def fromblast(args):
"""
%prog fromblast blastfile subject.fasta
Generate path from BLAST file. If multiple subjects map to the same query,
an edge is constructed between them (with the link provided by the query).
The BLAST file MUST be filtered, chained, supermapped.
"""
from jcvi.formats.blast import sort
from jcvi.utils.range import range_distance
p = OptionParser(fromblast.__doc__)
p.add_option(
"--clique",
default=False,
action="store_true",
help="Populate clique instead of linear path",
)
p.add_option(
"--maxdist",
default=100000,
type="int",
help="Create edge within certain distance",
)
p.set_verbose(help="Print verbose reports to stdout")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
blastfile, subjectfasta = args
clique = opts.clique
maxdist = opts.maxdist
sort([blastfile, "--query"])
blast = BlastSlow(blastfile, sorted=True)
g = BiGraph()
for query, blines in groupby(blast, key=lambda x: x.query):
blines = list(blines)
iterator = combinations(blines, 2) if clique else pairwise(blines)
for a, b in iterator:
asub, bsub = a.subject, b.subject
if asub == bsub:
continue
arange = (a.query, a.qstart, a.qstop, "+")
brange = (b.query, b.qstart, b.qstop, "+")
dist, oo = range_distance(arange, brange, distmode="ee")
if dist > maxdist:
continue
atag = ">" if a.orientation == "+" else "<"
btag = ">" if b.orientation == "+" else "<"
g.add_edge(asub, bsub, atag, btag)
graph_to_agp(g, blastfile, subjectfasta, verbose=opts.verbose)
def fromblast(args):
"""
%prog fromblast blastfile subject.fasta
Generate path from BLAST file. If multiple subjects map to the same query,
an edge is constructed between them (with the link provided by the query).
The BLAST file MUST be filtered, chained, supermapped.
"""
from jcvi.formats.blast import sort
from jcvi.utils.range import range_distance
p = OptionParser(fromblast.__doc__)
p.add_option("--clique", default=False, action="store_true",
help="Populate clique instead of linear path [default: %default]")
p.add_option("--maxdist", default=100000, type="int",
help="Create edge within certain distance [default: %default]")
p.add_option("--verbose", default=False, action="store_true",
help="Print verbose reports to stdout [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
blastfile, subjectfasta = args
clique = opts.clique
maxdist = opts.maxdist
sort([blastfile, "--query"])
blast = BlastSlow(blastfile, sorted=True)
g = BiGraph()
for query, blines in groupby(blast, key=lambda x: x.query):
blines = list(blines)
iterator = combinations(blines, 2) if clique else pairwise(blines)
for a, b in iterator:
asub, bsub = a.subject, b.subject
if asub == bsub:
continue
arange = (a.query, a.qstart, a.qstop, "+")
brange = (b.query, b.qstart, b.qstop, "+")
dist, oo = range_distance(arange, brange, distmode="ee")
if dist > maxdist:
continue
atag = ">" if a.orientation == "+" else "<"
btag = ">" if b.orientation == "+" else "<"
g.add_edge(BiEdge(asub, bsub, atag, btag))
graph_to_agp(g, blastfile, subjectfasta, verbose=opts.verbose)
def fromblast(args):
"""
%prog fromblast blastfile subject.fasta
Generate path from BLAST file. If multiple subjects map to the same query,
an edge is constructed between them (with the link provided by the query).
The BLAST file MUST be filtered, chained, supermapped.
"""
from jcvi.formats.blast import sort
from jcvi.utils.range import range_distance
p = OptionParser(fromblast.__doc__)
p.add_option(
"--clique",
default=False,
action="store_true",
help="Populate clique instead of linear path [default: %default]")
p.add_option(
"--maxdist",
default=100000,
type="int",
help="Create edge within certain distance [default: %default]")
p.add_option("--verbose",
default=False,
action="store_true",
help="Print verbose reports to stdout [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
blastfile, subjectfasta = args
clique = opts.clique
maxdist = opts.maxdist
sort([blastfile, "--query"])
blast = BlastSlow(blastfile, sorted=True)
g = BiGraph()
for query, blines in groupby(blast, key=lambda x: x.query):
blines = list(blines)
iterator = combinations(blines, 2) if clique else pairwise(blines)
for a, b in iterator:
asub, bsub = a.subject, b.subject
if asub == bsub:
continue
arange = (a.query, a.qstart, a.qstop, "+")
brange = (b.query, b.qstart, b.qstop, "+")
dist, oo = range_distance(arange, brange, distmode="ee")
if dist > maxdist:
continue
atag = ">" if a.orientation == "+" else "<"
btag = ">" if b.orientation == "+" else "<"
g.add_edge(BiEdge(asub, bsub, atag, btag))
g.write("graph.txt")
#g.draw("graph.pdf")
logging.debug(str(g))
paths = []
for path in g.iter_paths():
m, oo = g.path(path)
if len(oo) == 1: # Singleton path
continue
paths.append(oo)
if opts.verbose:
print m
print oo
npaths = len(paths)
ntigs = sum(len(x) for x in paths)
logging.debug("Graph decomposed to {0} paths with {1} components.".\
format(npaths, ntigs))
agpfile = blastfile + ".agp"
sizes = Sizes(subjectfasta)
fwagp = open(agpfile, "w")
scaffolded = set()
for i, oo in enumerate(paths):
ctgorder = [(str(ctg), ("+" if strand else "-")) \
for ctg, strand in oo]
scaffolded |= set(ctg for ctg, strand in ctgorder)
object = "pmol_{0:04d}".format(i)
order_to_agp(object, ctgorder, sizes.mapping, fwagp)
# Get the singletons as well
nsingletons = 0
for ctg, size in sizes.iter_sizes():
if ctg in scaffolded:
continue
ctgorder = [(ctg, "+")]
object = ctg
order_to_agp(object, ctgorder, sizes.mapping, fwagp)
nsingletons += 1
logging.debug("Written {0} unscaffolded singletons.".format(nsingletons))
fwagp.close()
logging.debug("AGP file written to `{0}`.".format(agpfile))
def supermap(blast_file, filter="intersection", dialect="blast", clip=0):
# filter by query
if filter != "ref":
logging.debug("filter by query")
ranges = list(
BlastOrCoordsLine(blast_file,
filter="query",
dialect=dialect,
clip=clip))
query_selected, query_score = range_chain(ranges)
query_idx = set(x.id for x in query_selected)
# filter by ref
if filter != "query":
logging.debug("filter by ref")
ranges = list(
BlastOrCoordsLine(blast_file,
filter="ref",
dialect=dialect,
clip=clip))
ref_selected, ref_score = range_chain(ranges)
ref_idx = set(x.id for x in ref_selected)
if filter == "ref":
selected_idx = ref_idx
elif filter == "query":
selected_idx = query_idx
elif filter == "intersection":
logging.debug("perform intersection")
selected_idx = ref_idx & query_idx
elif filter == "union":
logging.debug("perform union")
selected_idx = ref_idx | query_idx
assert len(selected_idx) != 0
# selected_idx is in fact the lineno in the BLAST file
fp = open(blast_file)
if filter == "intersection":
tag = ""
else:
tag = "." + filter
supermapfile = blast_file + tag + ".supermap"
fw = open(supermapfile, "w")
selected_idx = iter(sorted(selected_idx))
selected = next(selected_idx)
for i, row in enumerate(fp):
if i < selected:
continue
print(row.rstrip(), file=fw)
try:
selected = next(selected_idx)
except StopIteration:
break
logging.debug("Write output file to `{0}`".format(supermapfile))
fw.close()
from jcvi.formats.blast import sort
ofilter = "ref" if filter == "ref" else "query"
args = [supermapfile, "--" + ofilter]
if dialect == "coords":
args += ["--coords"]
sort(args)
return supermapfile
def supermap(blast_file, filter="intersection", dialect="blast", clip=0):
# filter by query
if filter != "ref":
logging.debug("filter by query")
ranges = list(BlastOrCoordsLine(blast_file, filter="query",
dialect=dialect, clip=clip))
query_selected, query_score = range_chain(ranges)
query_idx = set(x.id for x in query_selected)
# filter by ref
if filter != "query":
logging.debug("filter by ref")
ranges = list(BlastOrCoordsLine(blast_file, filter="ref",
dialect=dialect, clip=clip))
ref_selected, ref_score = range_chain(ranges)
ref_idx = set(x.id for x in ref_selected)
if filter == "ref":
selected_idx = ref_idx
elif filter == "query":
selected_idx = query_idx
elif filter == "intersection":
logging.debug("perform intersection")
selected_idx = ref_idx & query_idx
elif filter == "union":
logging.debug("perform union")
selected_idx = ref_idx | query_idx
assert len(selected_idx) != 0
# selected_idx is in fact the lineno in the BLAST file
fp = open(blast_file)
if filter == "intersection":
tag = ""
else:
tag = "." + filter
supermapfile = blast_file + tag + ".supermap"
fw = open(supermapfile, "w")
selected_idx = iter(sorted(selected_idx))
selected = selected_idx.next()
for i, row in enumerate(fp):
if i < selected:
continue
print >> fw, row.rstrip()
try:
selected = selected_idx.next()
except StopIteration:
break
logging.debug("Write output file to `{0}`".format(supermapfile))
fw.close()
from jcvi.formats.blast import sort
ofilter = "ref" if filter == "ref" else "query"
args = [supermapfile, "--" + ofilter]
if dialect == "coords":
args += ["--coords"]
sort(args)
return supermapfile
def fromblast(args):
"""
%prog fromblast blastfile subject.fasta
Generate path from BLAST file. If multiple subjects map to the same query,
an edge is constructed between them (with the link provided by the query).
The BLAST file MUST be filtered, chained, supermapped.
"""
from jcvi.formats.blast import sort
from jcvi.utils.range import range_distance
p = OptionParser(fromblast.__doc__)
p.add_option("--clique", default=False, action="store_true",
help="Populate clique instead of linear path [default: %default]")
p.add_option("--maxdist", default=100000, type="int",
help="Create edge within certain distance [default: %default]")
p.add_option("--verbose", default=False, action="store_true",
help="Print verbose reports to stdout [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
blastfile, subjectfasta = args
clique = opts.clique
maxdist = opts.maxdist
sort([blastfile, "--query"])
blast = BlastSlow(blastfile, sorted=True)
g = BiGraph()
for query, blines in groupby(blast, key=lambda x: x.query):
blines = list(blines)
iterator = combinations(blines, 2) if clique else pairwise(blines)
for a, b in iterator:
asub, bsub = a.subject, b.subject
if asub == bsub:
continue
arange = (a.query, a.qstart, a.qstop, "+")
brange = (b.query, b.qstart, b.qstop, "+")
dist, oo = range_distance(arange, brange, distmode="ee")
if dist > maxdist:
continue
atag = ">" if a.orientation == "+" else "<"
btag = ">" if b.orientation == "+" else "<"
g.add_edge(BiEdge(asub, bsub, atag, btag))
g.write("graph.txt")
#g.draw("graph.pdf")
logging.debug(str(g))
paths = []
for path in g.iter_paths():
m, oo = g.path(path)
if len(oo) == 1: # Singleton path
continue
paths.append(oo)
if opts.verbose:
print m
print oo
npaths = len(paths)
ntigs = sum(len(x) for x in paths)
logging.debug("Graph decomposed to {0} paths with {1} components.".\
format(npaths, ntigs))
agpfile = blastfile + ".agp"
sizes = Sizes(subjectfasta)
fwagp = open(agpfile, "w")
scaffolded = set()
for i, oo in enumerate(paths):
ctgorder = [(str(ctg), ("+" if strand else "-")) \
for ctg, strand in oo]
scaffolded |= set(ctg for ctg, strand in ctgorder)
object = "pmol_{0:04d}".format(i)
order_to_agp(object, ctgorder, sizes.mapping, fwagp)
# Get the singletons as well
nsingletons = 0
for ctg, size in sizes.iter_sizes():
if ctg in scaffolded:
continue
ctgorder = [(ctg, "+")]
object = ctg
order_to_agp(object, ctgorder, sizes.mapping, fwagp)
nsingletons += 1
logging.debug("Written {0} unscaffolded singletons.".format(nsingletons))
fwagp.close()
logging.debug("AGP file written to `{0}`.".format(agpfile))