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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PanExplorer_workflow/Perl/convertANI.pl	Thu May 30 11:16:08 2024 +0000
@@ -0,0 +1,54 @@
+#!/usr/bin/perl
+
+use strict;
+
+my $file = $ARGV[0];
+my $metadata = $ARGV[1];
+
+my %strains;
+open(F,$metadata);
+while(<F>){
+	my $line = $_;
+	$line =~s/\n//g;$line =~s/\r//g;
+	my ($path_genome,$strain) = split(/\t/,$line);
+	$strains{$path_genome} = $strain;
+}
+close(F);
+
+my %ANIs;
+my %genomes;
+my $num_line = 0;
+open(F,$file);
+<F>;
+while(<F>){
+	$num_line++;	
+	my $line = $_;
+	$line =~s/\n//g;$line =~s/\r//g;
+	my @infos = split(/\t/,$line);
+	my $genome = $infos[0];
+	$genome = $strains{$genome};
+	$genomes{$num_line} = $genome;
+	for (my $i = 1; $i <= $#infos; $i++){
+		$ANIs{$i}{$num_line} = $infos[$i];
+		$ANIs{$num_line}{$i} = $infos[$i];
+	}
+}
+close(F);
+
+print "Genomes";
+foreach my $i(sort keys(%ANIs)){
+	print "\t".$genomes{$i};
+}
+print "\n";
+foreach my $i(sort keys(%ANIs)){
+	print $genomes{$i};
+	foreach my $j(sort keys(%ANIs)){
+		my $ani = $ANIs{$i}{$j};
+		if ($ani eq "NA"){$ani = 0;}
+		if (!$ani && $i == $j){
+			$ani = 100;
+		}
+		print "\t".$ani;
+	}
+	print "\n";
+}