def blast(args):
"""
%prog blast fastafile
Run BLASTN against database (default is UniVec_Core). Output .bed format
on the vector/contaminant ranges.
"""
p = OptionParser(blast.__doc__)
p.add_option("--dist",
dest="dist",
default=100,
type="int",
help="Merge adjacent HSPs separated by [default: %default]")
p.add_option("--db",
dest="db",
default=None,
help="Use a different database rather than UniVec_Core")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
fastaprefix = fastafile.split(".", 1)[0]
univec = opts.db or download(
"ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core")
uniprefix = univec.split(".", 1)[0]
fastablast = fastaprefix + ".{0}.blast".format(uniprefix)
prog = run_megablast if opts.db else run_vecscreen
prog(infile=fastafile, outfile=fastablast, db=univec, pctid=95, hitlen=50)
fp = open(fastablast)
ranges = []
for row in fp:
b = BlastLine(row)
ranges.append((b.query, b.qstart, b.qstop))
merged_ranges = range_merge(ranges, dist=opts.dist)
bedfile = fastaprefix + ".{0}.bed".format(uniprefix)
fw = must_open(bedfile, "w")
for seqid, start, end in merged_ranges:
print >> fw, "\t".join(
str(x) for x in (seqid, start - 1, end, uniprefix))
return bedfile
def closest(args):
"""
%prog closest candidates.bed gaps.bed fastafile
Identify the nearest gaps flanking suggested regions.
"""
p = OptionParser(closest.__doc__)
p.add_option(
"--om",
default=False,
action="store_true",
help="The bedfile is OM blocks",
)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
candidates, gapsbed, fastafile = args
sizes = Sizes(fastafile).mapping
bed = Bed(candidates)
ranges = []
for b in bed:
r = range_parse(b.accn) if opts.om else b
ranges.append([r.seqid, r.start, r.end])
gapsbed = Bed(gapsbed)
granges = [(x.seqid, x.start, x.end) for x in gapsbed]
ranges = range_merge(ranges)
for r in ranges:
a = range_closest(granges, r)
b = range_closest(granges, r, left=False)
seqid = r[0]
if a is not None and a[0] != seqid:
a = None
if b is not None and b[0] != seqid:
b = None
mmin = 1 if a is None else a[1]
mmax = sizes[seqid] if b is None else b[2]
print("\t".join(str(x) for x in (seqid, mmin - 1, mmax)))
def blast(args):
"""
%prog blast fastafile
Run BLASTN against database (default is UniVec_Core). Output .bed format
on the vector/contaminant ranges.
"""
p = OptionParser(blast.__doc__)
p.add_option("--dist", default=100, type="int",
help="Merge adjacent HSPs separated by [default: %default]")
p.add_option("--db",
help="Use a different database rather than UniVec_Core")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
fastaprefix = fastafile.split(".", 1)[0]
univec = opts.db or download("ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core")
uniprefix = univec.split(".", 1)[0]
fastablast = fastaprefix + ".{0}.blast".format(uniprefix)
prog = run_megablast if opts.db else run_vecscreen
prog(infile=fastafile, outfile=fastablast, db=univec, pctid=95, hitlen=50)
fp = open(fastablast)
ranges = []
for row in fp:
b = BlastLine(row)
ranges.append((b.query, b.qstart, b.qstop))
merged_ranges = range_merge(ranges, dist=opts.dist)
bedfile = fastaprefix + ".{0}.bed".format(uniprefix)
fw = must_open(bedfile, "w")
for seqid, start, end in merged_ranges:
print("\t".join(str(x) for x in (seqid, start - 1, end, uniprefix)), file=fw)
return bedfile
def closest(args):
"""
%prog closest candidates.bed gaps.bed fastafile
Identify the nearest gaps flanking suggested regions.
"""
p = OptionParser(closest.__doc__)
p.add_option("--om", default=False, action="store_true",
help="The bedfile is OM blocks [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
candidates, gapsbed, fastafile = args
sizes = Sizes(fastafile).mapping
bed = Bed(candidates)
ranges = []
for b in bed:
r = range_parse(b.accn) if opts.om else b
ranges.append([r.seqid, r.start, r.end])
gapsbed = Bed(gapsbed)
granges = [(x.seqid, x.start, x.end) for x in gapsbed]
ranges = range_merge(ranges)
for r in ranges:
a = range_closest(granges, r)
b = range_closest(granges, r, left=False)
seqid = r[0]
if a is not None and a[0] != seqid:
a = None
if b is not None and b[0] != seqid:
b = None
mmin = 1 if a is None else a[1]
mmax = sizes[seqid] if b is None else b[2]
print "\t".join(str(x) for x in (seqid, mmin - 1, mmax))
def test_range_merge(ranges, dist, expected):
from jcvi.utils.range import range_merge
assert range_merge(ranges, dist) == expected
