def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-t",
"--test",
dest="test",
type="string",
help="supply help")
parser.add_option(
"--task",
dest="task",
type="choice",
choices=["mafs", "penetrance", "detect_duplicates", "allele_diff"],
help="task to perform")
parser.add_option("--ped-file",
dest="ped_file",
type="string",
help="plink format .ped file")
parser.add_option("--map-file",
dest="map_file",
type="string",
help="plink format .map file")
parser.add_option("--freq-file",
dest="mafs",
type="string",
help="text file containing populations minor "
"allele frequencies of variants. One row per "
"variant with ID MAF")
parser.add_option("--groups-file",
dest="group_file",
type="string",
help="file containing group labels for individuals "
"in the provided ped file")
parser.add_option("--ref-label",
dest="ref_label",
type="string",
help="group label to be used as the reference case")
parser.add_option("--test-label",
dest="test_label",
type="string",
help="group label to be used as the test case")
parser.add_option("--subset",
dest="subset",
type="choice",
choices=["cases", "gender"],
help="subset the "
"data by either case/control or gender")
parser.add_option("--take-last",
dest="take",
action="store_true",
help="if use duplicates will take the last variant, "
"default behaviour is to take the first")
parser.add_option("--outfile-pattern",
dest="out_pattern",
type="string",
help="outfile pattern to use for finding duplicates "
"and triallelic variants")
parser.add_option("--snp-set",
dest="snp_subset",
type="string",
help="list of SNPs to include")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
parser.set_defaults(mafs=None, subset=None, take_last=False)
if options.task == "mafs":
mafs = gwas.countByVariantAllele(options.ped_file, options.map_file)
mafs.to_csv(options.stdout, index_col=None, sep="\t")
elif options.task == "penetrance":
summary, pens = gwas.calcPenetrance(options.ped_file,
options.map_file,
subset=options.subset,
mafs=options.mafs,
snpset=options.snp_subset)
pens.to_csv(options.stdout, sep="\t", index_label="SNP")
summary.to_csv("/".join([os.getcwd(), "penetrance_summary.txt"]),
sep="\t",
index_label="SNP")
elif options.task == "allele_diff":
allele_diffs = gwas.calcMaxAlleleFreqDiff(
ped_file=options.ped_file,
map_file=options.map_file,
group_file=options.group_file,
test=options.test_label,
ref=options.ref_label)
allele_diffs.to_csv(options.stdout, sep="\t")
elif options.task == "detect_duplicates":
# find variants with duplicated position and shared reference
# allele indicative of triallelic variants - also same ID
# ouput to a filter list
infile = argv[-1]
dups, tris, oves = gwas.findDuplicateVariants(bim_file=infile,
take_last=options.take)
if os.path.isabs(options.out_pattern):
with open(options.out_pattern + ".triallelic", "w") as otfile:
for tvar in tris:
otfile.write("%s\n" % tvar)
with open(options.out_pattern + ".duplicates", "w") as odfile:
for dvar in dups:
odfile.write("%s\n" % dvar)
with open(options.out_pattern + ".overlapping", "w") as ovfile:
for ovar in oves:
ovfile.write("%s\n" % ovar)
else:
outpattern = os.path.abspath(options.out_pattern)
with open(outpattern + ".triallelic", "w") as otfile:
for tvar in tris:
otfile.write("%s\n" % tvar)
with open(outpattern + ".duplicates", "w") as odfile:
for dvar in dups:
odfile.write("%s\n" % dvar)
with open(outpattern + ".overlapping", "w") as ovfile:
for ovar in oves:
ovfile.write("%s\n" % ovar)
# write footer and output benchmark information.
E.Stop()
