--- a/mlstAddFields.pl	Fri Jan 19 11:47:53 2024 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-#!/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".$_;
-}