def main(): e = Environment(version=VERSION, doc=__doc__) parser = e.argument_parser parser.add_argument('--strip-after-barcode', default=1, type=int, help="""strip n bases after the barcode is removed (5' end) (by default this 1 now, and is ignored if GERALD handled the barcoding)""") parser.add_argument('--strip-before-barcode', default=0, type=int, help="""strip n bases before the barcode is removed (5' end) (by default this 0 now, and is ignored if GERALD handled the barcoding)""") parser.add_argument('--min-length', type=int, default=4, help='require sequences to be at least n total bases of non-N sequence (default: ignore)') parser.add_argument('--max-length', type=int, default=-1, help='truncate final sequences to n bases (default: ignore)') parser.add_argument('--no-gzip', default=False, action='store_true', help = 'Do not gzip output files') bgroup = parser.add_argument_group('barcodes', 'Specify sequence barcodes in the sample(s)') bgroup.add_argument('-b', '--barcodes', action='append', type=valid_seq, help="Specify a barcode sequence. May be invoked multiple times") bgroup.add_argument('--kry-barcodes', dest='barcodes', action='store_const', help='Alias for -bTCAT -bGACG -bAGTC -bCTGA', const=['TCAT', 'GACG', 'AGTC', 'CTGA']) parser.add_argument('--linker', default='', type=valid_seq, help="Specify a 3' adaptor/linker sequence that we should clip off of each read") parser.add_argument('--collapse', default=False, action='store_true', help='Collapse identical reads') parser.set_defaults(**{'target': 'processed'}) e.set_filename_parser(BarcodeFilenameParser) e.set_config_reader(read_config) e.set_config_writer(write_config) e.do_action(splitter) e.do_action(collapser)
def main(): e = Environment(doc=__doc__, version=VERSION) parser = e.argument_parser parser.add_argument('-g', '--genome-size', dest='user_gsize', default=None, help='Optional user-specified genome size (DEFAULT: ' 'script will try to auto-detect the genome)') parser.add_argument('--path-to-macs', default=path_to_executable("macs2"), help="optional path to macs2 executable") parser.add_argument('--no-subpeaks', dest='subpeaks', action='store_false', default=True, help='do not call subpeaks with --call-summits') parser.add_argument('-q', '--q-value', dest='qvalue', default='0.01', help='FDR/q-value cutoff (default is 0.01)') parser.add_argument('--passthru-args', nargs='*', help='A list of arguments to be passed through to ' 'MACS2. Substitute + for - (e.g., ' '--passthru-args +m 4 50') parser.set_defaults(**{'target': 'peaks'}) e.set_filename_parser(BAMFilenameParser) e.set_config_reader(read_setup_file) e.set_config_writer(write_setup_file) e.do_action(run_macs)