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comparison cutadapt_galaxy_wrapper.py @ 3:7ed26fc9fa8a

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Updated for cutadapt 0.9.4, no longer need python wrapper
author Lance Parsons <lparsons@princeton.edu>
date Wed, 25 May 2011 18:54:09 -0400
parents 8b064ea16722
children
comparison
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2:f6b94b76d16b 3:7ed26fc9fa8a
12 [-n count] 12 [-n count]
13 [-O overlap_length] 13 [-O overlap_length]
14 [--discard discard trimmed reads] 14 [--discard discard trimmed reads]
15 [-m minimum read length] 15 [-m minimum read length]
16 [-M maximum read length] 16 [-M maximum read length]
17 [-q quality cutoff]
17 [-h,--help] [-v,--verbose] [--version] 18 [-h,--help] [-v,--verbose] [--version]
18 19
19 DESCRIPTION 20 DESCRIPTION
20 21
21 Wrapper for cutadapt running as a galaxy tool 22 Wrapper for cutadapt running as a galaxy tool
62 params.append("--discard") 63 params.append("--discard")
63 if options.minimum_length != None: 64 if options.minimum_length != None:
64 params.append("-m %s" % options.minimum_length) 65 params.append("-m %s" % options.minimum_length)
65 if options.maximum_length != None: 66 if options.maximum_length != None:
66 params.append("-M %s" % options.maximum_length) 67 params.append("-M %s" % options.maximum_length)
68 if options.cutoff != None:
69 params.append("-q %s" % options.cutoff)
70
67 71
68 # cutadapt relies on the extension to determine file format: .fasta or .fastq 72 # cutadapt relies on the extension to determine file format: .fasta or .fastq
69 input_name = '.'.join((options.input,options.format)) 73 input_name = '.'.join((options.input,options.format))
70 # make temp directory 74 # make temp directory
71 tmp_dir = tempfile.mkdtemp() 75 tmp_dir = tempfile.mkdtemp()
105 parser.add_option ('-n', '--times', dest='count', help='Try to remove adapters COUNT times') 109 parser.add_option ('-n', '--times', dest='count', help='Try to remove adapters COUNT times')
106 parser.add_option ('-O', '--overlap', dest='overlap_length', help='Minimum overlap length') 110 parser.add_option ('-O', '--overlap', dest='overlap_length', help='Minimum overlap length')
107 parser.add_option ('--discard', '--discard-trimmed', dest='discard_trimmed', action='store_true', default=False, help='Discard reads that contain the adapter') 111 parser.add_option ('--discard', '--discard-trimmed', dest='discard_trimmed', action='store_true', default=False, help='Discard reads that contain the adapter')
108 parser.add_option ('-m', '--minimum-length', dest='minimum_length', help='Discard reads that are shorter than LENGTH') 112 parser.add_option ('-m', '--minimum-length', dest='minimum_length', help='Discard reads that are shorter than LENGTH')
109 parser.add_option ('-M', '--maximum-length', dest='maximum_length', help='Discard reads that are longer than LENGTH') 113 parser.add_option ('-M', '--maximum-length', dest='maximum_length', help='Discard reads that are longer than LENGTH')
114 parser.add_option ('-q', '--quality-cutoff', dest='cutoff', help='Trim
115 low quality ends from reads before adapter removal')
110 parser.add_option ('-o', '--output', dest='output_file', help='The modified sequences are written to the file') 116 parser.add_option ('-o', '--output', dest='output_file', help='The modified sequences are written to the file')
111 (options, args) = parser.parse_args() 117 (options, args) = parser.parse_args()
112 if options.input == None: 118 if options.input == None:
113 stop_err("Misssing option --input") 119 stop_err("Misssing option --input")
114 if options.output_file == None: 120 if options.output_file == None: