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

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author dereeper
date Thu, 30 May 2024 11:16:08 +0000
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0:3cbb01081cde 1:032f6b3806a3
1 #!/usr/bin/perl
2
3 use strict;
4
5 my $file = $ARGV[0];
6 my $metadata = $ARGV[1];
7
8 my %strains;
9 open(F,$metadata);
10 while(<F>){
11 my $line = $_;
12 $line =~s/\n//g;$line =~s/\r//g;
13 my ($path_genome,$strain) = split(/\t/,$line);
14 $strains{$path_genome} = $strain;
15 }
16 close(F);
17
18 my %ANIs;
19 my %genomes;
20 my $num_line = 0;
21 open(F,$file);
22 <F>;
23 while(<F>){
24 $num_line++;
25 my $line = $_;
26 $line =~s/\n//g;$line =~s/\r//g;
27 my @infos = split(/\t/,$line);
28 my $genome = $infos[0];
29 $genome = $strains{$genome};
30 $genomes{$num_line} = $genome;
31 for (my $i = 1; $i <= $#infos; $i++){
32 $ANIs{$i}{$num_line} = $infos[$i];
33 $ANIs{$num_line}{$i} = $infos[$i];
34 }
35 }
36 close(F);
37
38 print "Genomes";
39 foreach my $i(sort keys(%ANIs)){
40 print "\t".$genomes{$i};
41 }
42 print "\n";
43 foreach my $i(sort keys(%ANIs)){
44 print $genomes{$i};
45 foreach my $j(sort keys(%ANIs)){
46 my $ani = $ANIs{$i}{$j};
47 if ($ani eq "NA"){$ani = 0;}
48 if (!$ani && $i == $j){
49 $ani = 100;
50 }
51 print "\t".$ani;
52 }
53 print "\n";
54 }