# HG changeset patch
# User davidvanzessen
# Date 1415109574 18000
# Node ID 18ede27dc6b00ea44896677d3f61d92e801e8ec8
# Parent 6b348d07da4936758918b4bac7f25d48a4217463
Uploaded
diff -r 6b348d07da49 -r 18ede27dc6b0 demultiplex.xml
diff -r 6b348d07da49 -r 18ede27dc6b0 wrapper.sh
--- a/wrapper.sh Mon Jul 14 05:47:08 2014 -0400
+++ b/wrapper.sh Tue Nov 04 08:59:34 2014 -0500
@@ -38,7 +38,15 @@
workdir=$PWD
cd $outDir
echo "$3"
-result=`$dir/sff2fastq $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial`
+filetype=`file $input`
+result=""
+if [[ $filetype == *ASCII* ]]
+then
+ result=`cat $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial`
+else
+ result=`$dir/sff2fastq $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial`
+fi
+
echo "$result" | tail -n +2 | sed 's/\t/,/g' > output.txt
echo "$name demultiplex| ID | Count | FASTQ | FASTA | Trimmed FASTA | FASTQC |
|---|
" >> $output
while IFS=, read barcode count location
@@ -56,3 +64,14 @@
echo "| $barcode | $count | $file.fastq | $file.fasta | ${file}_trimmed.fasta | Report |
" >> $output
done < output.txt
echo "" >> $output
+
+:'
+mids = "mid\tforward\treverse"
+fal = "file with sequenses on single line (no multiline)"
+for mid in mids:
+ forwardmids = len([x for x in fal if re.match("^" + mid[1], x)])
+ reversemids = len([x for x in fal if re.match(mid[2] + "$", x)])
+ both = len([x for x in fal if re.match("^" + mid[1] + ".*" + mid[2] + "$", x)])
+ if (forwardmids + reversemids + both) > 0:
+ print "%s: %d - %d - %d" % (mid[0], forwardmids, reversemids, both)
+'