def populate_blastfile(blastfile, agp, outdir, opts):
assert not op.exists(blastfile)
all_oopts = []
for a, b, qreverse in agp.iter_paired_components():
aid = a.component_id
bid = b.component_id
oopts = get_overlap_opts(aid, bid, qreverse, outdir, opts)
all_oopts.append(oopts)
pool = WriteJobs(overlap_blastline_writer, all_oopts, \
blastfile, cpus=opts.cpus)
pool.run()
def populate_blastfile(blastfile, agp, outdir, opts):
assert not op.exists(blastfile)
all_oopts = []
for a, b, qreverse in agp.iter_paired_components():
aid = a.component_id
bid = b.component_id
oopts = get_overlap_opts(aid, bid, qreverse, outdir, opts)
all_oopts.append(oopts)
pool = WriteJobs(overlap_blastline_writer, all_oopts, \
blastfile, cpus=opts.cpus)
pool.run()
def populate_blastfile(blastfile, agp, outdir, opts):
assert not op.exists(blastfile)
all_oopts = []
for a, b, qreverse in agp.iter_paired_components():
aid = a.component_id
bid = b.component_id
oopts = [aid, bid, \
"--suffix", "fa", \
"--dir", outdir, \
"--pctid={0}".format(opts.pctid), \
"--hitlen={0}".format(opts.hitlen)]
if qreverse:
oopts += ["--qreverse"]
all_oopts.append(oopts)
pool = WriteJobs(overlap_blastline_writer, all_oopts, \
blastfile, cpus=opts.cpus)
pool.run()
def populate_blastfile(blastfile, agp, outdir, opts):
from jcvi.apps.grid import WriteJobs
assert not op.exists(blastfile)
all_oopts = []
for a, b, qreverse in agp.iter_paired_components():
aid = a.component_id
bid = b.component_id
oopts = [aid, bid, \
"--suffix", "fa", \
"--dir", outdir, \
"--pctid={0}".format(opts.pctid), \
"--hitlen={0}".format(opts.hitlen)]
if qreverse:
oopts += ["--qreverse"]
all_oopts.append(oopts)
pool = WriteJobs(overlap_blastline_writer, all_oopts, \
blastfile, cpus=opts.cpus)
pool.run()
