ){
            $flag  = 2;
        }
        elsif ( $flag==1 && $line =~ /^.*<Id>(\d+)<\/Id>.*$/ ){
            my $match = $1;
            $ntGIs  .= "$match,$match,";
        }
        elsif ( $flag==2 && $line =~ /^.*<Id>(\d+)<\/Id>.*$/ ){
            my $match = $1;
            $geneID .= "$match,$match,";
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        }
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    }

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    #Remove redundancy if any
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    chop $ntGIs; #Remove last ','
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    my %hash_NT = split(',', $ntGIs);
    $ntGIs      = join(',',  keys(%hash_NT) );
    chop $geneID;
    my %hash_GE = split(',', $geneID);
    $geneID     = join(',',  keys(%hash_GE) );

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    return($ntGIs, $geneID);
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}

sub geneID2Chr{
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    my ($geneID, $blastHit) = @_;
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    my $chr   = '';
    my ($amont, $aval) = ('', '');
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#   my $content = fetch("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=$geneID&retmode=xml&tool=ProtoGene&email=smoretti\@unil.ch");
    my $content = fetch("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id=$geneID&retmode=xml&tool=ProtoGene&email=smoretti\@unil.ch");

    my @xml  = split("\n", $content);
    my $flag = 0;
    GENE_INFO:
    for my $line (@xml){
        if ( $flag==0    && $line =~ /<Item Name="GenomicInfoType" Type="Structure">/ ){
            $flag = 1;
        }
        elsif ( $flag==1 && $line =~ /<Item Name="ChrAccVer" Type="String">([^<]+?)\.?\d*<\/Item>/ ){
            $chr   = $1;
            $flag  = 3;
        }
        elsif ( $flag==3 && $line =~ /<Item Name="ChrStart" Type="Integer">(\d+)<\/Item>/ ){
            $amont = $1;
            $flag  = 4;
        }
        elsif ( $flag==4 && $line =~ /<Item Name="ChrStop" Type="Integer">(\d+)<\/Item>/ ){
            $aval  = $1;
            last GENE_INFO;
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        }
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    }
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    if ( $amont eq '' || $aval eq '' ){
        $amont = '';
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        $aval  = '';
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    }
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    elsif ( $amont ne '' && $aval ne '' ){
        if ( $amont > $aval ){
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            $amont = $amont + 5000;
            $aval  = $aval  - 5000;
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        }
        else{
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            $amont = $amont - 5000;
            $aval  = $aval  + 5000;
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        }
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    }
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    $amont = 1 if ( $amont ne '' && $amont <= 0 );
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    $aval  = 1 if ( $aval  ne '' && $aval  <= 0 );
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    return($chr, $amont, $aval);
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}

sub downloadSeqFromGIs{
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    my ($cache, $amont, $aval, @acc) = @_;
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    GET_SEQ:
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    for(my $a=0; $a<=$#acc; $a++){
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        if ( $amont =~ /^\d+$/ && $aval =~ /^\d+$/ ){
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            fetch_fasta("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$acc[$a]&rettype=fasta&retmode=text&from=$amont&to=$aval&tool=ProtoGene&email=smoretti\@unil.ch", "$cache/$acc[$a]-$amont.fas") ;
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        }
        else{
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            fetch_fasta("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$acc[$a]&rettype=fasta&retmode=text&tool=ProtoGene&email=smoretti\@unil.ch'", "$cache/$acc[$a].fas");
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        }
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    }
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    return;
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}

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sub download_seq{
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    my ($cache, $amont, $aval, @acc) = @_;
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    my $cp   = 0;
    my $from = $amont;