diff PanExplorer_workflow/Perl/ConvertPanacotaMatrix.pl @ 1:032f6b3806a3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PanExplorer_workflow/Perl/ConvertPanacotaMatrix.pl	Thu May 30 11:16:08 2024 +0000
@@ -0,0 +1,120 @@
+#!/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);