Mercurial > repos > dereeper > pangenome_explorer
view Perl/ConvertPGAPMatrix.pl @ 14:5a5c9a6b047b draft
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author | dereeper |
---|---|
date | Tue, 10 Dec 2024 16:20:53 +0000 |
parents | e42d30da7a74 |
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#!/usr/bin/perl use strict; my $indir = $ARGV[0]; my $matrix = $ARGV[1]; my $out = $ARGV[2]; my $strain_names = $ARGV[3]; my %strains_of_gb; open(F,$strain_names); while(<F>){ my $line = $_; $line =~s/\n//g;$line =~s/\r//g; my ($gb,$strain) = split(/\t/,$line); $strains_of_gb{$gb} = $strain; } close(F); my %corr; open(D,"ls $indir/*rmdup.gff |"); while(<D>){ my $file = $_; open(F,"$file"); while(<F>){ my @infos = split(/\t/,$_); if ($infos[2] eq 'CDS' && /ID=([^;]*);.*protein_id=([^;]*);/){ my $id = $1; my $protid = $2; $corr{$id} = $protid; } } close(F); } close(D); my $cl_num = 0; my $nb_strains = 1; open(O,">$out"); open(F,$matrix); my $firstline = <F>; $firstline =~s/\n//g;$firstline =~s/\r//g; my @infos = split(/\t/,$firstline); print O "ClutserID"; print U "ClutserID"; print M "Gene"; for (my $j=1; $j <= $#infos; $j++){ my $gbfile = $infos[$j]; $gbfile =~s/\"//g; $gbfile =~s/\.gb\.filt//g; $gbfile =~s/\.gb\.rmdup//g; my $strain = $strains_of_gb{$gbfile}; print O "\t".$strain; print U "\t".$strain; print M "\t".$strain; $nb_strains++; } print O "\n"; while(<F>){ print O $_; } close(F); close(O);