def bed2chain(args):
from maize.formats.sizes import Sizes
tdic = Sizes(args.tsize)
qdic = Sizes(args.qsize)
firstline = True
cid0, tName0, qName0, srd0, locs = '', '', '', '', []
for line in must_open(args.fi):
line = line.rstrip("\n")
if not line:
continue
tName, tStart, tEnd, srd, qName, qStart, qEnd, cid = line.split()[:8]
tStart, tEnd, qStart, qEnd = int(tStart), int(tEnd), int(qStart), int(qEnd)
if firstline:
cid0, tName0, qName0, srd0 = cid, tName, qName, srd
locs.append([tStart, tEnd, qStart, qEnd])
firstline = False
elif cid0 == cid:
assert tName == tName0 and qName == qName0 and srd == srd0, "inconsistent info in chain"
locs.append([tStart, tEnd, qStart, qEnd])
else:
print_chain(cid0, tName0, qName0, srd0, tdic.get_size(tName0), qdic.get_size(qName0), locs)
cid0, tName0, qName0, srd0 = cid, tName, qName, srd
locs = [[tStart, tEnd, qStart, qEnd]]
print_chain(cid0, tName0, qName0, srd0, tdic.get_size(tName0), qdic.get_size(qName0), locs)
def bed2chain(args):
from jcvi.formats.sizes import Sizes
tdic = Sizes(args.tsize)
qdic = Sizes(args.qsize)
firstline = True
cid0, tName0, qName0, srd0, locs = '', '', '', '', []
for line in must_open(args.fi):
line = line.rstrip("\n")
if not line:
continue
tName, tStart, tEnd, srd, qName, qStart, qEnd, cid = line.split()[:8]
tStart, tEnd, qStart, qEnd = int(tStart), int(tEnd), int(qStart), int(qEnd)
if firstline:
cid0, tName0, qName0, srd0 = cid, tName, qName, srd
locs.append([tStart, tEnd, qStart, qEnd])
firstline = False
elif cid0 == cid:
assert tName == tName0 and qName == qName0 and srd == srd0, "inconsistent info in chain"
locs.append([tStart, tEnd, qStart, qEnd])
else:
print_chain(cid0, tName0, qName0, srd0, tdic.get_size(tName0), qdic.get_size(qName0), locs)
cid0, tName0, qName0, srd0 = cid, tName, qName, srd
locs = [[tStart, tEnd, qStart, qEnd]]
print_chain(cid0, tName0, qName0, srd0, tdic.get_size(tName0), qdic.get_size(qName0), locs)
def main():
p = OptionParser(__doc__)
p.add_option("--order",
help="The order to plot the tracks, comma-separated")
opts, args, iopts = p.set_image_options()
if len(args) != 3:
sys.exit(not p.print_help())
chr, sizes, datadir = args
order = opts.order
hlsuffix = opts.hlsuffix
if order:
order = order.split(",")
sizes = Sizes(sizes)
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
canvas = (.12, .35, .8, .35)
chr_size = sizes.get_size(chr)
c = Coverage(fig, root, canvas, chr, (0, chr_size), datadir,
order=order, hlsuffix=hlsuffix)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = chr + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def main():
p = OptionParser(__doc__)
p.add_option("--order",
help="The order to plot the tracks, comma-separated")
opts, args, iopts = p.set_image_options()
if len(args) != 3:
sys.exit(not p.print_help())
chr, sizes, datadir = args
order = opts.order
hlsuffix = opts.hlsuffix
if order:
order = order.split(",")
sizes = Sizes(sizes)
fig = plt.figure(1, (iopts.w, iopts.h))
root = fig.add_axes([0, 0, 1, 1])
canvas = (.12, .35, .8, .35)
chr_size = sizes.get_size(chr)
Coverage(fig,
root,
canvas,
chr, (0, chr_size),
datadir,
order=order,
hlsuffix=hlsuffix)
root.set_xlim(0, 1)
root.set_ylim(0, 1)
root.set_axis_off()
image_name = chr + "." + iopts.format
savefig(image_name, dpi=iopts.dpi, iopts=iopts)
def coordT(args):
sizes = Sizes(args.fs)
for line in must_open(args.fi):
if not re.match(r'\d+', line[0]):
continue
p = PslLine(line)
tnames = p.tName.split("-")
if len(tnames) == 3:
x = p.tName
p.tName, tosStart, tosEnd = tnames[0], int(tnames[1]), int(
tnames[2])
assert tosEnd - tosStart + 1 == p.tSize
cSize = sizes.get_size(p.tName)
p.tStart += tosStart - 1
p.tEnd += tosStart - 1
p.tStarts = [x + tosStart - 1 for x in p.tStarts]
p.tSize = cSize
print(str(p))
def coordQ(args):
sizes = Sizes(args.fs)
for line in must_open(args.fi):
if not re.match(r'\d+', line[0]):
continue
p = PslLine(line)
qnames = p.qName.split("-")
if len(qnames) == 3:
x = p.qName
p.qName, qosStart, qosEnd = qnames[0], int(qnames[1]), int(
qnames[2])
assert qosEnd - qosStart + 1 == p.qSize
cSize = sizes.get_size(p.qName)
p.qStart += qosStart - 1
p.qEnd += qosStart - 1
if p.qstrand == "-":
p.qStarts = [x + cSize - qosEnd for x in p.qStarts]
else:
p.qStarts = [x + qosStart - 1 for x in p.qStarts]
p.qSize = cSize
print(str(p))
def bambus(args):
"""
%prog bambus bambus.bed bambus.mates total.fasta
Insert unplaced scaffolds based on mates.
"""
from jcvi.formats.bed import BedLine
from jcvi.formats.posmap import MatesFile
p = OptionParser(bambus.__doc__)
p.add_option(
"--prefix",
default="scaffold",
help="Prefix of the unplaced scaffolds",
)
p.add_option(
"--minlinks",
default=3,
type="int",
help="Minimum number of links to place",
)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
bedfile, matesfile, fastafile = args
pf = matesfile.rsplit(".", 1)[0]
logfile = pf + ".log"
log = open(logfile, "w")
mf = MatesFile(matesfile)
maxdist = max(x.max for x in mf.libraries.values())
logging.debug("Max separation: {0}".format(maxdist))
prefix = opts.prefix
minlinks = opts.minlinks
is_unplaced = lambda x: x.startswith(prefix)
bed = Bed(bedfile, sorted=False)
beds = []
unplaced = defaultdict(list)
for a, b in pairwise(bed):
aname, bname = a.accn, b.accn
aseqid, bseqid = a.seqid, b.seqid
if aname not in mf:
continue
pa, la = mf[aname]
if pa != bname:
continue
ia = is_unplaced(aseqid)
ib = is_unplaced(bseqid)
if ia == ib:
continue
if ia:
a, b = b, a
unplaced[b.seqid].append((a, b))
beds.extend([a, b])
sizes = Sizes(fastafile)
candidatebed = Bed()
cbeds = []
# For each unplaced scaffold, find most likely placement and orientation
for scf, beds in sorted(unplaced.items()):
print(file=log)
ranges = []
for a, b in beds:
aname, astrand = a.accn, a.strand
bname, bstrand = b.accn, b.strand
aseqid, bseqid = a.seqid, b.seqid
pa, lib = mf[aname]
print(a, file=log)
print(b, file=log)
flip_b = astrand == bstrand
fbstrand = "-" if flip_b else "+"
if flip_b:
b.reverse_complement(sizes)
lmin, lmax = lib.min, lib.max
L = sizes.get_size(scf)
assert astrand in ("+", "-")
if astrand == "+":
offset = a.start - b.end
sstart, sstop = offset + lmin, offset + lmax
else:
offset = a.end - b.start + L
sstart, sstop = offset - lmax, offset - lmin
# Prevent out of range error
size = sizes.get_size(aseqid)
sstart = max(0, sstart)
sstop = max(0, sstop)
sstart = min(size - 1, sstart)
sstop = min(size - 1, sstop)
start_range = (aseqid, sstart, sstop, scf, 1, fbstrand)
print("*" + "\t".join(str(x) for x in start_range), file=log)
ranges.append(start_range)
mranges = [x[:3] for x in ranges]
# Determine placement by finding the interval with the most support
rd = ranges_depth(mranges, sizes.mapping, verbose=False)
alldepths = []
for depth in rd:
alldepths.extend(depth)
print(alldepths, file=log)
maxdepth = max(alldepths, key=lambda x: x[-1])[-1]
if maxdepth < minlinks:
print("Insufficient links ({0} < {1})".format(maxdepth, minlinks), file=log)
continue
candidates = [x for x in alldepths if x[-1] == maxdepth]
nseqids = len(set(x[0] for x in candidates))
if nseqids != 1:
msg = "Multiple conflicting candidates found"
print(msg, file=log)
continue
seqid, mmin, mmax, depth = candidates[0]
mmin, mmax = range_minmax([x[1:3] for x in candidates])
if mmin >= mmax:
msg = "Invalid (min, max) range"
print("Invalid (min, max) range", file=log)
continue
if (mmax - mmin) > maxdist:
msg = "(min, max) distance greater than library maxdist"
print(msg, file=log)
continue
# Determine orientation by voting
nplus, nminus = 0, 0
arange = (seqid, mmin, mmax)
for sid, start, end, sf, sc, fbstrand in ranges:
brange = (sid, start, end)
if range_overlap(arange, brange):
if fbstrand == "+":
nplus += 1
else:
nminus += 1
fbstrand = "+" if nplus >= nminus else "-"
candidate = (seqid, mmin, mmax, scf, depth, fbstrand)
bedline = BedLine("\t".join((str(x) for x in candidate)))
cbeds.append(bedline)
print("Plus: {0}, Minus: {1}".format(nplus, nminus), file=log)
print(candidate, file=log)
candidatebed.extend(cbeds)
logging.debug("A total of {0} scaffolds can be placed.".format(len(candidatebed)))
log.close()
candidatebedfile = pf + ".candidate.bed"
candidatebed.print_to_file(candidatebedfile, sorted=True)
def bambus(args):
"""
%prog bambus bambus.bed bambus.mates total.fasta
Insert unplaced scaffolds based on mates.
"""
from jcvi.utils.iter import pairwise
from jcvi.formats.posmap import MatesFile
p = OptionParser(bambus.__doc__)
p.add_option("--prefix", default="scaffold",
help="Prefix of the unplaced scaffolds [default: %default]")
p.add_option("--minlinks", default=3, type="int",
help="Minimum number of links to place [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
bedfile, matesfile, fastafile = args
pf = matesfile.rsplit(".", 1)[0]
logfile = pf + ".log"
log = open(logfile, "w")
mf = MatesFile(matesfile)
maxdist = max(x.max for x in mf.libraries.values())
logging.debug("Max separation: {0}".format(maxdist))
prefix = opts.prefix
minlinks = opts.minlinks
is_unplaced = lambda x: x.startswith(prefix)
bed = Bed(bedfile, sorted=False)
beds = []
unplaced = defaultdict(list)
for a, b in pairwise(bed):
aname, bname = a.accn, b.accn
aseqid, bseqid = a.seqid, b.seqid
if aname not in mf:
continue
pa, la = mf[aname]
if pa != bname:
continue
ia = is_unplaced(aseqid)
ib = is_unplaced(bseqid)
if ia == ib:
continue
if ia:
a, b = b, a
unplaced[b.seqid].append((a, b))
beds.extend([a, b])
sizes = Sizes(fastafile)
candidatebed = Bed()
cbeds = []
# For each unplaced scaffold, find most likely placement and orientation
for scf, beds in sorted(unplaced.items()):
print >> log
ranges = []
for a, b in beds:
aname, astrand = a.accn, a.strand
bname, bstrand = b.accn, b.strand
aseqid, bseqid = a.seqid, b.seqid
pa, lib = mf[aname]
print >> log, a
print >> log, b
flip_b = (astrand == bstrand)
fbstrand = '-' if flip_b else '+'
if flip_b:
b.reverse_complement(sizes)
lmin, lmax = lib.min, lib.max
L = sizes.get_size(scf)
assert astrand in ('+', '-')
if astrand == '+':
offset = a.start - b.end
sstart, sstop = offset + lmin, offset + lmax
else:
offset = a.end - b.start + L
sstart, sstop = offset - lmax, offset - lmin
# Prevent out of range error
size = sizes.get_size(aseqid)
sstart = max(0, sstart)
sstop = max(0, sstop)
sstart = min(size - 1, sstart)
sstop = min(size - 1, sstop)
start_range = (aseqid, sstart, sstop, scf, 1, fbstrand)
print >> log, "*" + "\t".join(str(x) for x in start_range)
ranges.append(start_range)
mranges = [x[:3] for x in ranges]
# Determine placement by finding the interval with the most support
rd = ranges_depth(mranges, sizes.mapping, verbose=False)
alldepths = []
for depth in rd:
alldepths.extend(depth)
print >> log, alldepths
maxdepth = max(alldepths, key=lambda x: x[-1])[-1]
if maxdepth < minlinks:
print >> log, "Insufficient links ({0} < {1})".format(maxdepth, minlinks)
continue
candidates = [x for x in alldepths if x[-1] == maxdepth]
nseqids = len(set(x[0] for x in candidates))
msg = "Multiple conflicting candidates found"
if nseqids != 1:
print >> log, msg
continue
seqid, mmin, mmax, depth = candidates[0]
mmin, mmax = range_minmax([x[1:3] for x in candidates])
if (mmax - mmin) > maxdist:
print >> log, msg
continue
# Determine orientation by voting
nplus, nminus = 0, 0
arange = (seqid, mmin, mmax)
for sid, start, end, sf, sc, fbstrand in ranges:
brange = (sid, start, end)
if range_overlap(arange, brange):
if fbstrand == '+':
nplus += 1
else:
nminus += 1
fbstrand = '+' if nplus >= nminus else '-'
candidate = (seqid, mmin, mmax, scf, depth, fbstrand)
bedline = BedLine("\t".join((str(x) for x in candidate)))
cbeds.append(bedline)
print >> log, "Plus: {0}, Minus: {1}".format(nplus, nminus)
print >> log, candidate
candidatebed.extend(cbeds)
logging.debug("A total of {0} scaffolds can be placed.".\
format(len(candidatebed)))
log.close()
candidatebedfile = pf + ".candidate.bed"
candidatebed.print_to_file(candidatebedfile, sorted=True)
