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comparison genetrack.py @ 14:6ad44f393892 draft

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author greg
date Wed, 16 Dec 2015 12:43:22 -0500
parents 1a9f1a4fa36c
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13:7deceb5e2062 14:6ad44f393892
18 parser.add_option('-i', '--input', dest='inputs', type='string', action='append', nargs=2, help='Input datasets') 18 parser.add_option('-i', '--input', dest='inputs', type='string', action='append', nargs=2, help='Input datasets')
19 parser.add_option('-s', '--sigma', dest='sigma', type='int', default=5, help='Sigma.') 19 parser.add_option('-s', '--sigma', dest='sigma', type='int', default=5, help='Sigma.')
20 parser.add_option('-e', '--exclusion', dest='exclusion', type='int', default=20, help='Exclusion zone.') 20 parser.add_option('-e', '--exclusion', dest='exclusion', type='int', default=20, help='Exclusion zone.')
21 parser.add_option('-u', '--up_width', dest='up_width', type='int', default=10, help='Upstream width of called peaks.') 21 parser.add_option('-u', '--up_width', dest='up_width', type='int', default=10, help='Upstream width of called peaks.')
22 parser.add_option('-d', '--down_width', dest='down_width', type='int', default=10, help='Downstream width of called peaks.') 22 parser.add_option('-d', '--down_width', dest='down_width', type='int', default=10, help='Downstream width of called peaks.')
23 parser.add_option('-f', '--filter', dest='filter', type='int', default=3, help='Absolute read filter.') 23 parser.add_option('-f', '--filter', dest='filter', type='int', default=1, help='Absolute read filter.')
24 options, args = parser.parse_args() 24 options, args = parser.parse_args()
25 25
26 os.mkdir('output') 26 os.mkdir('output')
27 for (dataset_path, hid) in options.inputs: 27 for (dataset_path, hid) in options.inputs:
28 if options.input_format == 'gff': 28 if options.input_format == 'gff':