ProtoGene.pl 52.3 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;
use Env qw(HOME);                          # Use only environmental (shell) HOME variable
use File::Basename;
use File::Copy qw(move);                   # Avoid external 'mv' command usage

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use lib '/mnt/common/share/ProtoGene/';    # Local path for ProtoGene's own perl modules
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use lib '/mnt/local/lib/tcoffee_perl/';
use Getopt::Long;                          # For options specifications
use File::Which qw(which);                 # Locate external executable programs in the PATH
#use Time::Format qw(%time);               # Use local time for part of pseudo-uniq temp file name
use Mail::Send;                            # Send warnings and errors files by e-mail ==> only if the $userEMail variable is defined

use loci_from_Exonerate;                   # Exonerate parser
#use output_checker;                       # Check output for cds consistancy with query



############## Specific to our server
#L'installer doit creer $HOME/.PACMAN/ and $HOME/.PACMAN/.perllib/
#et mettre les differents modules dans $HOME/.PACMAN/.perllib/
$ENV{'PATH'} .= ':/mnt/local/bin/'; # additional path for executable on the server
##############



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my $Version='3.0.2';
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my $uct=15;                                            # UpdateCacheThreshold: number of days before update
my $cachedir='/scratch/frt/tcoffee/ProtoGene_Cache';   # Cache directory
##### User settings ####################################
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my $userEMail='moretti.sebastien@gmail.com';           # To receive an e-mail with encountered problems; leave blank to inactive this option
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my $webblast_exe=which('webblast.pl') || '';           #
my $blast_prog='blastall';                             # Or wu-blastall for Wu-BLAST; for local blast usage
my $exonerate=which('exonerate-1.0') || '';            #
########################################################
my $blast_exe=which($blast_prog) || '';
my $doc=which('perldoc') || '';
#my $date=$time{'yy-mm-dd_hh\hmm-ss.mmm'}; #Used to get a unique file
my $date=`/usr/bin/env date +%y-%m-%d_%T`; #Used to get a unique file
chomp($date);
$date =~ s/\:/\-/g;

&checkProgramsPresence($webblast_exe,$exonerate); # Check external programs presence in the PATH
$blast_exe =~ s/${blast_prog}$//;

&checkCacheAccessibility($cachedir); # Check cache directory accessibility



##Options management
my ($msa,$species,$db,$athome,$revtrans,$pep,$hideBOJ)=('','All_organisms','refseq_protein',0,0,0,0);
my ($version,$help,${run_name},$Cache,$template,$lim,$tmp)=(0,0,'','update','',0,0);
my $giga=0;
GetOptions("msa|in=s"       => \$msa,        #Input sequences
           "orgm|species=s" => \$species,    #Organism(s) to blast against
           "db|database=s"  => \$db,         #Database to blast against
           "local"          => \$athome,     #Use to specify a local db query, definied in $local_db
           "giga"           => \$giga,       #Use GigaBlaster server
           "revtrans"       => \$revtrans,   #Use to reverse-translate sequences with no match
           "pep"            => \$pep,        #Add the original peptide query beneath the linked nt seq
           "version|v"      => \$version,    #Print version information
           "help|h"         => \$help,       #Print full help message
           "run_name=s"     => \${run_name}, #Use another name, instead of input seq name, for result files
           "cache=s"        => \$Cache,      #Specify what cache parameter
           "hideBOJ"        => \$hideBOJ,    
           "template=s"     => \$template,   #Use a template file
           "lim=i"          => \$lim,        #Limite number of input query sequences
           "tmp"            => \$tmp         #To keep traces of fake intermediate files like fake xml from NCBI, fake aln, ...
           );
$athome=2 if ($giga==1);
if ($version==1){
    print "\n\tPROTOGENE : Bona-Fide Back Translation of Protein Multiple Sequence Alignments\n\tversion   : $Version\n\n";
    exit;
}
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if ( $help==1 ){
    if ( $doc ne '' ){
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	system("$doc $0");
    }
    else{
	print STDERR "\n\tperldoc command doesn't seem to be available\n\tto see the documentation in pod format\n\n";
    }
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    exit(1);
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}
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if ( $blast_exe eq '' && $version==0 && $help==0 ){
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    print STDERR "\n\t$blast_prog program is not reachable\n\tIt could not be in your PATH or not installed\n\tIt is required only for local blast searches\n\n";
}

#Cache management
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my $cache = &cacheManagement($Cache) || '.';
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#Open and check template file
my ($templG,$templP,$templSeq);
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($templG,$templP,$templSeq) = &checkTemplate($template) if ($template);
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#Short help message
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if ( $msa eq '' || $species eq '' || $db eq '' || $cache eq '' ){
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    my $appli=basename($0);
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    print {*STDERR} "\n\tCannot open the MSA file in fasta format
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\tTry:  $appli --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, ...
\t                default is 'All_organisms'
\t         --db=nr, pdb, swissprot, refseq_protein
\t                default is 'refseq_protein'
\t         --local to execute a local BLAST query with
\t                --db=path_for_a_local_db_blast_formated
\t         --template to provide your own nucleotidic sequences
\t                following the cds file format
\t         --revtrans to reverse-translate sequences with no
\t                blast hit, in IUB (IUPAC) depiction code
\t                They are removed from the alignement by default
\t         --pep  to add the original peptide query beneath the
\t                back-translated sequence
\t         --cache=none, update, use, own_PATH_directory, old, empty
\t                to select the cache mode
\t                default is 'update'
\t         --version to print version information
\t         --help to print a full help message\n\n";
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    exit(1);
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}



##Open and Check the fasta file
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my $originalMSA   = $msa;
my $change        = 0;
($msa,$change)    = &checkFastaFile($msa,$change);
my $fasta_checker = -1;
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my (@input_order,@original_names,@original_seq); #Use 3 lists in parallel : original_names, seq, order(1->n)
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open( my $MSA, '<', "$msa") if ( -e "$msa" );
while(<$MSA>){
    if ( $_ =~ /^>/ ){
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	$fasta_checker++;
	my $name=$_;
	$name =~ s/\r\n//g; #Remove return lines from windows OS '^M'
	chomp($name);
	@original_names=(@original_names,$name);
	@input_order=(@input_order,$fasta_checker);
    }
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    elsif ( $_ !~ /^>/ ){
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	my $seqq=$_;
	$seqq =~ s/\r\n//g;
	$seqq =~ s/\./-/g; #for msa with '.' as gap
	$seqq =~ s/[^A-Za-z\-\*\n\r]//g; #Remove all the non-gap or non-alphabetic characters from the seq
	chomp($seqq);
        #fasta sequence on 1 line
	if ( ! exists( $original_seq[$fasta_checker] )){
	    @original_seq=(@original_seq,$seqq);
	}
	else {
	    $original_seq[$fasta_checker]=$original_seq[$fasta_checker].$seqq;
	}
    }
}
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close $MSA;
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if ( $fasta_checker == -1 ){
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    &failure;
    print STDERR "\tThe MSA file does NOT seem to be a protein fasta format\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;
    print STDERR "\tThe fasta file is too large, try with less than $lim sequences\n\n";
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    exit(1);
}
elsif ( exists( $original_seq[0] ) && $original_seq[0] =~ /[acgtu]/i){
    #Check if sequences are amino acids and not nucleotides
    my ( $a, $c, $g, $t, $non ) = ( 0, 0, 0, 0, 0 );
    $a   = ($original_seq[0] =~ s/[aA]//g);
    $c   = ($original_seq[0] =~ s/[cC]//g);
    $g   = ($original_seq[0] =~ s/[gG]//g);
    $t   = ($original_seq[0] =~ s/[tTuU]//g);
    $non = ($original_seq[0] =~ s/[^aAcCgGtTuU-]//g);
    if ( ($a+$c+$g+$t) >= (($a+$c+$g+$t+$non)*80/100) ){
        &failure();
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        print STDERR "\tYour sequences seem already to be nucleotides\n\tthis program purpose 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;



#Start main program with version # of programs and list original queries
print "\n\t   Protogene\t$Version\t$date\n\n";
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open(my $EXONERATEISHERE,"$exonerate --version |");
my $IsExonerateHere=<$EXONERATEISHERE>;
close $EXONERATEISHERE;
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print "\t   $IsExonerateHere\n";
undef $IsExonerateHere;
undef $Version;
for(my $m=0; $m<=$#original_names; $m++){
    print "\t$original_names[$m]\n";
}
$date.="_$$"; #Add PID



# run_name implementation for web server
${originalMSA}=${run_name} if (${run_name} ne '');

unlink("${originalMSA}.cds");
unlink("${originalMSA}.cdsP");
unlink("${originalMSA}.out");
unlink("${originalMSA}.boj");



# Remove old files from the cache directory
&cacheManagement('old','1'); #everytime ProtoGene is running




##Build the sequences, from the alignment, to perform webblast
my $quiet='';
for(my $r=0; $r<=$#input_order; $r++){
    my $right_name=$original_names[$r];
    my $templ_name=$original_names[$r];
    $right_name =~ s/^>//;
    $templ_name =~ s/^([^\s\t]+).*$/$1/;

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    open(my $READY2BLAST, '>', "$cache/${date}_seq2blast.fas${r}");
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    my $noGap=$original_seq[$r];
    $noGap =~ s/[\.-]//g; #remove gaps
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    print {$READY2BLAST} ">$input_order[$r]\n$noGap\n";
    close $READY2BLAST;
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    undef $noGap;




    my @multipleequalblasthits;
    if ( exists($templG->{$templ_name}) and $templG->{$templ_name} ne ''){
	@multipleequalblasthits=(@multipleequalblasthits,'My_own_seq'); #To change for ?
	print "\n\n$r done\n\nNucleotidic template for $r:\t$templG->{$templ_name}\n\n**********************************************************************\n\n";
    }
    elsif ( exists($templP->{$templ_name}) and $templP->{$templ_name} ne ''){
	@multipleequalblasthits=(@multipleequalblasthits,$templP->{$templ_name});
	print "\n\n$r done\n\nBlastP template for $r:\t$templP->{$templ_name}\n\n**********************************************************************\n\n";
    }
    else{
	##   --> send them to webblast
	$quiet='-quiet=on ' if ($r>0); #Show webblast parameters only for the first webblast run
	&launchWebblast("$cache/${date}_seq2blast.fas${r}",$quiet,$athome,$db,$species,${blast_exe},"$cache/${date}.blastp${r}");

	##Get the BLASTp hit(s)  acc number
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	open(my $BLASTP, '<', "${cache}/${date}.blastp${r}");
	while(<$BLASTP>){
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	    @multipleequalblasthits=(@multipleequalblasthits,$1) if ($_ =~ /^>\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 or exists($multipleequalblasthits[0]) );
	if ( ! exists($multipleequalblasthits[0]) ){
	    print "\n$input_order[$r] ...\tNo blast result found above filter thresholds for $right_name\n\n";
	    &buildFailureOutputFiles($r,'No_BLASTp_Result','Unavailable','');
	    undef $original_seq[$r];
	    undef $original_names[$r];
	    undef $input_order[$r];
	    next;
	}
    }



    #When multiple equal blast hits  ==> use, and add, every hits
    my ($resultPOS,$resultBOJ)=('','');
    my @failureStatus=('');
    my @intronStatus=('');
    for(my $qq=0; $qq<=$#multipleequalblasthits; $qq++){
	print "\n${right_name}  -->  [${multipleequalblasthits[$qq]}]\n";


	my @nt_GIs;
	my $intronStep=0;
	if ( exists($templG->{$templ_name}) and $templG->{$templ_name} ne '' and $templG->{$templ_name} !~ /^My_Seq$/i){
	    &downloadSeq($cache,$date,'','',$templG->{$templ_name});
	    @nt_GIs=$templG->{$templ_name};
	}
	elsif ( exists($templG->{$templ_name}) and $templG->{$templ_name} ne '' and $templG->{$templ_name} =~ /^My_Seq$/i){
	    open(MYSEQ,">$cache/My_Seq-$$.fas");
	    print MYSEQ ">My_Seq-$$ for $templ_name\n".$templSeq->{$templ_name}."\n";
	    close MYSEQ;
	    @nt_GIs="My_Seq-$$";
	}
	else{
	    #Prot ACC -> PUID
	    my $protGI=&blastPAcc2PGI($multipleequalblasthits[$qq]);
	    if ($protGI eq ''){
		print "\tNo protein (prot GI) link found for ${multipleequalblasthits[$qq]} in $right_name\n\n";
		@failureStatus=('PUI_unavailable',${multipleequalblasthits[$qq]});
		next;
	    }
#           print "\t$protGI\n";

	    #PUID -> nt GIs & GeneID
	    my ($ntGIs,$geneID)=&protGI2NTGIs($protGI,$multipleequalblasthits[$qq]);
	    if ($ntGIs eq '' and $geneID eq ''){
		print "\tNo nucleotide (nt GIs) link found for ${multipleequalblasthits[$qq]} in $right_name\n\n";
		@failureStatus=('No_nt_link',${multipleequalblasthits[$qq]});
		next;
	    }
	    print " linked with [$ntGIs $geneID]\n";


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

		if ($chr ne ''){
		    #Get Chr seq
		    &downloadSeq($cache,$date,$amont,$aval,$chr);
		    $intronStep=1;

		    @nt_GIs=("$chr:$amont-$aval",@nt_GIs);
		}
	    }
	}


	#Align Nt seq with our protein query seq
	my ($POS,$BOJ)=&runExonerate($exonerate,$cache,$date,${input_order[$r]},${original_seq[$r]},${right_name},$multipleequalblasthits[$qq],$r,@nt_GIs);

	my ($POSresult,$bestNucleotide)=&prepareResults4CDS($POS,$multipleequalblasthits[$qq],${original_seq[$r]},${right_name});
	$resultPOS.=$POSresult if ($bestNucleotide ne '' and $POSresult ne '' and $resultPOS !~ /_G_$bestNucleotide/);

	@intronStatus=($POS->{0},${multipleequalblasthits[$qq]},'') if ($intronStep==1 and exists($POS->{0}) and $POS->{0} ne '' and $POS->{0} =~ /\:/);
        @intronStatus=($POS->{0},${multipleequalblasthits[$qq]},$bestNucleotide) if ($intronStep==0 and ($bestNucleotide =~ /^N[CTWZG]_/ or $bestNucleotide =~ /^AC_/));

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


    if ($resultPOS eq ''){
	&buildFailureOutputFiles($r,$failureStatus[1],$failureStatus[0],'') if ($failureStatus[0] ne '');
	&buildFailureOutputFiles($r,$multipleequalblasthits[0],'Failed_Aln','') if ($failureStatus[0] eq '');
	next;
    }
    elsif ($resultBOJ eq ''){
	if ($failureStatus[0] eq 'PUI_unavailable' or $failureStatus[0] eq 'No_nt_link'){
	    &buildFailureBOJOutputFile($failureStatus[1],$failureStatus[0],${right_name},${original_seq[$r]});
	}
	elsif ($failureStatus[0] eq '' and $intronStatus[0] ne ''){
	    &buildIntronlessBOJOutputFile($intronStatus[1],$intronStatus[0],$intronStatus[2],${right_name},${original_seq[$r]});
	}
	else{
	    &buildFailureBOJOutputFile($multipleequalblasthits[0],'Unavailable',${right_name},${original_seq[$r]});
	}
	&createCDSOutputFile($resultPOS,${original_seq[$r]},${right_name});
    }
    else {
	&createCDSOutputFile($resultPOS,${original_seq[$r]},${right_name});
	&createBOJOutputFile($resultBOJ,${original_seq[$r]});
    }


    undef $original_seq[$r];
    undef $original_names[$r];
    undef $input_order[$r];
}


&checkAndCleanStderrFiles("$cache/${date}_ExonerateError") if ( -e "$cache/${date}_ExonerateError" );
&checkOutputFiles();
unlink("$msa") if ($change==1);
my @tmpFiles=glob($cache."/${date}*");
if ( exists($tmpFiles[0]) ){
    mkdir("$cache/${date}_TMP");
    move("$_","$cache/${date}_TMP") while(<@tmpFiles>);
}


#Ouput Checker


#STDOUT Log output for our server
if ( -s "${originalMSA}.cds" or -s "${originalMSA}.out"){
    print "\n\nTERMINATION STATUS: SUCCESS\n";
    print "OUTPUT RESULTS\n";
    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= 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" and -s "${originalMSA}.cds" and $hideBOJ==0);
}
else{
    &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

=item empty: empty the whole cache directory $HOME/.ProtoGene/

=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 3.0.2
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=item on June 15th, 2007
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=back

=head1 AUTHORS

=over 8

=item Sebastien MORETTI

=item Sebastien.Moretti@igs.cnrs-mrs.fr

=item Frederic REINIER

=item Frederic.Reinier@igs.cnrs-mrs.fr

=item Lab. Information Genomique et Structurale - IGS

=item CNRS - Life Sciences

=item Marseille, France

=item http://www.igs.cnrs-mrs.fr/

=back

=cut


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

#Failure declaration
    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
sub checkProgramsPresence{
    my ($webblast_exe,$exonerate)=@_;

    if ($webblast_exe eq ''){
	&failure;
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	print {*STDERR} "\twebblast.pl program is not reachable\n\tIt could not be in your PATH or not installed\n\n";
	exit(1);
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    }
    if ($exonerate eq ''){
	&failure;
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	print {*STDERR} "\texonerate program is not reachable\n\tIt could not be in your PATH or not installed\n\n";
	exit(1);
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    }
}

#Check cache directory accessibility: Test and change rights, if needs, of the $HOME/.ProtoGene/ cache directory
sub checkCacheAccessibility{
    my ($cachedir)=@_;

    if ( -d "$cachedir/" and -w "$cachedir/" and -x "$cachedir/" and -r "$cachedir/" ){
    }
    elsif ( -d "$cachedir/" ){
	if ( -o "$cachedir/" ){
	    chmod 0754, "$cachedir/";
	}
	else{
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	    print {*STDERR} "\n\t** Warning ** :\n\tPermissions do NOT seem to be valide for the current cache directory\n\n";
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	}
    }
    else{
	mkdir "$cachedir/";
	if ( -o "$cachedir/" ){
	    chmod 0754, "$cachedir/"; #0754 est en octal, donc 754 ou '0754' ne sont pas bons !
	}
	else{
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	    print {*STDERR} "\n\t** Warning ** :\n\tPermissions do NOT seem to be valide for the current cache directory\n\n";
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	}
    }
}

#Cache Management
sub cacheManagement{
    my ($Cache,$inScript)=@_;
    $inScript=0 if ( !defined $inScript);

    if ($Cache eq 'empty'){
	my @temp_files=glob($cachedir.'/*.fas');
	if ( exists ($temp_files[0]) ){
	    unlink $_ while(<@temp_files>);
	}
	@temp_files=glob($cachedir.'/*_ExonerateError');
	if ( exists ($temp_files[0]) ){
	    unlink $_ while(<@temp_files>);
	}
	unlink("$cachedir/webblast.log","$cachedir/web_tempo.result","$cachedir/debug.tempo");
	print "\n\tcache directory [$cachedir] is empty\n\n";
	exit;
    }
    elsif ($Cache eq 'old'){
	my @temp_files=glob($cachedir.'/*.fas');
	my @tempFiles=grep { -M $_ > $uct } @temp_files; #Sort list only with $uct days old files
	if ( exists ($tempFiles[0]) ){
	    unlink $_ while(<@tempFiles>);
	}
	print "\n\tcache directory [$cachedir] is empty of its old files\n\n" if ($inScript==0);
	exit if ($inScript==0);
    }
    elsif ($Cache eq 'update' or $Cache eq 'use'){
	$cache=$cachedir; #Limit cache files to less than $uct days old ones for 'update'
    }
    elsif ($Cache eq 'none'){
    }
    elsif ( -d $Cache ){
	die "\n\tPACMAN cannot access to your directory\n\n" if ( ! -x $Cache );
	die "\n\tPACMAN cannot write into your directory\n\n" if ( ! -w $Cache );
	die "\n\tPACMAN cannot read into your directory\n\n" if ( ! -r $Cache );
	$cache=$Cache;
    }
    else {
	die "\n\tWrong cache argument, or your cache folder doesn't seem to exist\n\n";
    }

    return($cache);
}

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


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

#Check input aln
sub checkFastaFile{
    my ($msa,$change)=@_;

    if ( -e "$msa"){
    #Convert no fasta format to fasta with seq_reformat if available
	my $seqreformat=which('t_coffeeX') || ''; #desactive tant que t_coffee seq_reformat pose prob
	if ($seqreformat ne ''){
	    my @formatType=`$seqreformat -other_pg seq_reformat -in $msa -print_format`;
	    my $format='';
	    while(<@formatType>){
		if ($_ =~ /FORMAT:/){
		    $format=$_;
		    chomp($format);
		    last;
		}
	    }
	    if ($format ne '' and $format !~ /FORMAT:fasta_/){
		system("$seqreformat -other_pg seq_reformat -in $msa -output fasta_aln -out=${msa}.007") if ($format =~ /_aln *$/);
		system("$seqreformat -other_pg seq_reformat -in $msa -output fasta_seq -out=${msa}.007") if ($format =~ /_seq *$/);
		$msa.='.007';
		$change=1;
	    }
	}
    }
    else {
	&failure;
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	print {*STDERR} "\tThe file \'$msa\' doesn't not seem to be reachable\n\n";
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	exit(1);
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    }

    return($msa,$change);
}

#Prepare Fasta Header of the query name to incorporate our annotations
sub fastaHeaders4ProtoGene{
    my ($QueryName)=@_;

    $QueryName =~ s/  +/ /g;
    my ($cqacc,$cqdesc)=($QueryName,$QueryName);
    $cqacc =~ s/^ *([^ ]*) .*$/$1/;
    $cqacc =~ s/[\s\t]*$//g;
    $cqacc=$cqacc.'_G_@@';
    $cqdesc =~ s/^ *[^ ]* *(.*)$/$1/;
    $cqdesc =~ s/^[\| \.]*//;
    $cqdesc =~ s/[\|\. ]*$//;

    $QueryName=$cqacc.$cqdesc;
    return($QueryName);
}

#Prepare Fasta Header to put it on the fasta header of the result outputs
sub getFastaHeaderAnnot{
    my ($bestTarget)=@_;

    #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{
    my ($aa)=@_;

    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

    my $triplet='nnn';
    while(my ($x,$y) =each(%reverse_code)){
	if (uc($aa) eq $x){
	    $triplet=$y;
	    last;
	}
    }

    return($triplet);
}

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


####################### webblast #######################
sub launchWebblast{
    my ($infile,$quiet,$whatBlast,$db,$species,${blast_exe},$outfile)=@_;
    my $blast_at='';

    $blast_at="-database=$db" if ($whatBlast==0);
    $blast_at="-database=$db -blast_dir=${blast_exe}" if ($whatBlast==1);
    $blast_at="-database=$db -gigablast=yes" if ($whatBlast==2);

#    print "             Evalue treshold : 0.05
#             Matrix : BLOSUM62
#             Filter : F
#             **********************
#             For RefSeq Protein db:
#             Blast_identity_threshold : 100
#             Cover threshold : 100
#             **********************
#             For NR Protein db:
#             Blast_identity_threshold : 95
#             Cover threshold : 95";

    system("$webblast_exe -program=blastp ${blast_at} -infile=$infile -matrix=BLOSUM62 -evalue=0.05 -method=geneid -filter=Off -organism=$species -identity=100 -cover=100 $quiet -outfile=$outfile");


    if ( -z "$outfile"){ #Another blastP query if no hit with refseq and db was not nr !
	$quiet='-quiet=on';
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	print {*STDERR} "run BLAST.. against NR because there was no acceptable hit against $db\n" if ($whatBlast != 1 and $db ne 'nr');
	print {*STDERR} "run BLAST.. again, with decreased thresholds, because there was no acceptable hit against $db\n" if ($whatBlast == 1 or $db eq 'nr');
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	$blast_at =~ s/-database=[^\s]*/-database=nr/ if ($whatBlast != 1);
	system("$webblast_exe -program=blastp ${blast_at} -infile=$infile -matrix=BLOSUM62 -evalue=0.05 -method=geneid -filter=Off -organism=$species -identity=95 -cover=95 $quiet -outfile=$outfile");
    }

    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");
}


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


##################### NCBI requests #####################

#Prot ACC -> PUID
sub blastPAcc2PGI{
    my ($blastHit)=@_;

    my $protGI='';
    my $count=0;
    for(my $rep=0;$rep <= 4; $rep++){
	$count++;
	system("wget -q -O $cache/${date}_${blastHit}protGi.tmp 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=protein&term=${blastHit}[pacc]&retmode=xml'");
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	open(my $GIP, '<', "$cache/${date}_${blastHit}protGi.tmp");
	while(<$GIP>){
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	    if ($_ =~ /^.*\<Id\>(\d+)\<\/Id\>.*$/){
		$protGI=$1;
		last;		#OK if only one PUID
	    }
	}
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	close $GIP;
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	$rep=$rep-15 if ( -z "$cache/${date}_${blastHit}protGi.tmp" and $count==1);
	last if ($protGI =~ /^\d+$/);
    }
    unlink("$cache/${date}_${blastHit}protGi.tmp") if ($tmp == 0 or $protGI ne '');

    return($protGI);
}

#PUID -> nt GIs
sub protGI2NTGIs{
    my ($protGI,$blastHit)=@_;

    my $ntGIs='';
    my $geneID='';
    my $count=0;
    for(my $rep=0;$rep <= 4; $rep++){
	$count++;
        #nt GIs
	system("wget -q -O $cache/${date}_${blastHit}nucleo.tmp 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=protein&db=nucleotide,gene&id=$protGI&retmode=xml'");
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	open(my $GIN, '<', "$cache/${date}_${blastHit}nucleo.tmp");
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	my $flag=0;
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	while(<$GIN>){
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	    if ($_ =~ /\<LinkName\>protein_nucleotide\<\/LinkName\>/){
		$flag=1;
	    }
	    elsif ($_ =~ /\<LinkName\>protein_gene\<\/LinkName\>/){
		$flag=2;
	    }
	    elsif ($flag==1 and $_ =~ /^.*\<Id\>(\d+)\<\/Id\>.*$/){
		$ntGIs.=",$1" if ($ntGIs ne '');
		$ntGIs=$1 if ($ntGIs eq '');
	    }
	    elsif ($flag==2 and $_ =~ /^.*\<Id\>(\d+)\<\/Id\>.*$/){
		$geneID.=",$1" if ($geneID ne '');
		$geneID=$1 if ($geneID eq '');
	    }
	}
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	close $GIN;
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	$rep=$rep-15 if ( -z "$cache/${date}_${blastHit}nucleo.tmp" and $count==1);
	last if ($ntGIs ne '' or $geneID ne '');
    }
    unlink("$cache/${date}_${blastHit}nucleo.tmp") if ($tmp == 0 or ($ntGIs ne '' or $geneID ne ''));

    return($ntGIs,$geneID);
}

sub geneID2Chr{
    my ($geneID,$blastHit)=@_;

    my $chr='';
    my ($amont,$aval)=('','');
    my $count=0;
    for(my $rep=0;$rep <= 8; $rep++){
	$count++;
        #Gene Acc
	system("wget -q -O $cache/${date}_${blastHit}gene.tmp 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=$geneID&retmode=xml'");
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	open(my $GACC, '<', "$cache/${date}_${blastHit}gene.tmp");
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	my $flag=0;
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	while(<$GACC>){
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	    if ($_ =~ /\<ERROR\>Empty id list \- nothing todo\<\/ERROR\>/ and $flag==0){
		$rep=$rep-15 if ($count==1);
	    }
	    if ($_ =~ /\<Entrezgene_locus\>/ and $flag==0){
		$flag=1;
	    }
	    elsif ($_ =~ /\<Gene-commentary_type value=\"genomic\"\>/ and $flag==1){
		$flag=2;
	    }
	    elsif ($_ =~ /\<Gene-commentary_type value=/ and $flag==2){
		last;
	    }
	    elsif ($_ =~ /\<Gene-commentary_accession\>([\w\_\-\.]+)\<\/Gene-commentary_accession\>/ and $flag==2){
		$chr=$1;
		$flag=3;
	    }
	    elsif ($_ =~ /\<Seq-interval_from\>(\d+)\<\/Seq-interval_from\>/ and $flag==3){
		$amont=$1;
		$flag=4;
	    }
	    elsif ($_ =~ /\<Seq-interval_to\>(\d+)\<\/Seq-interval_to\>/ and $flag==4){
		$aval=$1;
		last;
	    }
	}
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	close $GACC;
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	$rep=$rep-15 if ( -z "$cache/${date}_${blastHit}gene.tmp" and $count==1);
	last if ($chr ne '' and $amont =~ /^\d+$/ and $aval =~ /^\d+$/);
    }
    unlink("$cache/${date}_${blastHit}gene.tmp") if ($tmp == 0 or $chr ne '');
    if ($amont eq '' or $aval eq ''){
	$amont='';
	$aval='';
    }
    elsif ($amont ne '' and $aval ne ''){
	if ($amont > $aval){
	    $amont=$amont+5000;
	    $aval=$aval-5000;
	}
	else{
	    $amont=$amont-5000;
	    $aval=$aval+5000;
	}
    }
    $amont=1 if ($amont ne '' and $amont <= 0);
    $aval=1 if ($aval ne '' and $aval <= 0);

    return($chr,$amont,$aval);
}

sub downloadSeqFromGIs{
    my ($cache,$date,$amont,$aval,@acc)=@_;

    for(my $a=0; $a<=$#acc; $a++){
	my $whatNumber=0;
	if ($amont =~ /^\d+$/ and $aval =~ /^\d+$/){
	    for(my $rep=0;$rep <= 4; $rep++){
		system("wget -q -O $cache/${acc[$a]}-${amont}.fas 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${acc[$a]}&rettype=fasta&retmode=text&from=$amont&to=$aval'") if ( ! -e "$cache/${acc[$a]}-${amont}.fas" or -z "$cache/${acc[$a]}-${amont}.fas" or $Cache eq 'none' or ($Cache eq 'update' and -M "$cache/${acc[$a]}-${amont}.fas" > $uct ));
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		open(my $CIBLE, '<', "$cache/${acc[$a]}-${amont}.fas");
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		my $counter=0;
		my $lines=0;
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		while(<$CIBLE>){
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		    $lines++ if ($_ !~ /^>/);
		    $counter=$counter+2 if ($counter==1 and $_ !~ /^\w/ and $lines==1 and $_ !~ /^>/);
		    $counter++ if ($_ =~ /^>/);
		    $counter=$counter+2 if ($_ !~ /^>/ and ($_ =~ /Error:/ or $_ =~ /[<>]/) );
#		    last if ($_ !~ /^>/ and $counter==1 and $_ =~ /^\w/);
		}
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		close $CIBLE;
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		$whatNumber++;
		last if ($whatNumber==20);
		if ($counter != 1){
		    $rep=$rep-1;
		    unlink("$cache/${acc[$a]}-${amont}.fas");
		}
	    }
	}
	else {
	    for(my $rep=0;$rep <= 4; $rep++){
		system("wget -q -O $cache/${acc[$a]}.fas 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${acc[$a]}&rettype=fasta&retmode=text'") if ( ! -e "$cache/${acc[$a]}.fas" or -z "$cache/${acc[$a]}.fas" or $Cache eq 'none' or ($Cache eq 'update' and -M "$cache/${acc[$a]}.fas" > $uct ));
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		open(my $CIBLE, '<', "$cache/${acc[$a]}.fas");
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		my $counter=0;
		my $lines=0;
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		while(<$CIBLE>){
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		    $lines++ if ($_ !~ /^>/);
		    $counter=$counter+2 if ($counter==1 and $_ !~ /^\w/ and $lines==1 and $_ !~ /^>/);
		    $counter++ if ($_ =~ /^>/);
		    $counter=$counter+2 if ($_ !~ /^>/ and ($_ =~ /Error:/ or $_ =~ /[<>]/) );
		}
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		close $CIBLE;
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		$whatNumber++;
		last if ($whatNumber==20);
		if ($counter != 1){
		    $rep=$rep-1;
		    unlink("$cache/${acc[$a]}.fas");
		}
	    }
	}
    }
}

sub downloadSeq{
    my ($cache,$date,$amont,$aval,@acc)=@_;

    my $cp=0;
    my $from=$amont;
    my $to=$aval;
    for(my $a=0; $a<=$#acc; $a++){
	my $pacc2puid=$acc[$a];
	if ($pacc2puid !~ /^[NAX][CGTWZM]_/){
            #pacc = primary acc NOT prot acc !   #265666 -> S55551
	    system("wget -q -O $cache/${date}_${acc[$a]}.gui 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?&db=nucleotide&term=${pacc2puid}[pacc]'");
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	    open(my $GUI, '<', "$cache/${date}_${acc[$a]}.gui");
	    while(<$GUI>){
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		if ($_ =~ /\<Id\>(\d+)\<\/Id\>/){
		    $pacc2puid=$1;
		    last;
		}
	    }
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	    close $GUI;
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	    unlink("$cache/${date}_${acc[$a]}.gui") if ($tmp == 0 or $pacc2puid =~ /^\d+$/);
	}
	my $whatNumber=0;
	if ($amont =~ /^\d+$/ and $aval =~ /^\d+$/){
	    for(my $rep=0;$rep <= 4; $rep++){
		system("wget -q -O $cache/${acc[$a]}:${from}-${to}.fas 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${pacc2puid}&rettype=fasta&retmode=text&from=$amont&to=$aval'") if ( ! -e "$cache/${acc[$a]}:${from}-${to}.fas" or -z "$cache/${acc[$a]}:${from}-${to}.fas" or $Cache eq 'none' or ($Cache eq 'update' and -M "$cache/${acc[$a]}:${from}-${to}.fas" > $uct ));
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		open(my $CIBLE, '<', "$cache/${acc[$a]}:${amont}-${aval}.fas");
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		my $counter=0;
		my $lines=0;
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		while(<$CIBLE>){
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		    $lines++ if ($_ !~ /^>/);
		    $counter=$counter+2 if ($counter==1 and $_ !~ /^\w/ and $lines==1 and $_ !~ /^>/);
		    $counter++ if ($_ =~ /^>/);
		    $counter=$counter+2 if ($_ !~ /^>/ and ($_ =~ /Error:/ or $_ =~ /[<>]/) );
		}
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		close $CIBLE;
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		$whatNumber++;
		last if ($whatNumber==20);
		if ($counter != 1){
		    $rep=$rep-1;
		    unlink("$cache/${acc[$a]}:${amont}-${aval}.fas");
		}
	    }
	}
	else {
	    for(my $rep=0;$rep <= 4; $rep++){
		system("wget -q -O $cache/${acc[$a]}.fas 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=${pacc2puid}&rettype=fasta&retmode=text'") if ( ! -e "$cache/${acc[$a]}.fas" or -z "$cache/${acc[$a]}.fas" or $Cache eq 'none' or ($Cache eq 'update' and -M "$cache/${acc[$a]}.fas" > $uct ));
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		open(my $CIBLE, '<', "$cache/${acc[$a]}.fas");
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		my $counter=0;
		my $lines=0;
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		while(<$CIBLE>){