Mercurial > repos > estrain > microrunqc
changeset 13:59e137488c63 draft
Uploaded
| author | estrain |
|---|---|
| date | Wed, 24 May 2023 17:24:23 +0000 |
| parents | 50867379763d |
| children | d326e0177a2a |
| files | ._median_size.py ._microrunqc.xml ._mlstAddFields.pl ._run_fastq_scan.py ._sum_mlst.py microrunqc.xml mlstAddFields.pl |
| diffstat | 7 files changed, 58 insertions(+), 2 deletions(-) [+] |
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--- 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 ${fqscan};
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mlstAddFields.pl Wed May 24 17:24:23 2023 +0000 @@ -0,0 +1,54 @@ +#!/usr/bin/perl +# + +use List::MoreUtils qw(first_index indexes); + +open MLST,$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".$_; +}