Repository 'msp_sr_readmap_and_size_histograms'
hg clone https://toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms

Changeset 4:4efe210c91f3 (2016-02-03)
Previous changeset 3:9b62e6b0d219 (2016-02-03) Next changeset 5:bcc0c7093e7a (2016-02-04)
Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 9237338d798251fb2667280d597746e852f3ffcc-dirty
modified:
readmap.py
readmap.xml
b
diff -r 9b62e6b0d219 -r 4efe210c91f3 readmap.py
--- 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))
b
diff -r 9b62e6b0d219 -r 4efe210c91f3 readmap.xml
--- a/readmap.xml Wed Feb 03 11:07:25 2016 -0500
+++ b/readmap.xml Wed Feb 03 11:35:00 2016 -0500
b
@@ -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>