def insert(args):
"""
%prog insert candidates.bed gaps.bed chrs.fasta unplaced.fasta
Insert scaffolds into assembly.
"""
from jcvi.formats.agp import mask, bed
from jcvi.formats.sizes import agp
p = OptionParser(insert.__doc__)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
candidates, gapsbed, chrfasta, unplacedfasta = args
refinedbed = refine([candidates, gapsbed])
sizes = Sizes(unplacedfasta).mapping
cbed = Bed(candidates)
corder = cbed.order
gbed = Bed(gapsbed)
gorder = gbed.order
gpbed = Bed()
gappositions = {} # (chr, start, end) => gapid
fp = open(refinedbed)
gap_to_scf = defaultdict(list)
seen = set()
for row in fp:
atoms = row.split()
if len(atoms) <= 6:
continue
unplaced = atoms[3]
strand = atoms[5]
gapid = atoms[9]
if gapid not in seen:
seen.add(gapid)
gi, gb = gorder[gapid]
gpbed.append(gb)
gappositions[(gb.seqid, gb.start, gb.end)] = gapid
gap_to_scf[gapid].append((unplaced, strand))
gpbedfile = "candidate.gaps.bed"
gpbed.print_to_file(gpbedfile, sorted=True)
agpfile = agp([chrfasta])
maskedagpfile = mask([agpfile, gpbedfile])
maskedbedfile = maskedagpfile.rsplit(".", 1)[0] + ".bed"
bed([maskedagpfile, "--outfile={0}".format(maskedbedfile)])
mbed = Bed(maskedbedfile)
finalbed = Bed()
for b in mbed:
sid = b.seqid
key = (sid, b.start, b.end)
if key not in gappositions:
finalbed.add("{0}\n".format(b))
continue
gapid = gappositions[key]
scfs = gap_to_scf[gapid]
# For scaffolds placed in the same gap, sort according to positions
scfs.sort(key=lambda x: corder[x[0]][1].start + corder[x[0]][1].end)
for scf, strand in scfs:
size = sizes[scf]
finalbed.add("\t".join(str(x) for x in (scf, 0, size, sid, 1000, strand)))
finalbedfile = "final.bed"
finalbed.print_to_file(finalbedfile)
# Clean-up
toclean = [gpbedfile, agpfile, maskedagpfile, maskedbedfile]
FileShredder(toclean)
def insert(args):
"""
%prog insert candidates.bed gaps.bed chrs.fasta unplaced.fasta
Insert scaffolds into assembly.
"""
from jcvi.formats.agp import mask, bed
from jcvi.formats.sizes import agp
p = OptionParser(insert.__doc__)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
candidates, gapsbed, chrfasta, unplacedfasta = args
refinedbed = refine([candidates, gapsbed])
sizes = Sizes(unplacedfasta).mapping
cbed = Bed(candidates)
corder = cbed.order
gbed = Bed(gapsbed)
gorder = gbed.order
gpbed = Bed()
gappositions = {} # (chr, start, end) => gapid
fp = open(refinedbed)
gap_to_scf = defaultdict(list)
seen = set()
for row in fp:
atoms = row.split()
unplaced = atoms[3]
strand = atoms[5]
gapid = atoms[9]
if gapid not in seen:
seen.add(gapid)
gi, gb = gorder[gapid]
gpbed.append(gb)
gappositions[(gb.seqid, gb.start, gb.end)] = gapid
gap_to_scf[gapid].append((unplaced, strand))
gpbedfile = "candidate.gaps.bed"
gpbed.print_to_file(gpbedfile, sorted=True)
agpfile = agp([chrfasta])
maskedagpfile = mask([agpfile, gpbedfile])
maskedbedfile = maskedagpfile.rsplit(".", 1)[0] + ".bed"
bed([maskedagpfile, "--outfile={0}".format(maskedbedfile)])
mbed = Bed(maskedbedfile)
beds = []
for b in mbed:
sid = b.seqid
key = (sid, b.start, b.end)
if key not in gappositions:
beds.append(b)
continue
gapid = gappositions[key]
scfs = gap_to_scf[gapid]
# For scaffolds placed in the same gap, sort according to positions
scfs.sort(key=lambda x: corder[x[0]][1].start + corder[x[0]][1].end)
for scf, strand in scfs:
size = sizes[scf]
beds.append(BedLine("\t".join(str(x) for x in \
(scf, 0, size, sid, 1000, strand))))
finalbed = Bed()
finalbed.extend(beds)
finalbedfile = "final.bed"
finalbed.print_to_file(finalbedfile)
# Clean-up
toclean = [gpbedfile, agpfile, maskedagpfile, maskedbedfile]
FileShredder(toclean)