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#!/usr/local/bin/perl
my $P=1;
my $N=-1;
my %hash = ();# hash des strand
open (DESC2, "coco_cds");
while(<DESC2>){
next if /^\#/;
chomp;
my ($id,$strand,$coord)=(split/\t/)[1,3,-1];
my @cds=();
foreach my $exon (split/,/,$coord){
my ($s,$e)=split(/\.\./,$exon);
push @cds,($s..$e)
}
if ($strand eq "-"){
$strand=$N;
@cds=reverse(@cds);
}
else{
$strand=$P;
}
$hash{$id}=$strand;# hash des strand pour coco
my $count=0;
for (my $i=0;$i<@cds;$i+=3){
$count++;
$aa2geno{$id}{$count}=$cds[$i];# hash des genomes pour coco
}
}
open (DESC3, "aster_cds");
while(<DESC3>){
next if /^\#/;
chomp;
my ($id,$strand,$coord)=(split/\t/)[1,3,-1];
my @cds=();
foreach my $exon (split/,/,$coord){
my ($s,$e)=split(/\.\./,$exon);
push @cds,($s..$e)
}
if ($strand eq "-"){
$strand=$N;
@cds=reverse(@cds);
}
else{
$strand=$P;
}
$hash{$id}=$strand;# hash des strand pour aster
my $count=0;
for (my $i=0;$i<@cds;$i+=3){
$count++;
$aa2geno{$id}{$count}=$cds[$i];# hash des genomes pour aster
}
}
open my $fh, '<', 'gene.txt' or die;
while (<$fh>){
chomp;
my ($A,$C,$a1,$a2,$c1,$c2,$B,$D,$b1,$b2,$d1,$d2)=split(/\t/);#split pour avoir les donnees
my $cocco1;
my $cocco2;
my $orth1;
my $orth2;
#print $D,"\t",$d1,"\t",$d2,"\n" ;
my ($geneA,$asterC,$geneB,$asterD) = map { /(\d+)$/ } (split/\t/)[0,1,6,7] ;#split par rapport aux chiffres pour pouvoir faire la comparaison
#print "$A: start $gene{$A}->{start}, end $gene{$A}->{end}\n" ;
my $SScocco = $hash{$A}*$hash{$B};
my $SSaster = $hash{$C}*$hash{$D};#construction des strand
#debut des filtrages
if ($SScocco>0 && ($SScocco==$SSaster)){
if ($hash{$A}==1 && $hash{$B}==1 ){
$cocco1=$a2;
$cocco2=$b1;
$orth1=$c2;
$orth2=$d1;
}
if ($hash{$A}==-1 && $hash{$B}==-1 ){
$cocco1=$a1;
$cocco2=$b2;
$orth1=$c1;
$orth2=$d2;
}
}
elsif($SScocco<1 && ($SScocco==$SSaster)){
if ($hash{$A}==-1 && $hash{$B}==1){
$cocco1=$a1;
$cocco2=$b1;
$orth1=$c1;
$orth2=$d1;
}
if ($hash{$A}==1 && $hash{$B}==-1){
$cocco1=$a2;
$cocco2=$b2;
$orth1=$c2;
$orth2=$d2;
}
}
print join("\t",$A,$B,abs($aa2geno{$B}{$cocco2}-$aa2geno{$A}{$cocco1}+1),$C,$D,abs($aa2geno{$D}{$orthococco2}-$aa2geno{$C}{$$orthcocco}+1))."\n";
}
#print $aa2geno{$B}{$cocco2};
#print join("\t",$A,$B,abs($aa2geno{$B}{$cocco2}-$aa2geno{$A}{$cocco1}+1),$C,$D,abs($aa2geno{$D}{$orthococco2}-$aa2geno{$C}{$$orthcocco}+1))."\n";
__END__ |
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