Mercurial > repos > davidvanzessen > sff_extract_demultiplex
changeset 7:18ede27dc6b0 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 04 Nov 2014 08:59:34 -0500 |
| parents | 6b348d07da49 |
| children | cd56ce86c4bf |
| files | demultiplex.xml wrapper.sh |
| diffstat | 1 files changed, 20 insertions(+), 1 deletions(-) [+] |
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--- 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 "<html><head><title>$name demultiplex</title></head><body><table border='1'><thead><tr><th>ID</th><th>Count</th><th>FASTQ</th><th>FASTA</th><th>Trimmed FASTA</th><th>FASTQC</th></tr></thead><tbody>" >> $output while IFS=, read barcode count location @@ -56,3 +64,14 @@ echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td><td><a href='${file}_trimmed.fasta'>${file}_trimmed.fasta</a></td><td><a href='${name}_${barcode}_fastqc.html'>Report</a></td></tr>" >> $output done < output.txt echo "</tbody></body></html>" >> $output + +:' +mids = "mid\tforward\treverse" +fal = "file with sequenses on single line (no multiline)" +for mid in mids: + forwardmids = len([x for x in fal if re.match("^" + mid[1], x)]) + reversemids = len([x for x in fal if re.match(mid[2] + "$", 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) +'