Mercurial > repos > lparsons > cutadapt
diff cutadapt_galaxy_wrapper.py @ 3:7ed26fc9fa8a
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 |
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--- a/cutadapt_galaxy_wrapper.py Mon May 16 16:34:09 2011 -0400 +++ b/cutadapt_galaxy_wrapper.py Wed May 25 18:54:09 2011 -0400 @@ -14,6 +14,7 @@ [--discard discard trimmed reads] [-m minimum read length] [-M maximum read length] + [-q quality cutoff] [-h,--help] [-v,--verbose] [--version] DESCRIPTION @@ -64,6 +65,9 @@ params.append("-m %s" % options.minimum_length) if options.maximum_length != None: params.append("-M %s" % options.maximum_length) + if options.cutoff != None: + params.append("-q %s" % options.cutoff) + # cutadapt relies on the extension to determine file format: .fasta or .fastq input_name = '.'.join((options.input,options.format)) @@ -107,6 +111,8 @@ parser.add_option ('--discard', '--discard-trimmed', dest='discard_trimmed', action='store_true', default=False, help='Discard reads that contain the adapter') parser.add_option ('-m', '--minimum-length', dest='minimum_length', help='Discard reads that are shorter than LENGTH') parser.add_option ('-M', '--maximum-length', dest='maximum_length', help='Discard reads that are longer than LENGTH') + parser.add_option ('-q', '--quality-cutoff', dest='cutoff', help='Trim + low quality ends from reads before adapter removal') parser.add_option ('-o', '--output', dest='output_file', help='The modified sequences are written to the file') (options, args) = parser.parse_args() if options.input == None: