def nucmer(args):
"""
%prog nucmer mappings.bed MTR.fasta assembly.fasta chr1 3
Select specific chromosome region based on MTR mapping. The above command
will extract chr1:2,000,001-3,000,000.
"""
p = OptionParser(nucmer.__doc__)
opts, args = p.parse_args(args)
if len(args) != 5:
sys.exit(not p.print_help())
mapbed, mtrfasta, asmfasta, chr, idx = args
idx = int(idx)
m1 = 1000000
bedfile = "sample.bed"
bed = Bed()
bed.add("\t".join(str(x) for x in (chr, (idx - 1) * m1, idx * m1)))
bed.print_to_file(bedfile)
cmd = "intersectBed -a {0} -b {1} -nonamecheck -sorted | cut -f4".format(mapbed, bedfile)
idsfile = "query.ids"
sh(cmd, outfile=idsfile)
sfasta = fastaFromBed(bedfile, mtrfasta)
qfasta = "query.fasta"
cmd = "faSomeRecords {0} {1} {2}".format(asmfasta, idsfile, qfasta)
sh(cmd)
cmd = "nucmer {0} {1}".format(sfasta, qfasta)
sh(cmd)
mummerplot_main(["out.delta", "--refcov=0"])
sh("mv out.pdf {0}.{1}.pdf".format(chr, idx))
def bed(args):
"""
%prog bed anchorsfile
Convert ANCHORS file to BED format.
"""
from collections import defaultdict
from jcvi.compara.synteny import AnchorFile, check_beds
from jcvi.formats.bed import Bed
from jcvi.formats.base import get_number
p = OptionParser(bed.__doc__)
p.add_option("--switch", default=False, action="store_true",
help="Switch reference and aligned map elements")
p.add_option("--scale", type="float",
help="Scale the aligned map distance by factor")
p.set_beds()
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
anchorsfile, = args
switch = opts.switch
scale = opts.scale
ac = AnchorFile(anchorsfile)
pairs = defaultdict(list)
for a, b, block_id in ac.iter_pairs():
pairs[a].append(b)
qbed, sbed, qorder, sorder, is_self = check_beds(anchorsfile, p, opts)
bd = Bed()
for q in qbed:
qseqid, qstart, qend, qaccn = q.seqid, q.start, q.end, q.accn
if qaccn not in pairs:
continue
for s in pairs[qaccn]:
si, s = sorder[s]
sseqid, sstart, send, saccn = s.seqid, s.start, s.end, s.accn
if switch:
qseqid, sseqid = sseqid, qseqid
qstart, sstart = sstart, qstart
qend, send = send, qend
qaccn, saccn = saccn, qaccn
if scale:
sstart /= scale
try:
newsseqid = get_number(sseqid)
except ValueError:
raise ValueError, "`{0}` is on `{1}` with no number to extract".\
format(saccn, sseqid)
bedline = "\t".join(str(x) for x in (qseqid, qstart - 1, qend,
"{0}:{1}".format(newsseqid, sstart)))
bd.add(bedline)
bd.print_to_file(filename=opts.outfile, sorted=True)
def nucmer(args):
"""
%prog nucmer mappings.bed MTR.fasta assembly.fasta chr1 3
Select specific chromosome region based on MTR mapping. The above command
will extract chr1:2,000,001-3,000,000.
"""
p = OptionParser(nucmer.__doc__)
opts, args = p.parse_args(args)
if len(args) != 5:
sys.exit(not p.print_help())
mapbed, mtrfasta, asmfasta, chr, idx = args
idx = int(idx)
m1 = 1000000
bedfile = "sample.bed"
bed = Bed()
bed.add("\t".join(str(x) for x in (chr, (idx - 1) * m1, idx * m1)))
bed.print_to_file(bedfile)
cmd = "intersectBed -a {0} -b {1} -nonamecheck -sorted | cut -f4".format(
mapbed, bedfile)
idsfile = "query.ids"
sh(cmd, outfile=idsfile)
sfasta = fastaFromBed(bedfile, mtrfasta)
qfasta = "query.fasta"
cmd = "faSomeRecords {0} {1} {2}".format(asmfasta, idsfile, qfasta)
sh(cmd)
cmd = "nucmer {0} {1}".format(sfasta, qfasta)
sh(cmd)
mummerplot_main(["out.delta", "--refcov=0"])
sh("mv out.pdf {0}.{1}.pdf".format(chr, idx))
def insert(args):
"""
%prog insert candidates.bed gaps.bed chrs.fasta unplaced.fasta
Insert scaffolds into assembly.
"""
from jcvi.formats.agp import mask, bed
from jcvi.formats.sizes import agp
p = OptionParser(insert.__doc__)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
candidates, gapsbed, chrfasta, unplacedfasta = args
refinedbed = refine([candidates, gapsbed])
sizes = Sizes(unplacedfasta).mapping
cbed = Bed(candidates)
corder = cbed.order
gbed = Bed(gapsbed)
gorder = gbed.order
gpbed = Bed()
gappositions = {} # (chr, start, end) => gapid
fp = open(refinedbed)
gap_to_scf = defaultdict(list)
seen = set()
for row in fp:
atoms = row.split()
if len(atoms) <= 6:
continue
unplaced = atoms[3]
strand = atoms[5]
gapid = atoms[9]
if gapid not in seen:
seen.add(gapid)
gi, gb = gorder[gapid]
gpbed.append(gb)
gappositions[(gb.seqid, gb.start, gb.end)] = gapid
gap_to_scf[gapid].append((unplaced, strand))
gpbedfile = "candidate.gaps.bed"
gpbed.print_to_file(gpbedfile, sorted=True)
agpfile = agp([chrfasta])
maskedagpfile = mask([agpfile, gpbedfile])
maskedbedfile = maskedagpfile.rsplit(".", 1)[0] + ".bed"
bed([maskedagpfile, "--outfile={0}".format(maskedbedfile)])
mbed = Bed(maskedbedfile)
finalbed = Bed()
for b in mbed:
sid = b.seqid
key = (sid, b.start, b.end)
if key not in gappositions:
finalbed.add("{0}\n".format(b))
continue
gapid = gappositions[key]
scfs = gap_to_scf[gapid]
# For scaffolds placed in the same gap, sort according to positions
scfs.sort(key=lambda x: corder[x[0]][1].start + corder[x[0]][1].end)
for scf, strand in scfs:
size = sizes[scf]
finalbed.add("\t".join(str(x) for x in (scf, 0, size, sid, 1000, strand)))
finalbedfile = "final.bed"
finalbed.print_to_file(finalbedfile)
# Clean-up
toclean = [gpbedfile, agpfile, maskedagpfile, maskedbedfile]
FileShredder(toclean)
def bed(args):
"""
%prog bed anchorsfile
Convert ANCHORS file to BED format.
"""
from collections import defaultdict
from jcvi.compara.synteny import AnchorFile, check_beds
from jcvi.formats.bed import Bed
from jcvi.formats.base import get_number
p = OptionParser(bed.__doc__)
p.add_option(
"--switch",
default=False,
action="store_true",
help="Switch reference and aligned map elements",
)
p.add_option(
"--scale", type="float", help="Scale the aligned map distance by factor"
)
p.set_beds()
p.set_outfile()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(anchorsfile,) = args
switch = opts.switch
scale = opts.scale
ac = AnchorFile(anchorsfile)
pairs = defaultdict(list)
for a, b, block_id in ac.iter_pairs():
pairs[a].append(b)
qbed, sbed, qorder, sorder, is_self = check_beds(anchorsfile, p, opts)
bd = Bed()
for q in qbed:
qseqid, qstart, qend, qaccn = q.seqid, q.start, q.end, q.accn
if qaccn not in pairs:
continue
for s in pairs[qaccn]:
si, s = sorder[s]
sseqid, sstart, send, saccn = s.seqid, s.start, s.end, s.accn
if switch:
qseqid, sseqid = sseqid, qseqid
qstart, sstart = sstart, qstart
qend, send = send, qend
qaccn, saccn = saccn, qaccn
if scale:
sstart /= scale
try:
newsseqid = get_number(sseqid)
except ValueError:
raise ValueError(
"`{0}` is on `{1}` with no number to extract".format(saccn, sseqid)
)
bedline = "\t".join(
str(x)
for x in (qseqid, qstart - 1, qend, "{0}:{1}".format(newsseqid, sstart))
)
bd.add(bedline)
bd.print_to_file(filename=opts.outfile, sorted=True)
def ancestral(args):
"""
%prog ancestral vplanifoliaA.vplanifoliaA.anchors > vplanifoliaA_blocks.bed
Paint 14 chromosomes following alpha WGD.
"""
p = OptionParser(ancestral.__doc__)
p.set_beds()
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(anchorsfile, ) = args
qbed, sbed, qorder, sorder, is_self = check_beds(anchorsfile, p, opts)
# We focus on the following chromosome pairs
target_pairs = {
(1, 1),
(1, 6),
(1, 8),
(1, 13),
(2, 4),
(3, 12),
(3, 14),
(5, 6),
(5, 8),
(7, 9),
(7, 11),
(9, 10),
(10, 11),
}
def get_target(achr, bchr):
if "chr" not in achr and "chr" not in bchr:
return None
achr, bchr = get_number(achr), get_number(bchr)
if achr > bchr:
achr, bchr = bchr, achr
if (achr, bchr) in target_pairs:
return achr, bchr
return None
def build_bedline(astart, aend, target_pair):
# target_name = "{:02d}-{:02d}".format(*target_pair)
target_name = [
str(x) for x in target_pair if x in (1, 2, 3, 5, 7, 10)
][0]
return "\t".join(
str(x)
for x in (astart.seqid, astart.start, aend.end, target_name))
# Iterate through the blocks, store any regions that has hits to one of the
# target_pairs
ac = AnchorFile(anchorsfile)
blocks = ac.blocks
outbed = Bed()
for i, block in enumerate(blocks):
a, b, scores = zip(*block)
a = [qorder[x] for x in a]
b = [sorder[x] for x in b]
astart, aend = min(a)[1], max(a)[1]
bstart, bend = min(b)[1], max(b)[1]
# Now convert to BED lines with new accn
achr, bchr = astart.seqid, bstart.seqid
target = get_target(achr, bchr)
if target is None:
continue
outbed.add(build_bedline(astart, aend, target))
outbed.add(build_bedline(bstart, bend, target))
outbed.print_to_file(sorted=True)
def insert(args):
"""
%prog insert candidates.bed gaps.bed chrs.fasta unplaced.fasta
Insert scaffolds into assembly.
"""
from jcvi.formats.agp import mask, bed
from jcvi.formats.sizes import agp
p = OptionParser(insert.__doc__)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
candidates, gapsbed, chrfasta, unplacedfasta = args
refinedbed = refine([candidates, gapsbed])
sizes = Sizes(unplacedfasta).mapping
cbed = Bed(candidates)
corder = cbed.order
gbed = Bed(gapsbed)
gorder = gbed.order
gpbed = Bed()
gappositions = {} # (chr, start, end) => gapid
fp = open(refinedbed)
gap_to_scf = defaultdict(list)
seen = set()
for row in fp:
atoms = row.split()
if len(atoms) <= 6:
continue
unplaced = atoms[3]
strand = atoms[5]
gapid = atoms[9]
if gapid not in seen:
seen.add(gapid)
gi, gb = gorder[gapid]
gpbed.append(gb)
gappositions[(gb.seqid, gb.start, gb.end)] = gapid
gap_to_scf[gapid].append((unplaced, strand))
gpbedfile = "candidate.gaps.bed"
gpbed.print_to_file(gpbedfile, sorted=True)
agpfile = agp([chrfasta])
maskedagpfile = mask([agpfile, gpbedfile])
maskedbedfile = maskedagpfile.rsplit(".", 1)[0] + ".bed"
bed([maskedagpfile, "--outfile={0}".format(maskedbedfile)])
mbed = Bed(maskedbedfile)
finalbed = Bed()
for b in mbed:
sid = b.seqid
key = (sid, b.start, b.end)
if key not in gappositions:
finalbed.add("{0}\n".format(b))
continue
gapid = gappositions[key]
scfs = gap_to_scf[gapid]
# For scaffolds placed in the same gap, sort according to positions
scfs.sort(key=lambda x: corder[x[0]][1].start + corder[x[0]][1].end)
for scf, strand in scfs:
size = sizes[scf]
finalbed.add("\t".join(str(x) for x in \
(scf, 0, size, sid, 1000, strand)))
finalbedfile = "final.bed"
finalbed.print_to_file(finalbedfile)
# Clean-up
toclean = [gpbedfile, agpfile, maskedagpfile, maskedbedfile]
FileShredder(toclean)
def extract(args):
import re
from jcvi.formats.bed import Bed
db = ""
if op.isfile(args.db):
db = Fasta(args.db)
else:
f_db = "%s/data/%s/10_genome.fna" % (os.environ["genome"], args.db)
assert op.isfile(f_db), "cannot find %s" % args.db
db = Fasta(f_db)
reg1 = re.compile("^([\w\-]+)\:([\d,]+)(\-|\.{1,2})([\d,]+)$")
reg2 = re.compile("^([\w\-]+)$")
bed = Bed()
if op.isfile(args.loc):
if args.list:
fho = must_open(args.loc, 'r')
for line in fho:
sid = line.strip()
beg = 0
if sid in db:
end = len(db[sid])
bed.add("%s\t%d\t%d\n" % (sid, beg, end))
# else:
# logging.error("%s not in db => skipped" % sid)
else:
bed = Bed(args.loc, sorted=False)
else:
for loc in args.loc.split(","):
res = reg1.match(loc)
if res:
sid, beg, end = res.group(1), res.group(2), res.group(4)
beg = int(beg.replace(",", ""))
end = int(end.replace(",", ""))
bed.add("%s\t%d\t%d\n" % (sid, beg - 1, end))
else:
res = reg2.match(loc)
if res:
sid = res.group(1)
beg = 0
if sid in db:
end = len(db[sid])
bed.add("%s\t%d\t%d\n" % (sid, beg, end))
# else:
# logging.error("%s not in db => skipped" % sid)
else:
logging.error("%s: unknown locstr => skipped" % loc)
rcds = []
for b in bed:
sid, beg, end = b.seqid, b.start, b.end
oid = sid if args.list else f"{sid}-{beg}-{end}"
if b.accn:
oid = b.accn
if sid not in db:
print("%s not in db => skipped" % sid)
continue
size = end - beg + 1
bp_pad = 0
if beg < 1:
bp_pad += 1 - beg
beg = 1
if beg > len(db[sid]):
bp_pad = 1
beg = len(db[sid])
if end > len(db[sid]):
bp_pad += end - len(db[sid])
end = len(db[sid])
seq = db[sid][beg - 1:end].seq
if args.padding:
if bp_pad > 0:
if end - beg + 1 < 30:
seq = "N" * size
else:
seq += "N" * bp_pad
assert len(seq) == size, "error in seq size: %s:%d-%d %d" % (
sid, beg, end, bp_pad)
if args.tsv:
print("\t".join([sid, str(beg), str(end), seq]))
else:
rcd = SeqRecord(Seq(seq), id=oid, description='')
SeqIO.write([rcd], sys.stdout, 'fasta')
