def main(args):
p = OptionParser(__doc__)
p.set_beds()
p.add_option("--quota", default="1:1",
help="`quota mapping` procedure -- screen blocks to constrain mapping"\
" (useful for orthology), "\
"put in the format like (#subgenomes expected for genome X):"\
"(#subgenomes expected for genome Y) "\
"[default: %default]")
p.add_option("--Nm", dest="Nmax", type="int", default=10,
help="distance cutoff to tolerate two blocks that are "\
"slightly overlapping (cutoff for `quota mapping`) "\
"[default: %default units (gene or bp dist)]")
supported_solvers = ("SCIP", "GLPK")
p.add_option("--self", dest="self_match",
action="store_true", default=False,
help="you might turn this on when screening paralogous blocks, "\
"esp. if you have reduced mirrored blocks into non-redundant set")
p.add_option("--solver", default="SCIP", choices=supported_solvers,
help="use MIP solver [default: %default]")
p.add_option("--verbose", action="store_true",
default=False, help="show verbose solver output")
p.add_option("--screen", default=False, action="store_true",
help="generate new anchors file [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
qa_file, = args
qbed, sbed, qorder, sorder, is_self = check_beds(qa_file, p, opts)
# sanity check for the quota
if opts.quota:
try:
qa, qb = opts.quota.split(":")
qa, qb = int(qa), int(qb)
except:
print >> sys.stderr, "quota string should be the form x:x (2:4, 1:3, etc.)"
sys.exit(1)
if opts.self_match and qa != qb:
raise Exception, "when comparing genome to itself, " \
"quota must be the same number " \
"(like 1:1, 2:2) you have %s" % opts.quota
quota = (qa, qb)
self_match = opts.self_match
clusters = read_clusters(qa_file, qorder, sorder)
for cluster in clusters:
assert len(cluster) > 0
# below runs `quota mapping`
work_dir = op.join(op.dirname(op.abspath(qa_file)), "work")
selected_ids = solve_lp(clusters, quota, work_dir=work_dir, \
Nmax=opts.Nmax, self_match=self_match, \
solver=opts.solver, verbose=opts.verbose)
logging.debug("Selected {0} blocks.".format(len(selected_ids)))
prefix = qa_file.rsplit(".", 1)[0]
suffix = "{0}x{1}".format(qa, qb)
outfile = ".".join((prefix, suffix))
fw = must_open(outfile, "w")
print >> fw, ",".join(str(x) for x in selected_ids)
fw.close()
logging.debug("Screened blocks ids written to `{0}`.".format(outfile))
if opts.screen:
from jcvi.compara.synteny import screen
new_qa_file = ".".join((prefix, suffix, "anchors"))
largs = [qa_file, new_qa_file, "--ids", outfile]
if opts.qbed and opts.sbed:
largs += ["--qbed={0}".format(opts.qbed)]
largs += ["--sbed={0}".format(opts.sbed)]
screen(largs)
def main(args):
p = OptionParser(__doc__)
p.set_beds()
p.add_option(
"--quota",
default="1:1",
help="`quota mapping` procedure -- screen blocks to constrain mapping"
" (useful for orthology), "
"put in the format like (#subgenomes expected for genome X):"
"(#subgenomes expected for genome Y) "
"[default: %default]")
p.add_option("--Nm",
dest="Nmax",
type="int",
default=10,
help="distance cutoff to tolerate two blocks that are "
"slightly overlapping (cutoff for `quota mapping`) "
"[default: %default units (gene or bp dist)]")
supported_solvers = ("SCIP", "GLPK")
p.add_option(
"--self",
dest="self_match",
action="store_true",
default=False,
help="you might turn this on when screening paralogous blocks, "
"esp. if you have reduced mirrored blocks into non-redundant set")
p.add_option("--solver",
default="SCIP",
choices=supported_solvers,
help="use MIP solver [default: %default]")
p.set_verbose(help="Show verbose solver output")
p.add_option("--screen",
default=False,
action="store_true",
help="generate new anchors file [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
qa_file, = args
qbed, sbed, qorder, sorder, is_self = check_beds(qa_file, p, opts)
# sanity check for the quota
if opts.quota:
try:
qa, qb = opts.quota.split(":")
qa, qb = int(qa), int(qb)
except:
print("quota string should be the form x:x (2:4, 1:3, etc.)",
file=sys.stderr)
sys.exit(1)
if opts.self_match and qa != qb:
raise Exception("when comparing genome to itself, "
"quota must be the same number "
"(like 1:1, 2:2) you have %s" % opts.quota)
quota = (qa, qb)
self_match = opts.self_match
clusters = read_clusters(qa_file, qorder, sorder)
for cluster in clusters:
assert len(cluster) > 0
# below runs `quota mapping`
work_dir = op.join(op.dirname(op.abspath(qa_file)), "work")
selected_ids = solve_lp(clusters,
quota,
work_dir=work_dir,
Nmax=opts.Nmax,
self_match=self_match,
solver=opts.solver,
verbose=opts.verbose)
logging.debug("Selected {0} blocks.".format(len(selected_ids)))
prefix = qa_file.rsplit(".", 1)[0]
suffix = "{0}x{1}".format(qa, qb)
outfile = ".".join((prefix, suffix))
fw = must_open(outfile, "w")
print(",".join(str(x) for x in selected_ids), file=fw)
fw.close()
logging.debug("Screened blocks ids written to `{0}`.".format(outfile))
if opts.screen:
from jcvi.compara.synteny import screen
new_qa_file = ".".join((prefix, suffix, "anchors"))
largs = [qa_file, new_qa_file, "--ids", outfile]
if opts.qbed and opts.sbed:
largs += ["--qbed={0}".format(opts.qbed)]
largs += ["--sbed={0}".format(opts.sbed)]
screen(largs)