def gaps(args):
"""
%prog gaps OM.bed fastafile
Create patches around OM gaps.
"""
from jcvi.formats.bed import uniq
p = OptionParser(gaps.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
ombed, fastafile = args
ombed = uniq([ombed])
bed = Bed(ombed)
for a, b in pairwise(bed):
om_a = (a.seqid, a.start, a.end, "+")
om_b = (b.seqid, b.start, b.end, "+")
ch_a = range_parse(a.accn)
ch_b = range_parse(b.accn)
ch_a = (ch_a.seqid, ch_a.start, ch_a.end, "+")
ch_b = (ch_b.seqid, ch_b.start, ch_b.end, "+")
om_dist, x = range_distance(om_a, om_b, distmode="ee")
ch_dist, x = range_distance(ch_a, ch_b, distmode="ee")
if om_dist <= 0 and ch_dist <= 0:
continue
print(a)
print(b)
print(om_dist, ch_dist)
def chimera(args):
"""
%prog chimera bedfile
Scan the bed file to break scaffolds that multi-maps.
"""
p = OptionParser(chimera.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
bedfile, = args
bed = Bed(bedfile)
selected = select_bed(bed)
mapped = defaultdict(set) # scaffold => chr
chimerabed = "chimera.bed"
fw = open(chimerabed, "w")
for b in selected:
scf = range_parse(b.accn).seqid
chr = b.seqid
mapped[scf].add(chr)
nchimera = 0
for s, chrs in sorted(mapped.items()):
if len(chrs) == 1:
continue
print >> sys.stderr, "=" * 80
print >> sys.stderr, "{0} mapped to multiple locations: {1}".\
format(s, ",".join(sorted(chrs)))
ranges = []
for b in selected:
rr = range_parse(b.accn)
scf = rr.seqid
if scf == s:
print >> sys.stderr, b
ranges.append(rr)
# Identify breakpoints
ranges.sort(key=lambda x: (x.seqid, x.start, x.end))
for a, b in pairwise(ranges):
seqid = a.seqid
if seqid != b.seqid:
continue
start, end = a.end, b.start
if start > end:
start, end = end, start
chimeraline = "\t".join(str(x) for x in (seqid, start, end))
print >> fw, chimeraline
print >> sys.stderr, chimeraline
nchimera += 1
fw.close()
logging.debug("A total of {0} junctions written to `{1}`.".\
format(nchimera, chimerabed))
def patcher(args):
"""
%prog patcher backbone.bed other.bed
Given optical map alignment, prepare the patchers. Use --backbone to suggest
which assembly is the major one, and the patchers will be extracted from
another assembly.
"""
from jcvi.formats.bed import uniq
p = OptionParser(patcher.__doc__)
p.add_option("--backbone",
default="OM",
help="Prefix of the backbone assembly [default: %default]")
p.add_option("--object",
default="object",
help="New object name [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
backbonebed, otherbed = args
backbonebed = uniq([backbonebed])
otherbed = uniq([otherbed])
bb = opts.backbone
pf = backbonebed.split(".")[0]
key = lambda x: (x.seqid, x.start, x.end)
is_bb = lambda x: x.startswith(bb)
# Make a uniq bed keeping backbone at redundant intervals
cmd = "intersectBed -v -wa"
cmd += " -a {0} -b {1}".format(otherbed, backbonebed)
outfile = otherbed.rsplit(".", 1)[0] + ".not." + backbonebed
sh(cmd, outfile=outfile)
uniqbed = Bed()
uniqbedfile = pf + ".merged.bed"
uniqbed.extend(Bed(backbonebed))
uniqbed.extend(Bed(outfile))
uniqbed.print_to_file(uniqbedfile, sorted=True)
# Condense adjacent intervals, allow some chaining
bed = uniqbed
key = lambda x: range_parse(x.accn).seqid
bed_fn = pf + ".patchers.bed"
bed_fw = open(bed_fn, "w")
for k, sb in groupby(bed, key=key):
sb = list(sb)
chr, start, end, strand = merge_ranges(sb)
id = "{0}:{1}-{2}".format(chr, start, end)
print >> bed_fw, "\t".join(str(x) for x in \
(chr, start, end, opts.object, 1000, strand))
bed_fw.close()
def patcher(args):
"""
%prog patcher backbone.bed other.bed
Given optical map alignment, prepare the patchers. Use --backbone to suggest
which assembly is the major one, and the patchers will be extracted from
another assembly.
"""
from jcvi.formats.bed import uniq
p = OptionParser(patcher.__doc__)
p.add_option("--backbone", default="OM",
help="Prefix of the backbone assembly [default: %default]")
p.add_option("--object", default="object",
help="New object name [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
backbonebed, otherbed = args
backbonebed = uniq([backbonebed])
otherbed = uniq([otherbed])
pf = backbonebed.split(".")[0]
key = lambda x: (x.seqid, x.start, x.end)
# Make a uniq bed keeping backbone at redundant intervals
cmd = "intersectBed -v -wa"
cmd += " -a {0} -b {1}".format(otherbed, backbonebed)
outfile = otherbed.rsplit(".", 1)[0] + ".not." + backbonebed
sh(cmd, outfile=outfile)
uniqbed = Bed()
uniqbedfile = pf + ".merged.bed"
uniqbed.extend(Bed(backbonebed))
uniqbed.extend(Bed(outfile))
uniqbed.print_to_file(uniqbedfile, sorted=True)
# Condense adjacent intervals, allow some chaining
bed = uniqbed
key = lambda x: range_parse(x.accn).seqid
bed_fn = pf + ".patchers.bed"
bed_fw = open(bed_fn, "w")
for k, sb in groupby(bed, key=key):
sb = list(sb)
chr, start, end, strand = merge_ranges(sb)
print >> bed_fw, "\t".join(str(x) for x in \
(chr, start, end, opts.object, 1000, strand))
bed_fw.close()
def gaps(args):
"""
%prog gaps OM.bed fastafile
Create patches around OM gaps.
"""
from jcvi.formats.bed import uniq
from jcvi.utils.iter import pairwise
p = OptionParser(gaps.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
ombed, fastafile = args
ombed = uniq([ombed])
bed = Bed(ombed)
for a, b in pairwise(bed):
om_a = (a.seqid, a.start, a.end, "+")
om_b = (b.seqid, b.start, b.end, "+")
ch_a = range_parse(a.accn)
ch_b = range_parse(b.accn)
ch_a = (ch_a.seqid, ch_a.start, ch_a.end, "+")
ch_b = (ch_b.seqid, ch_b.start, ch_b.end, "+")
om_dist, x = range_distance(om_a, om_b, distmode="ee")
ch_dist, x = range_distance(ch_a, ch_b, distmode="ee")
if om_dist <= 0 and ch_dist <= 0:
continue
print a
print b
print om_dist, ch_dist
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 merge_ranges(beds):
m = [x.accn for x in beds]
mr = [range_parse(x) for x in m]
mc = set(x.seqid for x in mr)
if len(mc) != 1:
logging.error("Multiple seqid found in pocket. Aborted.")
return
mc = list(mc)[0]
ms = min(x.start for x in mr)
me = max(x.end for x in mr)
neg_strands = sum(1 for x in beds if x.strand == "-")
pos_strands = len(beds) - neg_strands
strand = "-" if neg_strands > pos_strands else "+"
return mc, ms, me, strand
def merge_ranges(beds):
m = [x.accn for x in beds]
mr = [range_parse(x) for x in m]
mc = set(x.seqid for x in mr)
if len(mc) != 1:
logging.error("Multiple seqid found in pocket. Aborted.")
return
mc = list(mc)[0]
ms = min(x.start for x in mr)
me = max(x.end for x in mr)
neg_strands = sum(1 for x in beds if x.strand == '-')
pos_strands = len(beds) - neg_strands
strand = '-' if neg_strands > pos_strands else '+'
return mc, ms, me, strand
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 fasta(args):
"""
%prog fasta bedfile scf.fasta pseudomolecules.fasta
Use OM bed to scaffold and create pseudomolecules. bedfile can be generated
by running jcvi.assembly.opticalmap bed --blockonly
"""
from jcvi.formats.sizes import Sizes
from jcvi.formats.agp import OO, build
p = OptionParser(fasta.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
bedfile, scffasta, pmolfasta = args
pf = bedfile.rsplit(".", 1)[0]
bed = Bed(bedfile)
selected = select_bed(bed)
oo = OO()
seen = set()
sizes = Sizes(scffasta).mapping
agpfile = pf + ".agp"
agp = open(agpfile, "w")
for b in selected:
scf = range_parse(b.accn).seqid
chr = b.seqid
cs = (chr, scf)
if cs not in seen:
oo.add(chr, scf, sizes[scf], b.strand)
seen.add(cs)
else:
logging.debug("Seen {0}, ignored.".format(cs))
oo.write_AGP(agp, gaptype="contig")
agp.close()
build([agpfile, scffasta, pmolfasta])
def fasta(args):
"""
%prog fasta bedfile scf.fasta pseudomolecules.fasta
Use OM bed to scaffold and create pseudomolecules. bedfile can be generated
by running jcvi.assembly.opticalmap bed --blockonly
"""
from jcvi.formats.sizes import Sizes
from jcvi.formats.agp import OO, build
p = OptionParser(fasta.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
bedfile, scffasta, pmolfasta = args
pf = bedfile.rsplit(".", 1)[0]
bed = Bed(bedfile)
selected = select_bed(bed)
oo = OO()
seen = set()
sizes = Sizes(scffasta).mapping
agpfile = pf + ".agp"
agp = open(agpfile, "w")
for b in selected:
scf = range_parse(b.accn).seqid
chr = b.seqid
cs = (chr, scf)
if cs not in seen:
oo.add(chr, scf, sizes[scf], b.strand)
seen.add(cs)
else:
logging.debug("Seen {0}, ignored.".format(cs))
oo.write_AGP(agp, gaptype="contig")
agp.close()
build([agpfile, scffasta, pmolfasta])
def test_range_parse(input, expected):
from jcvi.utils.range import range_parse
assert range_parse(input) == expected
