Esempio n. 1
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        execution.add_task(tools.filter_bed_by_contig,
                           tags=dict(in_bam=bam_path,
                                     in_bed=target_bed_path,
                                     contig=contig),
                           out_dir='work/{contig}') for contig in contigs
    ]

    freebayes_tasks = one2one(tools.freebayes, bed_tasks,
                              dict(max_complex_gap=max_complex_gap))

    merge_vcf_tasks = many2one(tools.vcf_concat_parts, freebayes_tasks)

    execution.run()


if __name__ == '__main__':
    p = argparse.ArgumentParser()
    p.add_argument('bam_path')
    p.add_argument('target_bed_path')
    p.add_argument('--max_complex_gap', type=int, default=2)
    add_execution_args(p)
    start_kwargs, variant_call_args = pop_execution_args(vars(p.parse_args()))

    cosmos = Cosmos('sqlite:///%s/sqlite.db' %
                    os.path.dirname(os.path.abspath(__file__)))
    cosmos.initdb()
    execution = cosmos.start(output_dir='../analysis_output/variant_calling',
                             **start_kwargs)

    variant_call(execution, **variant_call_args)
Esempio n. 2
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    sp.set_defaults(func=cosmos.shell)

    sp = sps.add_parser('runweb', help=cosmos.runweb.__doc__)
    sp.add_argument('-p',
                    '--port',
                    type=int,
                    help='port to bind the server to')
    sp.add_argument('-H',
                    '--host',
                    default='localhost',
                    help='host to bind the server to')
    sp.set_defaults(func=cosmos.runweb)

    sp = sps.add_parser('ex1', help='Example1')
    sp.set_defaults(func=ex1.run_ex1)
    add_execution_args(sp)

    sp = sps.add_parser('ex2', help='Example2: A failed task')
    sp.set_defaults(func=ex_fail.run_ex2)
    add_execution_args(sp)

    sp = sps.add_parser('ex3',
                        help='Example3: Twitter (note you must edit the file)')
    sp.set_defaults(func=ex_email.run_ex3)
    add_execution_args(sp)

    args = parser.parse_args()
    kwargs = dict(args._get_kwargs())
    func = kwargs.pop('func')
    growl = kwargs.pop('growl')
    debug = kwargs.pop('debug')
Esempio n. 3
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    sp.set_defaults(func=cosmos.resetdb)

    sp = sps.add_parser('initdb', help=cosmos.initdb.__doc__)
    sp.set_defaults(func=cosmos.initdb)

    sp = sps.add_parser('shell', help=cosmos.shell.__doc__)
    sp.set_defaults(func=cosmos.shell)

    sp = sps.add_parser('runweb', help=cosmos.runweb.__doc__)
    sp.add_argument('-p', '--port', type=int, help='port to bind the server to')
    sp.add_argument('-H', '--host', default='localhost', help='host to bind the server to')
    sp.set_defaults(func=cosmos.runweb)

    sp = sps.add_parser('ex1', help='Example1')
    sp.set_defaults(func=ex1.run_ex1)
    add_execution_args(sp)

    sp = sps.add_parser('ex2', help='Example2: A failed task')
    sp.set_defaults(func=ex_fail.run_ex2)
    add_execution_args(sp)

    sp = sps.add_parser('ex3', help='Example3: Twitter (note you must edit the file)')
    sp.set_defaults(func=ex_email.run_ex3)
    add_execution_args(sp)

    args = parser.parse_args()
    kwargs = dict(args._get_kwargs())
    func = kwargs.pop('func')
    growl = kwargs.pop('growl')
    debug = kwargs.pop('debug')
    if growl:
Esempio n. 4
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def variant_call(execution, bam_path, target_bed_path, max_complex_gap):
    """
    Bioinformatics variant calling workflow
    """
    contigs = sp.check_output("cat %s |cut -f1|uniq" % target_bed_path, shell=True).strip().split("\n")

    bed_tasks = [execution.add_task(tools.filter_bed_by_contig, tags=dict(in_bam=bam_path, in_bed=target_bed_path, contig=contig), out_dir='work/{contig}')
                 for contig in contigs ]

    freebayes_tasks = one2one(tools.freebayes, bed_tasks, dict(max_complex_gap=max_complex_gap))

    merge_vcf_tasks = many2one(tools.vcf_concat_parts, freebayes_tasks)

    execution.run()


if __name__ == '__main__':
    p = argparse.ArgumentParser()
    p.add_argument('bam_path')
    p.add_argument('target_bed_path')
    p.add_argument('--max_complex_gap', type=int, default=2)
    add_execution_args(p)
    start_kwargs, variant_call_args = pop_execution_args(vars(p.parse_args()))

    cosmos = Cosmos('sqlite:///%s/sqlite.db' % os.path.dirname(os.path.abspath(__file__)))
    cosmos.initdb()
    execution = cosmos.start(output_dir='../analysis_output/variant_calling', **start_kwargs)

    variant_call(execution, **variant_call_args)