Mercurial > repos > artbio > bamparse

changeset 1:ae9ea0488850 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 9aec415b3fcc66bf3ed2aad43fd70b57bfe2fb18
author artbio
date Sun, 15 Oct 2017 19:14:29 -0400
parents 2a1a2bc6ae8b
children 8ea06787c08a
files bamparse.py bamparse.xml
diffstat 2 files changed, 3 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/bamparse.py	Fri Oct 13 02:59:36 2017 -0400
+++ b/bamparse.py	Sun Oct 15 19:14:29 2017 -0400
@@ -62,13 +62,13 @@
     countlists = []
     for dic in diclist:
         counts = sorted(dic.items())
-        counts = [j for (i,j) in counts]
+        counts = [j for (i, j) in counts]
         countlists.append(counts)
     if number == "unique":
         out = open("outputdir/table.tabular", "w")
         out.write("gene\t%s\n" % "\t".join(labels))
         for countline in zip(sorted(diclist[0]), *countlists):
-            line = [ str(i) for i in countline]
+            line = [str(i) for i in countline]
             out.write("%s\n" % "\t".join(line))
         out.close()
     else:
@@ -80,7 +80,6 @@
             out.close()
 
 
-
 def main(alignments, labels, polarity, output, number):
     diclist = []
     for file in alignments:
--- a/bamparse.xml	Fri Oct 13 02:59:36 2017 -0400
+++ b/bamparse.xml	Sun Oct 15 19:14:29 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bamparse" name="Count alignments" version="2.0.0">
+<tool id="bamparse" name="Count alignments" version="2.0.1">
     <description>in a BAM file</description>
     <requirements>
 	        <requirement type="package" version="1.1.2">bowtie</requirement>