def liftover(args):
"""
%prog liftover agpfile bedfile
Given coordinates in components, convert to the coordinates in chromosomes.
"""
p = OptionParser(liftover.__doc__)
p.add_option("--prefix",
default=False,
action="store_true",
help="Prepend prefix to accn names [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(p.print_help())
agpfile, bedfile = args
agp = AGP(agpfile).order
bed = Bed(bedfile)
newbed = Bed()
for b in bed:
component = b.seqid
if component not in agp:
newbed.append(b)
continue
i, a = agp[component]
assert a.component_beg < a.component_end
arange = a.component_beg, a.component_end
assert b.start < b.end
brange = b.start, b.end
st = range_intersect(arange, brange)
if not st:
continue
start, end = st
assert start <= end
if a.orientation == '-':
d = a.object_end + a.component_beg
s, t = d - end, d - start
else:
d = a.object_beg - a.component_beg
s, t = d + start, d + end
name = b.accn.replace(" ", "_")
if opts.prefix:
name = component + "_" + name
bline = "\t".join(str(x) for x in (a.object, s - 1, t, name))
newbed.append(BedLine(bline))
newbed.print_to_file(sorted=True)
def liftover(args):
"""
%prog liftover agpfile bedfile
Given coordinates in components, convert to the coordinates in chromosomes.
"""
p = OptionParser(liftover.__doc__)
p.add_option("--prefix", default=False, action="store_true",
help="Prepend prefix to accn names [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(p.print_help())
agpfile, bedfile = args
agp = AGP(agpfile).order
bed = Bed(bedfile)
newbed = Bed()
for b in bed:
component = b.seqid
if component not in agp:
newbed.append(b)
continue
i, a = agp[component]
assert a.component_beg < a.component_end
arange = a.component_beg, a.component_end
assert b.start < b.end
brange = b.start, b.end
st = range_intersect(arange, brange)
if not st:
continue
start, end = st
assert start <= end
if a.orientation == '-':
d = a.object_end + a.component_beg
s, t = d - end, d - start
else:
d = a.object_beg - a.component_beg
s, t = d + start, d + end
name = b.accn.replace(" ", "_")
if opts.prefix:
name = component + "_" + name
bline = "\t".join(str(x) for x in (a.object, s - 1, t, name))
newbed.append(BedLine(bline))
newbed.sort(key=newbed.nullkey)
newbed.print_to_file()
def refine(args):
"""
%prog refine bedfile1 bedfile2 refinedbed
Refine bed file using a second bed file. The final bed is keeping all the
intervals in bedfile1, but refined by bedfile2 whenever they have
intersection.
"""
p = OptionParser(refine.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
abedfile, bbedfile, refinedbed = args
fw = open(refinedbed, "w")
intersected = refined = 0
for a, b in intersectBed_wao(abedfile, bbedfile):
if b is None:
print >> fw, a
continue
intersected += 1
aspan_before = a.span
arange = (a.start, a.end)
brange = (b.start, b.end)
irange = range_intersect(arange, brange)
a.start, a.end = irange
aspan_after = a.span
if aspan_before > aspan_after:
refined += 1
print >> fw, a
fw.close()
print >> sys.stderr, "Total intersected: {0}".format(intersected)
print >> sys.stderr, "Total refined: {0}".format(refined)
summary([abedfile])
summary([refinedbed])
def refine(args):
"""
%prog refine bedfile1 bedfile2 refinedbed
Refine bed file using a second bed file. The final bed is keeping all the
intervals in bedfile1, but refined by bedfile2 whenever they have
intersection.
"""
p = OptionParser(refine.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
abedfile, bbedfile, refinedbed = args
fw = open(refinedbed, "w")
intersected = refined = 0
for a, b in intersectBed_wao(abedfile, bbedfile):
if b is None:
print >> fw, a
continue
intersected += 1
aspan_before = a.span
arange = (a.start, a.end)
brange = (b.start, b.end)
irange = range_intersect(arange, brange)
a.start, a.end = irange
aspan_after = a.span
if aspan_before > aspan_after:
refined += 1
print >> fw, a
fw.close()
print >> sys.stderr, "Total intersected: {0}".format(intersected)
print >> sys.stderr, "Total refined: {0}".format(refined)
summary([abedfile])
summary([refinedbed])
def connect(args):
"""
%prog connect assembly.fasta read_mapping.blast
Connect contigs using long reads.
"""
p = OptionParser(connect.__doc__)
p.add_option(
"--clip",
default=2000,
type="int",
help="Only consider end of contigs",
)
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 "<"
g.add_edge(asub, bsub, atag, btag)
graph_to_agp(g, blastfile, fastafile, verbose=False)
def mask(args):
"""
%prog mask agpfile bedfile
Mask given ranges in componets to gaps.
"""
p = OptionParser(mask.__doc__)
p.add_option("--split", default=False, action="store_true",
help="Split object and create new names [default: %default]")
p.add_option("--log", default=False, action="store_true",
help="Write verbose logs to .masklog file [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(p.print_help())
agpfile, bedfile = args
agp = AGP(agpfile)
bed = Bed(bedfile)
simple_agp = agp.order
# agp lines to replace original ones, keyed by the component
agp_fixes = defaultdict(list)
newagpfile = agpfile.replace(".agp", ".masked.agp")
logfile = bedfile.replace(".bed", ".masklog")
fw = open(newagpfile, "w")
if opts.log:
fwlog = open(logfile, "w")
for component, intervals in bed.sub_beds():
if opts.log:
print >> fwlog, "\n".join(str(x) for x in intervals)
i, a = simple_agp[component]
object = a.object
component_span = a.component_span
orientation = a.orientation
if opts.log:
print >> fwlog, a
assert a.component_beg, a.component_end
arange = a.component_beg, a.component_end
# Make sure `ivs` contain DISJOINT ranges, and located within `arange`
ivs = []
for i in intervals:
iv = range_intersect(arange, (i.start, i.end))
if iv is not None:
ivs.append(iv)
# Sort the ends of `ivs` as well as the arange
arange = a.component_beg - 1, a.component_end + 1
endpoints = sorted(flatten(ivs + [arange]))
# reverse if component on negative strand
if orientation == '-':
endpoints.reverse()
sum_of_spans = 0
# assign complements as sequence components
for i, (a, b) in enumerate(pairwise(endpoints)):
if orientation == '-':
a, b = b, a
if orientation not in ('+', '-'):
orientation = '+'
oid = object + "_{0}".format(i / 2) if opts.split else object
aline = [oid, 0, 0, 0]
if i % 2 == 0:
cspan = b - a - 1
aline += ['D', component, a + 1, b - 1, orientation]
is_gap = False
else:
cspan = b - a + 1
aline += ["N", cspan, "fragment", "yes"]
is_gap = True
if cspan <= 0:
continue
sum_of_spans += cspan
aline = "\t".join(str(x) for x in aline)
if not (opts.split and is_gap):
agp_fixes[component].append(aline)
if opts.log:
print >> fwlog, aline
assert component_span == sum_of_spans
if opts.log:
print >> fwlog
# Finally write the masked agp
for a in agp:
if not a.is_gap and a.component_id in agp_fixes:
print >> fw, "\n".join(agp_fixes[a.component_id])
else:
print >> fw, a
fw.close()
# Reindex
idxagpfile = reindex([newagpfile])
shutil.move(idxagpfile, newagpfile)
return newagpfile
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 mask(args):
"""
%prog mask agpfile bedfile
Mask given ranges in components to gaps.
"""
p = OptionParser(mask.__doc__)
p.add_option("--split",
default=False,
action="store_true",
help="Split object and create new names [default: %default]")
p.add_option(
"--log",
default=False,
action="store_true",
help="Write verbose logs to .masklog file [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(p.print_help())
agpfile, bedfile = args
agp = AGP(agpfile)
bed = Bed(bedfile)
simple_agp = agp.order
# agp lines to replace original ones, keyed by the component
agp_fixes = defaultdict(list)
newagpfile = agpfile.replace(".agp", ".masked.agp")
logfile = bedfile.replace(".bed", ".masklog")
fw = open(newagpfile, "w")
if opts.log:
fwlog = open(logfile, "w")
for component, intervals in bed.sub_beds():
if opts.log:
print >> fwlog, "\n".join(str(x) for x in intervals)
i, a = simple_agp[component]
object = a.object
component_span = a.component_span
orientation = a.orientation
if opts.log:
print >> fwlog, a
assert a.component_beg, a.component_end
arange = a.component_beg, a.component_end
# Make sure `ivs` contain DISJOINT ranges, and located within `arange`
ivs = []
for i in intervals:
iv = range_intersect(arange, (i.start, i.end))
if iv is not None:
ivs.append(iv)
# Sort the ends of `ivs` as well as the arange
arange = a.component_beg - 1, a.component_end + 1
endpoints = sorted(flatten(ivs + [arange]))
# reverse if component on negative strand
if orientation == '-':
endpoints.reverse()
sum_of_spans = 0
# assign complements as sequence components
for i, (a, b) in enumerate(pairwise(endpoints)):
if orientation == '-':
a, b = b, a
if orientation not in ('+', '-'):
orientation = '+'
oid = object + "_{0}".format(i / 2) if opts.split else object
aline = [oid, 0, 0, 0]
if i % 2 == 0:
cspan = b - a - 1
aline += ['D', component, a + 1, b - 1, orientation]
is_gap = False
else:
cspan = b - a + 1
aline += ["N", cspan, "fragment", "yes"]
is_gap = True
if cspan <= 0:
continue
sum_of_spans += cspan
aline = "\t".join(str(x) for x in aline)
if not (opts.split and is_gap):
agp_fixes[component].append(aline)
if opts.log:
print >> fwlog, aline
#assert component_span == sum_of_spans
if opts.log:
print >> fwlog
# Finally write the masked agp
for a in agp:
if not a.is_gap and a.component_id in agp_fixes:
print >> fw, "\n".join(agp_fixes[a.component_id])
else:
print >> fw, a
fw.close()
# Reindex
idxagpfile = reindex([newagpfile])
shutil.move(idxagpfile, newagpfile)
return newagpfile
def test_range_intersect(a, b, expected):
from jcvi.utils.range import range_intersect
assert range_intersect(a, b) == expected
