Mercurial > repos > artbio > bamparse
changeset 1:ae9ea0488850 draft
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(-) [+] |
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--- 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>