Mercurial > repos > dereeper > pangenome_explorer
view Perl/ConvertRoaryMatrix.pl @ 7:2c65d4257fe6 draft
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author | dereeper |
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date | Thu, 30 May 2024 12:30:04 +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(U,">$out.upsetr.txt"); open(M,">$out.accessory_01matrix.txt"); open(F,$matrix); my $firstline = <F>; $firstline =~s/\n//g;$firstline =~s/\r//g; my @infos = split(/","/,$firstline); print O "ClutserID"; print U "ClutserID"; print M "Gene"; for (my $j=14; $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"; print U "\n"; print M "\n"; while(<F>){ $cl_num++; my $line = $_; $line =~s/\n//g;$line =~s/\r//g; my @infos = split(/","/,$line); print O $cl_num; print U $cl_num; my $concat_accessory = ""; for (my $i = 14; $i <= $#infos; $i++){ my $val = $infos[$i]; $val =~s/\"//g; if ($val =~/\w+/){ print U "\t1"; $concat_accessory .= "\t1"; } else{ print U "\t0"; $concat_accessory .= "\t0"; } my @genes = split(/\t/,$val); my $concat = ""; foreach my $gene(@genes){ my $prot_id = $corr{$gene}; if (!$prot_id){$prot_id = $gene;} $concat .= "$prot_id," } chop($concat); if (scalar @genes == 0){ $concat = "-"; } print O "\t".$concat; } if ($concat_accessory =~/0/){ print M $cl_num.$concat_accessory."\n"; } print O "\n"; print U "\n"; } close(F); close(O); close(U); close(M);