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13
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1 #!/usr/bin/perl
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2 #
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3
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4 use List::MoreUtils qw(first_index indexes);
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5
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6 open MLST,$ARGV[0];
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7
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8 @mlstout=split(/\t/,<MLST>);
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9
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10 $schema=$mlstout[1];
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11 $mlstST=$mlstout[2];
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12
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13 # Assumes mlst command is installed and available in the path
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14 # Retrieve the location of the MLST databases
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15 $mlstdesc=`mlst -h | grep \"db/pubmlst\"`;
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16 @vals = split(/\'/,$mlstdesc);
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17 $mlstloc=$vals[1];
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18 $mlstloc=~s/bin\/\.\.//g;
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19
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20 my(%schema);
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21
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22 $mlstfile = "$mlstloc/$schema/$schema.txt";
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23 open IN,$mlstfile;
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24 @headers=split(/\t/,<IN>);
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25 my $clonal = first_index { /clonal\_complex/ } @headers;
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26 my $cc = first_index { /CC/ } @headers;
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27 my $lineage = first_index { /Lineage/ } @headers;
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28 my $species = first_index { /species/ } @headers;
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29 while($line=<IN>) {
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30 chomp($line);
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31 my(@vals)=split(/\t/,$line);
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32 my(@desc);
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33 if ($clonal>0 && length($vals[$clonal])>0) {
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34 push(@desc,"clonal_complex=".$vals[$clonal]);
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35 }
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36 if ($cc>0 && length($vals[$clonal])>0) {
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37 push(@desc,"CC=".$vals[$cc]);
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38 }
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39 if ($lineage>0 && length($vals[$linage])>0) {
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40 push(@desc,"Lineage=".$vals[$lineage]);
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41 }
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42 if ($species>0 && length($vals[$species])>0) {
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43 push(@desc,"species=".$vals[$species]);
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44 }
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45 $schema{$vals[0]}=join(',',@desc);
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46 }
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47
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48 print shift(@mlstout)."\t".shift(@mlstout)."\t".shift(@mlstout)."\t";
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49 if(exists($schema{$mlstST})) {
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50 print $schema{$mlstST};
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51 }
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52 foreach(@mlstout) {
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53 print "\t".$_;
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54 }
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