Mercurial > repos > davidvanzessen > baseline_fasta_generator

changeset 4:aa4b95abef11 draft

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Uploaded
author davidvanzessen
date Wed, 23 Jul 2014 10:13:05 -0400
parents be17e1e7dc2b
children 048f8cdbb6d2
files baseline_generator.xml script_imgt.py
diffstat 2 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/baseline_generator.xml	Wed Jul 23 07:51:10 2014 -0400
+++ b/baseline_generator.xml	Wed Jul 23 10:13:05 2014 -0400
@@ -4,7 +4,7 @@
 		wrapper.sh $in_file $reference $out_file
 	</command>
 	<inputs>
-		<param name="in_file" type="data" label="Input excel file" />
+		<param name="in_file" type="data" label="Input excel or IMGT zip file" />
 		<param name="reference" type="data" format="fasta" label="Reference fasta file" />
 	</inputs>
 	<outputs>
--- a/script_imgt.py	Wed Jul 23 07:51:10 2014 -0400
+++ b/script_imgt.py	Wed Jul 23 10:13:05 2014 -0400
@@ -54,7 +54,7 @@
 		for line in i.readlines()[1:]:
 			linesplt = line.split("\t")
 			ref = filterGene(linesplt[1], vPattern)
-			if not ref:
+			if not ref or not linesplt[2].rstrip():
 				continue
 			if ref in outputdic:
 				outputdic[ref] += [(linesplt[0].replace(">", ""), linesplt[2].replace(">", "").rstrip())]