Mercurial > repos > davidvanzessen > sff_extract_demultiplex

changeset 8:cd56ce86c4bf draft

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Uploaded
author davidvanzessen
date Tue, 04 Nov 2014 09:03:22 -0500
parents 18ede27dc6b0
children 7973dd7a39ab
files wrapper.sh
diffstat 1 files changed, 0 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/wrapper.sh	Tue Nov 04 08:59:34 2014 -0500
+++ b/wrapper.sh	Tue Nov 04 09:03:22 2014 -0500
@@ -64,14 +64,3 @@
 		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)
-'