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=["merge_exclusions", "flag_hets",
"find_inbreds", "flag_relations",
"discordant_gender"],
help="task to execute on phenotype file(s)")
parser.add_option("--gender-check-file", dest="gender_check",
type="string", help="output from gender checking "
"by Plink, suffix should be .sexcheck")
parser.add_option("--relationship-file", dest="relations",
type="string", help="output file from IBS "
"calculation. Should contain all pairwise "
"relationships.")
parser.add_option("--inbreeding-coef-file", dest="inbreed_file",
type="string", help="file containing either Plink "
"or GCTA estimates of F, inbreeding coefficient")
parser.add_option("--inbreeding-coefficient", dest="inbred_coeff", type="choice",
choices=["Fhat1", "Fhat2", "Fhat3", "F",
"ibc"], help="inbreeding coefficient "
"to use to identify highly inbred individuals")
parser.add_option("--inbred-cutoff", dest="inbred_cutoff", type="float",
help="threshold above which individuals are classed "
"as inbred.")
parser.add_option("--ibs-cutoff", dest="ibs_cutoff", type="float",
help="IBS threshold to flag individuals as being "
"closely related")
parser.add_option("--trimmed-relationships", dest="rel_cutoff",
type="string", help="output file from Plink "
"--rel-cutoff with trimmed data set of unrelated "
"individuals.")
parser.add_option("--heterozygotes-file", dest="hets_file", type="string",
help="file from heterozygote analysis containing observed "
"homozygosity and F coefficients")
parser.add_option("--auxillary-file", dest="aux_file", type="string",
help="a file of IIDs and FIDs for individuals that are "
"to be removed from analysis, unrelated to QC")
parser.add_option("--plotting-path", dest="plot_path", type="string",
help="PATH to save any plots to")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
if options.task == "flag_hets":
# calculate heterozygosity rates, find and flag
# individuals > 3 s.d. away from mean value
# rate = (nonissing - homs) / nonmissing
# i.e. non-homozygote rate
flags = gwas.flagExcessHets(options.hets_file,
plot=True,
plot_path=options.plot_path)
flags.to_csv(options.stdout, index=None, sep="\t")
elif options.task == "merge_exclusions":
exclusions = gwas.mergeQcExclusions(hets_file=options.hets_file,
inbred_file=options.inbreed_file,
related_file=options.relations,
gender_file=options.gender_check,
mask_file=options.aux_file)
exclusions.to_csv(options.stdout, index=None, sep="\t")
elif options.task == "find_inbreds":
inbreds = gwas.flagInbred(inbred_file=options.inbreed_file,
inbreeding_coefficient=options.inbred_coeff,
ibc_threshold=options.inbred_cutoff,
plot=True,
plot_path=options.plot_path)
inbreds.to_csv(options.stdout, sep="\t", index=None)
elif options.task == "flag_relations":
# the input file is likely to be huge! Ergo, read the file in chunks
# calculate any related individuals and store them, store
# an array of IBD values for plotting, drop the rest
relate = gwas.flagRelated(ibd_file=options.relations,
chunk_size=500000,
threshold=options.ibs_cutoff,
plot=True,
plotting_path=options.plot_path)
elif options.task == "discordant_gender":
sex_discord = gwas.flagGender(gender_file=options.gender_check,
plot=True,
plot_path=options.plot_path)
sex_discord.to_csv(options.stdout, index=None, sep="\t")
else:
pass
# write footer and output benchmark information.
E.Stop()
