def annotate(args):
"""
%prog annotate blastfile query.fasta subject.fasta
Annotate overlap types (dovetail, contained, etc) in BLAST tabular file.
"""
from jcvi.assembly.goldenpath import Cutoff, Overlap, Overlap_types
p = OptionParser(annotate.__doc__)
p.set_align(pctid=94, hitlen=500)
p.add_option("--hang",
default=500,
type="int",
help="Maximum overhang length")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
blastfile, afasta, bfasta = args
fp = must_open(blastfile)
asizes = Sizes(afasta).mapping
bsizes = Sizes(bfasta).mapping
cutoff = Cutoff(opts.pctid, opts.hitlen, opts.hang)
logging.debug(str(cutoff))
for row in fp:
b = BlastLine(row)
asize = asizes[b.query]
bsize = bsizes[b.subject]
if b.query == b.subject:
continue
ov = Overlap(b, asize, bsize, cutoff)
if ov.otype:
ov.print_graphic()
print "{0}\t{1}".format(b, Overlap_types[ov.otype])
def annotate(args):
"""
%prog annotate blastfile query.fasta subject.fasta
Annotate overlap types (dovetail, contained, etc) in BLAST tabular file.
"""
from jcvi.assembly.goldenpath import Cutoff, Overlap, Overlap_types
p = OptionParser(annotate.__doc__)
p.set_align(pctid=94, hitlen=500)
p.add_option("--hang", default=500, type="int",
help="Maximum overhang length")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
blastfile, afasta, bfasta = args
fp = open(blastfile)
asizes = Sizes(afasta).mapping
bsizes = Sizes(bfasta).mapping
cutoff = Cutoff(opts.pctid, opts.hitlen, opts.hang)
logging.debug(str(cutoff))
for row in fp:
b = BlastLine(row)
asize = asizes[b.query]
bsize = bsizes[b.subject]
if b.query == b.subject:
continue
ov = Overlap(b, asize, bsize, cutoff)
if ov.otype:
ov.print_graphic()
print "{0}\t{1}".format(b, Overlap_types[ov.otype])
def annotate(args):
"""
%prog annotate blastfile query.fasta subject.fasta
Annotate overlap types (dovetail, contained, etc) in BLAST tabular file.
"""
from jcvi.assembly.goldenpath import Overlap, Overlap_types
p = OptionParser(annotate.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
blastfile, afasta, bfasta = args
fp = open(blastfile)
asizes = Sizes(afasta).mapping
bsizes = Sizes(bfasta).mapping
for row in fp:
b = BlastLine(row)
asize = asizes[b.query]
bsize = bsizes[b.subject]
ov = Overlap(b, asize, bsize)
print "{0}\t{1}".format(b, Overlap_types[ov.get_otype()])
def annotate(args):
"""
%prog annotate blastfile query.fasta subject.fasta
Annotate overlap types (dovetail, contained, etc) in BLAST tabular file.
"""
from jcvi.assembly.goldenpath import Overlap, Overlap_types
p = OptionParser(annotate.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
blastfile, afasta, bfasta = args
fp = open(blastfile)
asizes = Sizes(afasta).mapping
bsizes = Sizes(bfasta).mapping
for row in fp:
b = BlastLine(row)
asize = asizes[b.query]
bsize = bsizes[b.subject]
ov = Overlap(b, asize, bsize)
print "{0}\t{1}".format(b, Overlap_types[ov.get_otype()])