subsmc

#!/usr/bin/env python

import optparse

import argweaver


o = optparse.OptionParser()
o.add_option("-s", "--smc", metavar="SMC_FILE", default="-")
o.add_option("-o", "--output", metavar="OUTPUT_FILE", default="-")
o.add_option("-r", "--region", metavar="START-END")
#o.add_option("-n", "--nseqs", metavar="NUMBER_OF_SEQS", type="int",
#             help="use a random subsst of sequences")
#o.add_option("--both-haps", action="store_true",
#             help="use both haplotypes for each individual")
#o.add_option("-i", "--ind", metavar="INDIVIDUALS")

conf, args = o.parse_args()

#=============================================================================


# read data
if conf.region:
    region = map(int, conf.region.split("-"))
else:
    region = None
smc = argweaver.iter_smc_file(conf.smc, region=region)

# write
argweaver.write_smc(conf.output, smc)