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comparison dapars.py @ 16:f8bb40b2ff31 draft

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planemo upload for repository https://github.com/mvdbeek/dapars commit b1b007c561ea6c9db145c88b6b128d66ecd05e24-dirty
author mvdbeek
date Fri, 30 Oct 2015 07:31:36 -0400
parents 8af6d4ad2f0a
children 917a2f7ab841
comparison
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15:8af6d4ad2f0a 16:f8bb40b2ff31
94 Use bedtools coverage to generate pileup data for all alignment files for the regions specified in utr_dict. 94 Use bedtools coverage to generate pileup data for all alignment files for the regions specified in utr_dict.
95 """ 95 """
96 cmds = [] 96 cmds = []
97 for alignment_file in self.all_alignments: 97 for alignment_file in self.all_alignments:
98 cmd = "sort -k1,1 -k2,2n tmp_bedfile.bed | " 98 cmd = "sort -k1,1 -k2,2n tmp_bedfile.bed | "
99 cmd = cmd + "bedtools coverage -d -s -abam {alignment_file} -b tmp_bedfile.bed |" \ 99 cmd = cmd + "bedtools coverage -d -s -abam {alignment_file} -b stdin |" \
100 " cut -f 4,7,8 > coverage_file_{alignment_name}".format( 100 " cut -f 4,7,8 > coverage_file_{alignment_name}".format(
101 alignment_file = alignment_file, alignment_name= self.alignment_names[alignment_file] ) 101 alignment_file = alignment_file, alignment_name= self.alignment_names[alignment_file] )
102 cmds.append(cmd) 102 cmds.append(cmd)
103 subprocesses = [subprocess.Popen([cmd], shell=True) for cmd in cmds] 103 subprocesses = [subprocess.Popen([cmd], shell=True) for cmd in cmds]
104 [p.wait() for p in subprocesses] 104 [p.wait() for p in subprocesses]