Mercurial > repos > mgarnier > pangenome_cog_analysis
changeset 4:db4e1e6850b0 draft
Uploaded
| author | mgarnier |
|---|---|
| date | Fri, 02 Jul 2021 17:32:59 +0000 |
| parents | 27c5a6f2301c |
| children | 3d565ddc7b95 |
| files | pangenomeCogAnalysis_V1.pl |
| diffstat | 1 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/pangenomeCogAnalysis_V1.pl Fri Jul 02 14:54:40 2021 +0000 +++ b/pangenomeCogAnalysis_V1.pl Fri Jul 02 17:32:59 2021 +0000 @@ -517,6 +517,8 @@ 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 $i (keys (%coregenes2)){ @@ -532,7 +534,7 @@ open (OUT5, "> Core/$strain_name.$specie_name.txt") or die "Cannot create file $!\n"; - print OUT5 "Orthogroup\tGene\tChromosome\tStart\tEnd\tCOG categories\n"; + print OUT5 "Orthogroup\tGene\tChromosome\tStart\tEnd\tCOG categories\tLetter assigned\n"; my $refcoregenes2 = $coregenes2{$i}; my %subhash = %$refcoregenes2; @@ -549,7 +551,7 @@ # if (!$subhash{$gene}){ # print "$gene\n"; # } - print OUT5 $subhash{$gene}."\t"."$gene\t".$Gene_position{$gene}."\t".$cat."\n"; + print OUT5 $subhash{$gene}."\t"."$gene\t".$Gene_position{$gene}."\t".$cat."\t".$Hash_Convert{$cat}."\n"; } @@ -568,7 +570,7 @@ 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"; + print OUT6 "Orthogroup\tGene\tChromosome\tStart\tEnd\tCOG categories\tLetter assigned\n"; my $refGenes_of_OG = $Genes_of_OG{$i}; my %subhash = %$refGenes_of_OG; @@ -581,7 +583,7 @@ if ($Cog_of_gene{$gene}){ $cat = $Cog_of_gene{$gene}; } - print OUT6 $orthogroup."\t".$subhash{$orthogroup}."\t".$Gene_position{$gene}."\t".$cat."\n"; + print OUT6 $orthogroup."\t".$subhash{$orthogroup}."\t".$Gene_position{$gene}."\t".$cat."\t".$Hash_Convert{$cat}."\n"; } }