def graph(args):
"""
%prog graph all.ov contigs.fasta
Load overlaps to create bidirectional graph.
"""
from jcvi.algorithms.graph import BiGraph, BiEdge
from jcvi.assembly.syntenypath import graph_to_agp
p = OptionParser(graph.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
allov, contigsfasta = args
g = BiGraph()
fp = open(allov)
# ctg7180000045865 - ctg7180000086408: a ~ b Overlap: 5108 Identity: 99.02%
# Orientation: +
contained = set()
for row in fp:
atoms = row.strip().split(":")
pair = atoms[0]
a, b = pair.split(" - ")
orientation = atoms[-1].strip()
tag = atoms[1].replace("Overlap", "").strip()
oa = ">"
ob = "<" if orientation == '-' else ">"
if tag == "a ~ b":
g.add_edge(BiEdge(a, b, oa, ob))
elif tag == "b ~ a":
g.add_edge(BiEdge(b, a, ob, oa))
elif tag == "a in b":
contained.add(a)
elif tag == "b in a":
contained.add(b)
graph_to_agp(g, allov, contigsfasta)
containedfile = "contained.ids"
fw = open(containedfile, "w")
print >> fw, "\n".join(contained)
fw.close()
def connect(args):
"""
%prog connect assembly.fasta read_mapping.blast
Connect contigs using long reads.
"""
from jcvi.formats.sizes import Sizes
from jcvi.formats.blast import Blast
from jcvi.utils.iter import pairwise
from jcvi.utils.range import range_intersect
from jcvi.algorithms.graph import BiGraph, BiEdge
from jcvi.assembly.syntenypath import graph_to_agp
p = OptionParser(connect.__doc__)
p.add_option("--clip", default=2000, type="int",
help="Only consider end of contigs [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
fastafile, blastfile = args
clip = opts.clip
sizes = Sizes(fastafile).mapping
blast = Blast(blastfile)
blasts = []
for b in blast:
seqid = b.subject
size = sizes[seqid]
start, end = b.sstart, b.sstop
cstart, cend = min(size, clip), max(0, size - clip)
if start > cstart and end < cend:
continue
blasts.append(b)
key = lambda x: x.query
blasts.sort(key=key)
g = BiGraph()
for query, bb in groupby(blasts, key=key):
bb = sorted(bb, key=lambda x: x.qstart)
nsubjects = len(set(x.subject for x in bb))
if nsubjects == 1:
continue
print "\n".join(str(x) for x in bb)
for a, b in pairwise(bb):
astart, astop = a.qstart, a.qstop
bstart, bstop = b.qstart, b.qstop
if a.subject == b.subject:
continue
arange = astart, astop
brange = bstart, bstop
ov = range_intersect(arange, brange)
alen = astop - astart + 1
blen = bstop - bstart + 1
if ov:
ostart, ostop = ov
ov = ostop - ostart + 1
print ov, alen, blen
if ov and (ov > alen / 2 or ov > blen / 2):
print "Too much overlap ({0})".format(ov)
continue
asub = a.subject
bsub = b.subject
atag = ">" if a.orientation == "+" else "<"
btag = ">" if b.orientation == "+" else "<"
e = BiEdge(asub, bsub, atag, btag)
g.add_edge(e)
print "=" * 5, e
graph_to_agp(g, blastfile, fastafile, verbose=False)
def connect(args):
"""
%prog connect assembly.fasta read_mapping.blast
Connect contigs using long reads.
"""
from jcvi.formats.sizes import Sizes
from jcvi.formats.blast import Blast
from jcvi.utils.iter import pairwise
from jcvi.utils.range import range_intersect
from jcvi.algorithms.graph import BiGraph, BiEdge
from jcvi.assembly.syntenypath import graph_to_agp
p = OptionParser(connect.__doc__)
p.add_option("--clip",
default=2000,
type="int",
help="Only consider end of contigs [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
fastafile, blastfile = args
clip = opts.clip
sizes = Sizes(fastafile).mapping
blast = Blast(blastfile)
blasts = []
for b in blast:
seqid = b.subject
size = sizes[seqid]
start, end = b.sstart, b.sstop
cstart, cend = min(size, clip), max(0, size - clip)
if start > cstart and end < cend:
continue
blasts.append(b)
key = lambda x: x.query
blasts.sort(key=key)
g = BiGraph()
for query, bb in groupby(blasts, key=key):
bb = sorted(bb, key=lambda x: x.qstart)
nsubjects = len(set(x.subject for x in bb))
if nsubjects == 1:
continue
print "\n".join(str(x) for x in bb)
for a, b in pairwise(bb):
astart, astop = a.qstart, a.qstop
bstart, bstop = b.qstart, b.qstop
if a.subject == b.subject:
continue
arange = astart, astop
brange = bstart, bstop
ov = range_intersect(arange, brange)
alen = astop - astart + 1
blen = bstop - bstart + 1
if ov:
ostart, ostop = ov
ov = ostop - ostart + 1
print ov, alen, blen
if ov and (ov > alen / 2 or ov > blen / 2):
print "Too much overlap ({0})".format(ov)
continue
asub = a.subject
bsub = b.subject
atag = ">" if a.orientation == "+" else "<"
btag = ">" if b.orientation == "+" else "<"
e = BiEdge(asub, bsub, atag, btag)
g.add_edge(e)
print "=" * 5, e
graph_to_agp(g, blastfile, fastafile, verbose=False)
