Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.py @ 2:316124e85b8d draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author mvdbeek
date Mon, 25 May 2015 12:44:36 -0400
parents b50d7228b678
children d123b6e6a633
comparison
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1:b50d7228b678 2:316124e85b8d
50 def bowtieCommandLiner(alignment_method="RNA", v_mis="1", out_type="tabular", 50 def bowtieCommandLiner(alignment_method="RNA", v_mis="1", out_type="tabular",
51 aligned="None", unaligned="None", input_format="fasta", input="path", 51 aligned="None", unaligned="None", input_format="fasta", input="path",
52 index="path", output="path", pslots="4"): 52 index="path", output="path", pslots="4"):
53 if input_format == "fasta": 53 if input_format == "fasta":
54 input_format = "-f" 54 input_format = "-f"
55 elif input_format == "fastq": 55 elif (input_format == "fastq") or (input_format == "fastqsanger"):
56 input_format = "-q" 56 input_format = "-q"
57 else: 57 else:
58 raise Exception('input format must be one of fasta or fastq') 58 raise Exception('input format must be one of fasta or fastq')
59 if alignment_method == "RNA": 59 if alignment_method == "RNA":
60 x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % ( 60 x = "-v %s -M 1 --best --strata -p %s --norc --suppress 6,7,8" % (