def main():
parser = argparse.ArgumentParser()
parser.add_argument('--config', dest='config',
help="parallyze config file", default='parallyze.conf')
parser.add_argument('--procedure', dest='procedure',
default='mutationTally', choices=['simulationRM',
'simulationEJB', 'dNdS', 'mutationTally', 'infoRegion',
'analyticalEJB'])
parser.add_argument('--nonsynonymous', action='store_true')
parser.add_argument('--synonymous', action='store_true')
parser.add_argument('--noncoding', action='store_true')
parser.add_argument('--pseudogene', action='store_true')
parser.add_argument('--intergenic', action='store_true')
parser.add_argument('--replicates', type=int)
parser.add_argument('--genes_to_display', type=int)
parser.add_argument('--fname')
parser.add_argument('--gene_product', action='store_true')
args = parser.parse_args()
# print args.fname
conf = SimpleConfig(config_keys, args.config)
for fn in conf.GENOMEDIFF_FILES:
assert os.path.isfile(fn)
'''
The user can override most of the options in config file
with (optional) flags at runtime.
'''
if args.nonsynonymous:
conf.NONSYNONYMOUS = True
if args.synonymous:
conf.SYNONYMOUS = True
if args.noncoding:
conf.NONCODING = True
if args.pseudogene:
conf.PSEUDOGENE = True
if args.intergenic:
conf.INTERGENIC = True
if args.gene_product:
conf.GENE_PRODUCT = True
if args.replicates and args.replicates > 0:
conf.REPLICATES = args.replicates
if args.genes_to_display and args.genes_to_display >= 0:
conf.GENES_TO_DISPLAY = args.genes_to_display
'''
Store the set of mutation types to use, for later reference
in the program.
'''
conf.snp_types = set()
if conf.NONSYNONYMOUS:
conf.snp_types.add('nonsynonymous')
if conf.SYNONYMOUS:
conf.snp_types.add('synonymous')
if conf.NONCODING:
conf.snp_types.add('noncoding')
if conf.PSEUDOGENE:
conf.snp_types.add('pseudogene')
if conf.INTERGENIC:
conf.snp_types.add('intergenic')
if args.procedure == 'simulationRM':
simulationRM(conf)
elif args.procedure == 'simulationEJB':
simulationEJB(conf)
elif args.procedure == 3:
proc3(conf)
elif args.procedure == 'dNdS':
dNdS(conf)
elif args.procedure == 'analyticalEJB':
analyticalEJB(conf)
elif args.procedure == 'mutationTally':
mutationTally(conf, args)
elif args.procedure == 'infoRegion':
infoRegion(conf)
