def anneal(args):
"""
%prog anneal agpfile contigs.fasta
Merge adjacent overlapping contigs and make new AGP file.
By default it will also anneal lines like these together (unless --nozipshreds):
scaffold4 1 1608 1 W ca-bacs.5638.frag11.22000-23608 1 1608 -
scaffold4 1609 1771 2 N 163 scaffold yes paired-ends
scaffold4 1772 3771 3 W ca-bacs.5638.frag10.20000-22000 1 2000 -
These are most likely shreds, which we look for based on names.
"""
p = OptionParser(anneal.__doc__)
p.set_align(pctid=GoodPct, hitlen=GoodOverlap)
p.add_option("--hang", default=GoodOverhang, type="int",
help="Maximum overhang length [default: %default]")
p.set_outdir(outdir="outdir")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
agpfile, contigs = args
outdir = opts.outdir
if not op.exists(outdir):
mkdir(outdir)
cmd = "faSplit byname {0} {1}/".format(contigs, outdir)
sh(cmd)
cutoff = Cutoff(opts.pctid, opts.hitlen, opts.hang)
logging.debug(str(cutoff))
agp = AGP(agpfile)
blastfile = agpfile.replace(".agp", ".blast")
if not op.exists(blastfile):
populate_blastfile(blastfile, agp, outdir, opts)
assert op.exists(blastfile)
logging.debug("File `{0}` found. Start loading.".format(blastfile))
blast = BlastSlow(blastfile).to_dict()
annealedagp = "annealed.agp"
annealedfasta = "annealed.fasta"
newagp = deepcopy(agp)
clrstore = {}
for a, b, qreverse in agp.iter_paired_components():
aid = a.component_id
bid = b.component_id
pair = (aid, bid)
if pair in blast:
bl = blast[pair]
else:
oopts = get_overlap_opts(aid, bid, qreverse, outdir, opts)
o = overlap(oopts)
if not o:
continue
bl = o.blastline
o = Overlap(bl, a.component_span, b.component_span,
cutoff, qreverse=qreverse)
if aid not in clrstore:
clrstore[aid] = CLR.from_agpline(a)
if bid not in clrstore:
clrstore[bid] = CLR.from_agpline(b)
aclr, bclr = clrstore[aid], clrstore[bid]
o.print_graphic()
if o.anneal(aclr, bclr):
newagp.delete_between(aid, bid, verbose=True)
if o.otype == 2: # b ~ a
o = o.swapped
o.print_graphic()
if o.anneal(bclr, aclr):
newagp.switch_between(bid, aid, verbose=True)
newagp.delete_between(bid, aid, verbose=True)
logging.debug("A total of {0} components with modified CLR.".\
format(len(clrstore)))
for cid, c in clrstore.items():
if c.is_valid:
continue
print >> sys.stderr, "Remove {0}".format(c)
newagp.convert_to_gap(cid, verbose=True)
# Update all ranges that has modified clr
for a in newagp:
if a.is_gap:
continue
aid = a.component_id
if aid in clrstore:
c = clrstore[aid]
a.component_beg = c.start
a.component_end = c.end
newagp.print_to_file(annealedagp)
tidyagp = tidy([annealedagp, contigs])
build([tidyagp, contigs, annealedfasta])
return annealedfasta
def anneal(args):
"""
%prog anneal agpfile contigs.fasta
Merge adjacent overlapping contigs and make new AGP file.
By default it will also anneal lines like these together (unless --nozipshreds):
scaffold4 1 1608 1 W ca-bacs.5638.frag11.22000-23608 1 1608 -
scaffold4 1609 1771 2 N 163 scaffold yes paired-ends
scaffold4 1772 3771 3 W ca-bacs.5638.frag10.20000-22000 1 2000 -
These are most likely shreds, which we look for based on names.
"""
p = OptionParser(anneal.__doc__)
p.set_align(pctid=GoodPct, hitlen=GoodOverlap)
p.add_option("--hang",
default=GoodOverhang,
type="int",
help="Maximum overhang length [default: %default]")
p.set_outdir(outdir="outdir")
p.set_cpus()
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
agpfile, contigs = args
outdir = opts.outdir
if not op.exists(outdir):
mkdir(outdir)
cmd = "faSplit byname {0} {1}/".format(contigs, outdir)
sh(cmd)
cutoff = Cutoff(opts.pctid, opts.hitlen, opts.hang)
logging.debug(str(cutoff))
agp = AGP(agpfile)
blastfile = agpfile.replace(".agp", ".blast")
if not op.exists(blastfile):
populate_blastfile(blastfile, agp, outdir, opts)
assert op.exists(blastfile)
logging.debug("File `{0}` found. Start loading.".format(blastfile))
blast = BlastSlow(blastfile).to_dict()
annealedagp = "annealed.agp"
annealedfasta = "annealed.fasta"
newagp = deepcopy(agp)
clrstore = {}
for a, b, qreverse in agp.iter_paired_components():
aid = a.component_id
bid = b.component_id
pair = (aid, bid)
if pair in blast:
bl = blast[pair]
else:
oopts = get_overlap_opts(aid, bid, qreverse, outdir, opts)
o = overlap(oopts)
if not o:
continue
bl = o.blastline
o = Overlap(bl,
a.component_span,
b.component_span,
cutoff,
qreverse=qreverse)
if aid not in clrstore:
clrstore[aid] = CLR.from_agpline(a)
if bid not in clrstore:
clrstore[bid] = CLR.from_agpline(b)
aclr, bclr = clrstore[aid], clrstore[bid]
o.print_graphic()
if o.anneal(aclr, bclr):
newagp.delete_between(aid, bid, verbose=True)
if o.otype == 2: # b ~ a
o = o.swapped
o.print_graphic()
if o.anneal(bclr, aclr):
newagp.switch_between(bid, aid, verbose=True)
newagp.delete_between(bid, aid, verbose=True)
logging.debug("A total of {0} components with modified CLR.".\
format(len(clrstore)))
for cid, c in clrstore.items():
if c.is_valid:
continue
print >> sys.stderr, "Remove {0}".format(c)
newagp.convert_to_gap(cid, verbose=True)
# Update all ranges that has modified clr
for a in newagp:
if a.is_gap:
continue
aid = a.component_id
if aid in clrstore:
c = clrstore[aid]
a.component_beg = c.start
a.component_end = c.end
newagp.print_to_file(annealedagp)
tidyagp = tidy([annealedagp, contigs])
build([tidyagp, contigs, annealedfasta])
return annealedfasta
