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
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 paste(args):
"""
%prog paste flanks.bed flanks_vs_assembly.blast backbone.fasta
Paste in good sequences in the final assembly.
"""
from jcvi.formats.bed import uniq
p = OptionParser(paste.__doc__)
p.add_option(
"--maxsize",
default=300000,
type="int",
help="Maximum size of patchers to be replaced",
)
p.add_option("--prefix", help="Prefix of the new object")
p.set_rclip(rclip=1)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
pbed, blastfile, bbfasta = args
maxsize = opts.maxsize # Max DNA size to replace gap
order = Bed(pbed).order
beforebed, afterbed = blast_to_twobeds(
blastfile, order, log=True, rclip=opts.rclip, maxsize=maxsize, flipbeds=True
)
beforebed = uniq([beforebed])
afbed = Bed(beforebed)
bfbed = Bed(afterbed)
shuffle_twobeds(afbed, bfbed, bbfasta, prefix=opts.prefix)
def paste(args):
"""
%prog paste flanks.bed flanks_vs_assembly.blast backbone.fasta
Paste in good sequences in the final assembly.
"""
from jcvi.formats.bed import uniq
p = OptionParser(paste.__doc__)
p.add_option("--maxsize", default=300000, type="int",
help="Maximum size of patchers to be replaced [default: %default]")
p.add_option("--prefix", help="Prefix of the new object [default: %default]")
p.set_rclip(rclip=1)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
pbed, blastfile, bbfasta = args
maxsize = opts.maxsize # Max DNA size to replace gap
order = Bed(pbed).order
beforebed, afterbed = blast_to_twobeds(blastfile, order, log=True,
rclip=opts.rclip, maxsize=maxsize,
flipbeds=True)
beforebed = uniq([beforebed])
afbed = Bed(beforebed)
bfbed = Bed(afterbed)
shuffle_twobeds(afbed, bfbed, bbfasta, prefix=opts.prefix)
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
