Mercurial > repos > mvdbeek > dapars

diff dapars.py @ 3:aca85eb3eb5b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/mvdbeek/dapars commit a02ced0b40d8946aa78a58321bd8f9771148391e-dirty
author mvdbeek
date Wed, 28 Oct 2015 06:05:21 -0400
parents 47b0044bc7f8
children 73b932244237
line wrap: on
line diff
--- a/dapars.py	Wed Oct 28 05:56:52 2015 -0400
+++ b/dapars.py	Wed Oct 28 06:05:21 2015 -0400
@@ -82,7 +82,7 @@
         cmds = []
         for alignment_file in self.all_alignments:
             cmd = "sort -k1,1 -k2,2n tmp_bedfile.bed | "
-            cmd = cmd + "~/bin/bedtools coverage -d -s -abam {alignment_file} -b stdin |" \
+            cmd = cmd + "bedtools coverage -d -s -abam {alignment_file} -b stdin |" \
                         " cut -f 4,7,8 > coverage_file_{alignment_name}".format(
                 alignment_file = alignment_file, alignment_name= self.alignment_names[alignment_file] )
             cmds.append(cmd)