Пример #1
0
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()
Пример #2
0
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()
Пример #3
0
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()
Пример #4
0
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()