Mercurial > repos > dereeper > pangenome_explorer
view Perl/ConvertPanacotaMatrix.pl @ 7:2c65d4257fe6 draft
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author | dereeper |
---|---|
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 @strains; my %corr; open(D,"ls $indir/*pep |"); while(<D>){ my $file = $_; my $prot_num = 0; my $strain; if ($file =~/\/([^\/]*).pep/){ $strain = $1; $strain = $strains_of_gb{$strain}; push(@strains,$strain); } open(F,"$file"); while(<F>){ if (/>(.*)/){ my $prot_id = $1; $prot_num++; my $new_id = "$strain"."_".$prot_num; $corr{$new_id} = $prot_id; } } 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); print O "ClutserID"; print U "ClutserID"; print M "Gene"; my %hash_place_strains; my $num_cell = 0; foreach my $strain(@strains){ $num_cell++; my @words = split(/_/,$strain); my $genus = $words[0]; my $species = $words[1]; my $shortname = substr($genus,0,3) . "_". substr($species,0,2); for (my $j = 2; $j <= $#words; $j++){ $shortname.="_".$words[$j]; } $shortname = substr($shortname,0,25); print O "\t".$strain; print U "\t".$shortname; print M "\t".$shortname; $hash_place_strains{$strain} = $num_cell; $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); my %cells; for (my $i = 1; $i <= $#infos; $i++){ my $new_id = $infos[$i]; my $prot_id = $corr{$new_id}; my $strain; if ($new_id =~/^(.*)_\d+$/){$strain=$1;} my $num_cell = $hash_place_strains{$strain}; #print "$strain $num_cell $prot_id $new_id\n"; $cells{$strain}.= $prot_id.","; } print O $cl_num; print U $cl_num; my $concat_accessory = ""; foreach my $strain(@strains){ my $val; if ($cells{$strain}){ $val = $cells{$strain}; chop($val); } else{ $val = "-"; } if ($val =~/\w+/){ print U "\t1"; $concat_accessory .= "\t1"; } else{ print U "\t0"; $concat_accessory .= "\t0"; } my $concat = $val; print O "\t".$concat; } if ($concat_accessory =~/0/){ print M $cl_num.$concat_accessory."\n"; } print O "\n"; print U "\n"; } close(F); close(O);