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3
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1 #!/usr/bin/perl
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2
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3 use strict;
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4
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5 my $file = $ARGV[0];
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6 my $metadata = $ARGV[1];
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7
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14
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8
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3
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9 my %strains;
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10 open(F,$metadata);
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11 while(<F>){
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12 my $line = $_;
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13 $line =~s/\n//g;$line =~s/\r//g;
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14 my ($path_genome,$strain) = split(/\t/,$line);
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15 $strains{$path_genome} = $strain;
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16 }
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17 close(F);
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18
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19 my %ANIs;
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20 my %genomes;
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14
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21 my %genome_names;
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3
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22 my $num_line = 0;
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23 open(F,$file);
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24 <F>;
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25 while(<F>){
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26 $num_line++;
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27 my $line = $_;
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28 $line =~s/\n//g;$line =~s/\r//g;
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29 my @infos = split(/\t/,$line);
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30 my $genome = $infos[0];
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31 $genome = $strains{$genome};
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14
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32 $genome_names{$genome}++;
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33 if ($genome_names{$genome} > 1){
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34 $genome = $genome . ".". $genome_names{$genome};
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35 }
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36
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3
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37 $genomes{$num_line} = $genome;
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38 for (my $i = 1; $i <= $#infos; $i++){
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39 $ANIs{$i}{$num_line} = $infos[$i];
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40 $ANIs{$num_line}{$i} = $infos[$i];
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41 }
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42 }
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43 close(F);
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44
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45 print "Genomes";
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14
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46
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3
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47 foreach my $i(sort keys(%ANIs)){
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48 print "\t".$genomes{$i};
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49 }
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50 print "\n";
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51 foreach my $i(sort keys(%ANIs)){
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52 print $genomes{$i};
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53 foreach my $j(sort keys(%ANIs)){
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54 my $ani = $ANIs{$i}{$j};
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55 if ($ani eq "NA"){$ani = 0;}
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56 if (!$ani && $i == $j){
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57 $ani = 100;
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58 }
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59 print "\t".$ani;
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60 }
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61 print "\n";
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62 }
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