def mergebam(args):
"""
%prog mergebam dir1 dir2 homo_outdir
or
%prog mergebam dir1 dir2/20.bam het_outdir
Merge sets of BAMs to make diploid. Two modes:
- Homozygous mode: pair-up the bams in the two folders and merge
- Heterozygous mode: pair the bams in first folder with a particular bam
"""
p = OptionParser(mergebam.__doc__)
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
idir1, idir2, outdir = args
dir1 = [idir1] if idir1.endswith(".bam") else iglob(idir1, "*.bam")
dir2 = [idir2] if idir2.endswith(".bam") else iglob(idir2, "*.bam")
nbams1 = len(dir1)
nbams2 = len(dir2)
# Make sure more or the same number of bams in first pile
if nbams1 < nbams2:
dir1, dir2 = dir2, dir1
if nbams1 == nbams2:
logging.debug("Homozygous mode")
elif nbams1 > nbams2:
assert nbams2 == 1, "Second pile must contain a single bam"
dir2 = [idir2] * nbams1
assert len(dir1) == len(dir2), "Two piles must contain same number of bams"
cmd = "samtools merge {} {} {} && samtools index {}"
cmds = []
mkdir(outdir)
for a, b in zip(dir1, dir2):
ia = op.basename(a).split(".")[0]
ib = op.basename(b).split(".")[0]
outfile = op.join(outdir, "{}_{}.bam".format(ia, ib))
cmds.append(cmd.format(outfile, a, b, outfile))
p = Parallel(cmds, cpus=opts.cpus)
p.run()
def batchlobstr(args):
"""
%prog batchlobstr bamlist
Run lobSTR on a list of BAMs. The corresponding batch command for TREDPARSE:
$ tred.py --toy bamlist --haploid CHR4 --workdir tredparse_results
"""
p = OptionParser(batchlobstr.__doc__)
p.add_option("--haploid",
default="chrY,chrM",
help="Use haploid model for these chromosomes")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bamlist, = args
cmd = "python -m jcvi.variation.str lobstr TOY"
cmd += " --input_bam_path {}"
cmd += " --haploid {}".format(opts.haploid)
cmds = [cmd.format(x.strip()) for x in open(bamlist).readlines()]
p = Parallel(cmds, cpus=opts.cpus)
p.run()