comparison pangenomeCogAnalysis_V1.pl @ 4:db4e1e6850b0 draft

Uploaded

3:27c5a6f2301c

    }
    
    close (G);
}

mkdir("Core");
foreach my $i (keys (%coregenes2)){

    if (!$hCol_Annotated{$i}) { # si le fichier GFF n'existe pas 
        next;

    my $specie_name = $hSpecies{$strain_name};



    open (OUT5, "> Core/$strain_name.$specie_name.txt") or die "Cannot create file $!\n";
    print OUT5 "Orthogroup\tGene\tChromosome\tStart\tEnd\tCOG categories\n";

    my $refcoregenes2 = $coregenes2{$i};
    my %subhash = %$refcoregenes2;
    foreach my $gene (keys (%subhash)){
    # print "$gene\n";

        # }
        
        # if (!$subhash{$gene}){
        #     print "$gene\n";
        # }
        print OUT5 $subhash{$gene}."\t"."$gene\t".$Gene_position{$gene}."\t".$cat."\n";
       
    }

    close (OUT5);
}

    my $strain_name = $hCol_Annotated{$i}; 
    
    my $specie_name = $hSpecies{$strain_name};

    open (OUT6, "> GroupSpecific/$strain_name.$specie_name.txt") or die "Cannot create file $!\n";
    print OUT6 "Orthogroup\tGene\tChromosome\tStart\tEnd\tCOG categories\n";

    my $refGenes_of_OG = $Genes_of_OG{$i};
    my %subhash = %$refGenes_of_OG;
    
    foreach my $orthogroup (keys (%subhash)){

            my $cat = "unknown";
            if ($Cog_of_gene{$gene}){
                $cat = $Cog_of_gene{$gene};
            }
            print OUT6 $orthogroup."\t".$subhash{$orthogroup}."\t".$Gene_position{$gene}."\t".$cat."\n";
        }
        
    }
    close (OUT6);
}

4:db4e1e6850b0

    }
    
    close (G);
}

my %Hash_Convert = ( "A"=>1, "B"=>2, "C"=>3, "D"=>4, "E"=>5, "F"=>6, "G"=>7, "H"=>8, "I"=>9, "J"=>10, "K"=>11, "L"=>12, "M"=>13, "N"=>14, "O"=>15, "P"=>16, "Q"=>17, "R"=>18,"S"=>19, "T"=>20, "U"=>21, "V"=>22, "W"=>23, "X"=>24, "Y"=>25, "Z"=>26, "unknown"=>27);

mkdir("Core");
foreach my $i (keys (%coregenes2)){

    if (!$hCol_Annotated{$i}) { # si le fichier GFF n'existe pas 
        next;

    my $specie_name = $hSpecies{$strain_name};



    open (OUT5, "> Core/$strain_name.$specie_name.txt") or die "Cannot create file $!\n";
    print OUT5 "Orthogroup\tGene\tChromosome\tStart\tEnd\tCOG categories\tLetter assigned\n";

    my $refcoregenes2 = $coregenes2{$i};
    my %subhash = %$refcoregenes2;
    foreach my $gene (keys (%subhash)){
    # print "$gene\n";

        # }
        
        # if (!$subhash{$gene}){
        #     print "$gene\n";
        # }
        print OUT5 $subhash{$gene}."\t"."$gene\t".$Gene_position{$gene}."\t".$cat."\t".$Hash_Convert{$cat}."\n";
       
    }

    close (OUT5);
}

    my $strain_name = $hCol_Annotated{$i}; 
    
    my $specie_name = $hSpecies{$strain_name};

    open (OUT6, "> GroupSpecific/$strain_name.$specie_name.txt") or die "Cannot create file $!\n";
    print OUT6 "Orthogroup\tGene\tChromosome\tStart\tEnd\tCOG categories\tLetter assigned\n";

    my $refGenes_of_OG = $Genes_of_OG{$i};
    my %subhash = %$refGenes_of_OG;
    
    foreach my $orthogroup (keys (%subhash)){

            my $cat = "unknown";
            if ($Cog_of_gene{$gene}){
                $cat = $Cog_of_gene{$gene};
            }
            print OUT6 $orthogroup."\t".$subhash{$orthogroup}."\t".$Gene_position{$gene}."\t".$cat."\t".$Hash_Convert{$cat}."\n";
        }
        
    }
    close (OUT6);
}