comparison mlstAddFields.pl @ 13:59e137488c63 draft

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13:59e137488c63

#!/usr/bin/perl
#

use List::MoreUtils qw(first_index indexes);

open MLST,$ARGV[0];

@mlstout=split(/\t/,<MLST>);

$schema=$mlstout[1];
$mlstST=$mlstout[2];

# Assumes mlst command is installed and available in the path
# Retrieve the location of the MLST databases
$mlstdesc=`mlst -h | grep \"db/pubmlst\"`;
@vals = split(/\'/,$mlstdesc);
$mlstloc=$vals[1];
$mlstloc=~s/bin\/\.\.//g;

my(%schema);

$mlstfile = "$mlstloc/$schema/$schema.txt";
open IN,$mlstfile;
@headers=split(/\t/,<IN>);
my $clonal = first_index { /clonal\_complex/ } @headers;
my $cc = first_index { /CC/ } @headers;
my $lineage = first_index { /Lineage/ } @headers;
my $species = first_index { /species/ } @headers;
while($line=<IN>) {
  chomp($line);
  my(@vals)=split(/\t/,$line);
  my(@desc);
  if ($clonal>0 && length($vals[$clonal])>0) {
    push(@desc,"clonal_complex=".$vals[$clonal]);
  }
  if ($cc>0 && length($vals[$clonal])>0) {
    push(@desc,"CC=".$vals[$cc]);
  }
  if ($lineage>0 && length($vals[$linage])>0) {
    push(@desc,"Lineage=".$vals[$lineage]);
  }
  if ($species>0 && length($vals[$species])>0) {
    push(@desc,"species=".$vals[$species]);
  } 
  $schema{$vals[0]}=join(',',@desc);
} 

print shift(@mlstout)."\t".shift(@mlstout)."\t".shift(@mlstout)."\t";
if(exists($schema{$mlstST})) {
  print $schema{$mlstST};
}
foreach(@mlstout) {
  print "\t".$_;
}