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)
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')
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:
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)