Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
changeset 4:4efe210c91f3 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 9237338d798251fb2667280d597746e852f3ffcc-dirty
| author | mvdbeek |
|---|---|
| date | Wed, 03 Feb 2016 11:35:00 -0500 |
| parents | 9b62e6b0d219 |
| children | bcc0c7093e7a |
| files | readmap.py readmap.xml |
| diffstat | 2 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/readmap.py Wed Feb 03 11:07:25 2016 -0500 +++ b/readmap.py Wed Feb 03 11:35:00 2016 -0500 @@ -77,7 +77,7 @@ return gene, coordinate, count, orientation def lookup_gene_length(gene, readDict): - return readDict[readDict.keys()[0]].instanceDict["size"] + return readDict[readDict.keys()[0]].instanceDict.values()[0].size def handle_start_stop_coordinates(plottable, readDict): """ @@ -91,9 +91,11 @@ new_line = "\t".join([gene, "0", "0", "F"]) plottable = [new_line] + plottable gene_length = str(lookup_gene_length(gene, readDict)) + gene, coordinate, count, orientation = listify_plottable_item(last_line) if not coordinate == gene_length: last_line = "\t".join([gene, gene_length, "0", "F"]) plottable = plottable + [last_line] + return plottable def write_readplot_dataframe(readDict, readmap_file): listoflines = [] @@ -106,7 +108,7 @@ dict=readDict[sample].instanceDict for gene in dict.keys(): plottable = dict[gene].readplot() - handle_start_stop_coordinates(plottable, readDict) + plottable = handle_start_stop_coordinates(plottable, readDict) for line in plottable: #print >>readmap, "%s\t%s" % (line, sample) listoflines.append ("%s\t%s" % (line, sample))
--- a/readmap.xml Wed Feb 03 11:07:25 2016 -0500 +++ b/readmap.xml Wed Feb 03 11:35:00 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.2"> +<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.3"> <description>from sRbowtie aligment</description> <requirements> <requirement type="package" version="0.12.7">bowtie</requirement>