# HG changeset patch
# User estrain
# Date 1684949063 0
# Node ID 59e137488c63978382822ee7ac9f6e62f2d1d612
# Parent  50867379763d60313431eb8c8aeb0d9b08981de4
Uploaded

diff -r 50867379763d -r 59e137488c63 ._median_size.py
Binary file ._median_size.py has changed
diff -r 50867379763d -r 59e137488c63 ._microrunqc.xml
Binary file ._microrunqc.xml has changed
diff -r 50867379763d -r 59e137488c63 ._mlstAddFields.pl
Binary file ._mlstAddFields.pl has changed
diff -r 50867379763d -r 59e137488c63 ._run_fastq_scan.py
Binary file ._run_fastq_scan.py has changed
diff -r 50867379763d -r 59e137488c63 ._sum_mlst.py
Binary file ._sum_mlst.py has changed
diff -r 50867379763d -r 59e137488c63 microrunqc.xml
--- a/microrunqc.xml	Fri Mar 10 17:01:21 2023 +0000
+++ b/microrunqc.xml	Wed May 24 17:24:23 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="microrunqc" name="microrunqc" version="1.0.0">
+<tool id="microrunqc" name="microrunqc" version="1.0.1">
 
   <requirements>
     <requirement type="package" version="2.4.0">skesa</requirement>
@@ -103,7 +103,9 @@
         --minscore $options.minscore
       #end if
     #end if
-    ${outname}.fasta > ${outname}.mlst.tsv;
+    ${outname}.fasta > ${outname}.mlst_raw.tsv;
+    
+    perl mlstAddFields.pl ${outname}.mlst_raw.tsv > ${outname}.mlst.tsv;
 
     python $__tool_directory__/run_fastq_scan.py --fastq ${bwalist} --out fq_out.tab --type ${fqscan};
 
diff -r 50867379763d -r 59e137488c63 mlstAddFields.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mlstAddFields.pl	Wed May 24 17:24:23 2023 +0000
@@ -0,0 +1,54 @@
+#!/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".$_;
+}