def pasteprepare(args):
"""
%prog pasteprepare bacs.fasta
Prepare sequences for paste.
"""
p = OptionParser(pasteprepare.__doc__)
p.add_option("--flank", default=5000, type="int",
help="Get the seq of size on two ends [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
goodfasta, = args
flank = opts.flank
pf = goodfasta.rsplit(".", 1)[0]
extbed = pf + ".ext.bed"
sizes = Sizes(goodfasta)
fw = open(extbed, "w")
for bac, size in sizes.iter_sizes():
print >> fw, "\t".join(str(x) for x in \
(bac, 0, min(flank, size), bac + "L"))
print >> fw, "\t".join(str(x) for x in \
(bac, max(size - flank, 0), size, bac + "R"))
fw.close()
fastaFromBed(extbed, goodfasta, name=True)
def pasteprepare(args):
"""
%prog pasteprepare bacs.fasta
Prepare sequences for paste.
"""
p = OptionParser(pasteprepare.__doc__)
p.add_option(
"--flank",
default=5000,
type="int",
help="Get the seq of size on two ends",
)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(goodfasta,) = args
flank = opts.flank
pf = goodfasta.rsplit(".", 1)[0]
extbed = pf + ".ext.bed"
sizes = Sizes(goodfasta)
fw = open(extbed, "w")
for bac, size in sizes.iter_sizes():
print("\t".join(str(x) for x in (bac, 0, min(flank, size), bac + "L")), file=fw)
print(
"\t".join(str(x) for x in (bac, max(size - flank, 0), size, bac + "R")),
file=fw,
)
fw.close()
fastaFromBed(extbed, goodfasta, name=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 fasta(args):
"""
%prog fasta map.out scaffolds.fasta
Extract marker sequences based on map.
"""
from jcvi.formats.sizes import Sizes
p = OptionParser(fasta.__doc__)
p.add_option(
"--extend",
default=1000,
type="int",
help="Extend seq flanking the gaps",
)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
mapout, sfasta = args
Flank = opts.extend
pf = mapout.split(".")[0]
mapbed = pf + ".bed"
bm = BinMap(mapout)
bm.print_to_bed(mapbed)
bed = Bed(mapbed, sorted=False)
markersbed = pf + ".markers.bed"
fw = open(markersbed, "w")
sizes = Sizes(sfasta).mapping
for b in bed:
accn = b.accn
scf, pos = accn.split(".")
pos = int(pos)
start = max(0, pos - Flank)
end = min(pos + Flank, sizes[scf])
print("\t".join(str(x) for x in (scf, start, end, accn)), file=fw)
fw.close()
fastaFromBed(markersbed, sfasta, name=True)
def flanks(args):
"""
%prog flanks gaps.bed fastafile
Create sequences flanking the gaps.
"""
p = OptionParser(flanks.__doc__)
p.add_option(
"--extend",
default=2000,
type="int",
help="Extend seq flanking the gaps",
)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
gapsbed, fastafile = args
Ext = opts.extend
sizes = Sizes(fastafile).mapping
bed = Bed(gapsbed)
pf = gapsbed.rsplit(".", 1)[0]
extbed = pf + ".ext.bed"
fw = open(extbed, "w")
for i, b in enumerate(bed):
seqid = b.seqid
gapname = b.accn
size = sizes[seqid]
prev_b = bed[i - 1] if i > 0 else None
next_b = bed[i + 1] if i + 1 < len(bed) else None
if prev_b and prev_b.seqid != seqid:
prev_b = None
if next_b and next_b.seqid != seqid:
next_b = None
start = prev_b.end + 1 if prev_b else 1
start, end = max(start, b.start - Ext), b.start - 1
print("\t".join(
str(x) for x in (b.seqid, start - 1, end, gapname + "L")),
file=fw)
end = next_b.start - 1 if next_b else size
start, end = b.end + 1, min(end, b.end + Ext)
print("\t".join(
str(x) for x in (b.seqid, start - 1, end, gapname + "R")),
file=fw)
fw.close()
extfasta = fastaFromBed(extbed, fastafile, name=True)
return extbed, extfasta
def fill(args):
"""
%prog fill gaps.bed bad.fasta
Perform gap filling of one assembly (bad) using sequences from another.
"""
p = OptionParser(fill.__doc__)
p.add_option(
"--extend",
default=2000,
type="int",
help="Extend seq flanking the gaps",
)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
gapsbed, badfasta = args
Ext = opts.extend
gapdist = 2 * Ext + 1 # This is to prevent to replacement ranges intersect
gapsbed = mergeBed(gapsbed, d=gapdist, nms=True)
bed = Bed(gapsbed)
sizes = Sizes(badfasta).mapping
pf = gapsbed.rsplit(".", 1)[0]
extbed = pf + ".ext.bed"
fw = open(extbed, "w")
for b in bed:
gapname = b.accn
start, end = max(0, b.start - Ext - 1), b.start - 1
print("\t".join(str(x) for x in (b.seqid, start, end, gapname + "L")),
file=fw)
start, end = b.end, min(sizes[b.seqid], b.end + Ext)
print("\t".join(str(x) for x in (b.seqid, start, end, gapname + "R")),
file=fw)
fw.close()
fastaFromBed(extbed, badfasta, name=True)
def fasta(args):
"""
%prog fasta map.out scaffolds.fasta
Extract marker sequences based on map.
"""
from jcvi.formats.sizes import Sizes
p = OptionParser(fasta.__doc__)
p.add_option("--extend", default=1000, type="int",
help="Extend seq flanking the gaps [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
mapout, sfasta = args
Flank = opts.extend
pf = mapout.split(".")[0]
mapbed = pf + ".bed"
bm = BinMap(mapout)
bm.print_to_bed(mapbed)
bed = Bed(mapbed, sorted=False)
markersbed = pf + ".markers.bed"
fw = open(markersbed, "w")
sizes = Sizes(sfasta).mapping
for b in bed:
accn = b.accn
scf, pos = accn.split(".")
pos = int(pos)
start = max(0, pos - Flank)
end = min(pos + Flank, sizes[scf])
print >> fw, "\t".join(str(x) for x in \
(scf, start, end, accn))
fw.close()
fastaFromBed(markersbed, sfasta, name=True)
def fill(args):
"""
%prog fill gaps.bed bad.fasta
Perform gap filling of one assembly (bad) using sequences from another.
"""
p = OptionParser(fill.__doc__)
p.add_option("--extend", default=2000, type="int",
help="Extend seq flanking the gaps [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
gapsbed, badfasta = args
Ext = opts.extend
gapdist = 2 * Ext + 1 # This is to prevent to replacement ranges intersect
gapsbed = mergeBed(gapsbed, d=gapdist, nms=True)
bed = Bed(gapsbed)
sizes = Sizes(badfasta).mapping
pf = gapsbed.rsplit(".", 1)[0]
extbed = pf + ".ext.bed"
fw = open(extbed, "w")
for b in bed:
gapname = b.accn
start, end = max(0, b.start - Ext - 1), b.start - 1
print >> fw, "\t".join(str(x) for x in \
(b.seqid, start, end, gapname + "L"))
start, end = b.end, min(sizes[b.seqid], b.end + Ext)
print >> fw, "\t".join(str(x) for x in \
(b.seqid, start, end, gapname + "R"))
fw.close()
fastaFromBed(extbed, badfasta, name=True)
def flanks(args):
"""
%prog flanks gaps.bed fastafile
Create sequences flanking the gaps.
"""
p = OptionParser(flanks.__doc__)
p.add_option("--extend", default=2000, type="int",
help="Extend seq flanking the gaps [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
gapsbed, fastafile = args
Ext = opts.extend
sizes = Sizes(fastafile).mapping
bed = Bed(gapsbed)
pf = gapsbed.rsplit(".", 1)[0]
extbed = pf + ".ext.bed"
fw = open(extbed, "w")
for i, b in enumerate(bed):
seqid = b.seqid
gapname = b.accn
size = sizes[seqid]
prev_b = bed[i - 1] if i > 0 else None
next_b = bed[i + 1] if i + 1 < len(bed) else None
if prev_b and prev_b.seqid != seqid:
prev_b = None
if next_b and next_b.seqid != seqid:
next_b = None
start = prev_b.end + 1 if prev_b else 1
start, end = max(start, b.start - Ext), b.start - 1
print >> fw, "\t".join(str(x) for x in \
(b.seqid, start - 1, end, gapname + "L"))
end = next_b.start - 1 if next_b else size
start, end = b.end + 1, min(end, b.end + Ext)
print >> fw, "\t".join(str(x) for x in \
(b.seqid, start - 1, end, gapname + "R"))
fw.close()
extfasta = fastaFromBed(extbed, fastafile, name=True)
return extbed, extfasta
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 install(args):
"""
%prog install patchers.bed patchers.fasta backbone.fasta alt.fasta
Install patches into backbone, using sequences from alternative assembly.
The patches sequences are generated via jcvi.assembly.patch.fill().
The output is a bedfile that can be converted to AGP using
jcvi.formats.agp.frombed().
"""
from jcvi.apps.align import blast
from jcvi.formats.fasta import SeqIO
p = OptionParser(install.__doc__)
p.set_rclip(rclip=1)
p.add_option(
"--maxsize",
default=300000,
type="int",
help="Maximum size of patchers to be replaced",
)
p.add_option("--prefix", help="Prefix of the new object")
p.add_option(
"--strict",
default=False,
action="store_true",
help="Only update if replacement has no gaps",
)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
pbed, pfasta, bbfasta, altfasta = args
maxsize = opts.maxsize # Max DNA size to replace gap
rclip = opts.rclip
blastfile = blast([altfasta, pfasta, "--wordsize=100", "--pctid=99"])
order = Bed(pbed).order
beforebed, afterbed = blast_to_twobeds(
blastfile, order, rclip=rclip, maxsize=maxsize
)
beforefasta = fastaFromBed(beforebed, bbfasta, name=True, stranded=True)
afterfasta = fastaFromBed(afterbed, altfasta, name=True, stranded=True)
# Exclude the replacements that contain more Ns than before
ah = SeqIO.parse(beforefasta, "fasta")
bh = SeqIO.parse(afterfasta, "fasta")
count_Ns = lambda x: x.seq.count("n") + x.seq.count("N")
exclude = set()
for arec, brec in zip(ah, bh):
an = count_Ns(arec)
bn = count_Ns(brec)
if opts.strict:
if bn == 0:
continue
elif bn < an:
continue
id = arec.id
exclude.add(id)
logging.debug(
"Ignore {0} updates because of decreasing quality.".format(len(exclude))
)
abed = Bed(beforebed, sorted=False)
bbed = Bed(afterbed, sorted=False)
abed = [x for x in abed if x.accn not in exclude]
bbed = [x for x in bbed if x.accn not in exclude]
abedfile = "before.filtered.bed"
bbedfile = "after.filtered.bed"
afbed = Bed()
afbed.extend(abed)
bfbed = Bed()
bfbed.extend(bbed)
afbed.print_to_file(abedfile)
bfbed.print_to_file(bbedfile)
shuffle_twobeds(afbed, bfbed, bbfasta, prefix=opts.prefix)
def pastegenes(args):
"""
%prog pastegenes coverage.list old.genes.bed new.genes.bed old.assembly
Paste in zero or low coverage genes. For a set of neighboring genes
missing, add the whole cassette as unplaced scaffolds. For singletons the
program will try to make a patch.
"""
from jcvi.formats.base import DictFile
from jcvi.utils.cbook import gene_name
p = OptionParser(pastegenes.__doc__)
p.add_option(
"--cutoff",
default=90,
type="int",
help="Coverage cutoff to call gene missing",
)
p.add_option(
"--flank",
default=2000,
type="int",
help="Get the seq of size on two ends",
)
p.add_option(
"--maxsize",
default=50000,
type="int",
help="Maximum size of patchers to be replaced",
)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
coveragefile, oldbed, newbed, oldassembly = args
cutoff = opts.cutoff
flank = opts.flank
maxsize = opts.maxsize
coverage = DictFile(coveragefile, valuepos=2, cast=float)
obed = Bed(oldbed)
order = obed.order
bed = [x for x in obed if x.accn in coverage]
key = lambda x: coverage[x.accn] >= cutoff
extrabed = "extra.bed"
extendbed = "extend.bed"
pastebed = "paste.bed"
fw = open(extrabed, "w")
fwe = open(extendbed, "w")
fwp = open(pastebed, "w")
fw_ids = open(extendbed + ".ids", "w")
singletons, large, large_genes = 0, 0, 0
for chr, chrbed in groupby(bed, key=lambda x: x.seqid):
chrbed = list(chrbed)
for good, beds in groupby(chrbed, key=key):
if good:
continue
beds = list(beds)
blocksize = len(set([gene_name(x.accn) for x in beds]))
if blocksize == 1:
singletons += 1
accn = beds[0].accn
gi, gb = order[accn]
leftb = obed[gi - 1]
rightb = obed[gi + 1]
leftr = leftb.range
rightr = rightb.range
cur = gb.range
distance_to_left, oo = range_distance(leftr, cur)
distance_to_right, oo = range_distance(cur, rightr)
span, oo = range_distance(leftr, rightr)
if distance_to_left <= distance_to_right and distance_to_left > 0:
label = "LEFT"
else:
label = "RIGHT"
if 0 < span <= maxsize:
print(
"\t".join(
str(x) for x in (chr, leftb.start, rightb.end, gb.accn)
),
file=fwp,
)
print(leftb, file=fwe)
print(gb, file=fwe)
print(rightb, file=fwe)
print(
"L:{0} R:{1} [{2}]".format(
distance_to_left, distance_to_right, label
),
file=fwe,
)
print(gb.accn, file=fw_ids)
continue
large += 1
large_genes += blocksize
ranges = [(x.start, x.end) for x in beds]
rmin, rmax = range_minmax(ranges)
rmin -= flank
rmax += flank
name = "-".join((beds[0].accn, beds[-1].accn))
print("\t".join(str(x) for x in (chr, rmin - 1, rmax, name)), file=fw)
fw.close()
fwe.close()
extrabed = mergeBed(extrabed, d=flank, nms=True)
fastaFromBed(extrabed, oldassembly, name=True)
summary([extrabed])
logging.debug("Singleton blocks : {0}".format(singletons))
logging.debug("Large blocks : {0} ({1} genes)".format(large, large_genes))
def install(args):
"""
%prog install patchers.bed patchers.fasta backbone.fasta alt.fasta
Install patches into backbone, using sequences from alternative assembly.
The patches sequences are generated via jcvi.assembly.patch.fill().
The output is a bedfile that can be converted to AGP using
jcvi.formats.agp.frombed().
"""
from jcvi.apps.align import blast
from jcvi.formats.fasta import SeqIO
p = OptionParser(install.__doc__)
p.set_rclip(rclip=1)
p.add_option("--maxsize", default=300000, type="int",
help="Maximum size of patchers to be replaced [default: %default]")
p.add_option("--prefix", help="Prefix of the new object [default: %default]")
p.add_option("--strict", default=False, action="store_true",
help="Only update if replacement has no gaps [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
pbed, pfasta, bbfasta, altfasta = args
maxsize = opts.maxsize # Max DNA size to replace gap
rclip = opts.rclip
blastfile = blast([altfasta, pfasta,"--wordsize=100", "--pctid=99"])
order = Bed(pbed).order
beforebed, afterbed = blast_to_twobeds(blastfile, order, rclip=rclip,
maxsize=maxsize)
beforefasta = fastaFromBed(beforebed, bbfasta, name=True, stranded=True)
afterfasta = fastaFromBed(afterbed, altfasta, name=True, stranded=True)
# Exclude the replacements that contain more Ns than before
ah = SeqIO.parse(beforefasta, "fasta")
bh = SeqIO.parse(afterfasta, "fasta")
count_Ns = lambda x: x.seq.count('n') + x.seq.count('N')
exclude = set()
for arec, brec in zip(ah, bh):
an = count_Ns(arec)
bn = count_Ns(brec)
if opts.strict:
if bn == 0:
continue
elif bn < an:
continue
id = arec.id
exclude.add(id)
logging.debug("Ignore {0} updates because of decreasing quality."\
.format(len(exclude)))
abed = Bed(beforebed, sorted=False)
bbed = Bed(afterbed, sorted=False)
abed = [x for x in abed if x.accn not in exclude]
bbed = [x for x in bbed if x.accn not in exclude]
abedfile = "before.filtered.bed"
bbedfile = "after.filtered.bed"
afbed = Bed()
afbed.extend(abed)
bfbed = Bed()
bfbed.extend(bbed)
afbed.print_to_file(abedfile)
bfbed.print_to_file(bbedfile)
shuffle_twobeds(afbed, bfbed, bbfasta, prefix=opts.prefix)
def pastegenes(args):
"""
%prog pastegenes coverage.list old.genes.bed new.genes.bed old.assembly
Paste in zero or low coverage genes. For a set of neighboring genes
missing, add the whole cassette as unplaced scaffolds. For singletons the
program will try to make a patch.
"""
from jcvi.formats.base import DictFile
from jcvi.utils.cbook import gene_name
p = OptionParser(pastegenes.__doc__)
p.add_option("--cutoff", default=90, type="int",
help="Coverage cutoff to call gene missing [default: %default]")
p.add_option("--flank", default=2000, type="int",
help="Get the seq of size on two ends [default: %default]")
p.add_option("--maxsize", default=50000, type="int",
help="Maximum size of patchers to be replaced [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
coveragefile, oldbed, newbed, oldassembly = args
cutoff = opts.cutoff
flank = opts.flank
maxsize = opts.maxsize
coverage = DictFile(coveragefile, valuepos=2, cast=float)
obed = Bed(oldbed)
order = obed.order
bed = [x for x in obed if x.accn in coverage]
key = lambda x: coverage[x.accn] >= cutoff
extrabed = "extra.bed"
extendbed = "extend.bed"
pastebed = "paste.bed"
fw = open(extrabed, "w")
fwe = open(extendbed, "w")
fwp = open(pastebed, "w")
fw_ids = open(extendbed + ".ids", "w")
singletons, large, large_genes = 0, 0, 0
for chr, chrbed in groupby(bed, key=lambda x: x.seqid):
chrbed = list(chrbed)
for good, beds in groupby(chrbed, key=key):
if good:
continue
beds = list(beds)
blocksize = len(set([gene_name(x.accn) for x in beds]))
if blocksize == 1:
singletons += 1
accn = beds[0].accn
gi, gb = order[accn]
leftb = obed[gi - 1]
rightb = obed[gi + 1]
leftr = leftb.range
rightr = rightb.range
cur = gb.range
distance_to_left, oo = range_distance(leftr, cur)
distance_to_right, oo = range_distance(cur, rightr)
span, oo = range_distance(leftr, rightr)
if distance_to_left <= distance_to_right and \
distance_to_left > 0:
label = "LEFT"
else:
label = "RIGHT"
if 0 < span <= maxsize:
print >> fwp, "\t".join(str(x) for x in \
(chr, leftb.start, rightb.end, gb.accn))
print >> fwe, leftb
print >> fwe, gb
print >> fwe, rightb
print >> fwe, "L:{0} R:{1} [{2}]".format(distance_to_left, \
distance_to_right, label)
print >> fw_ids, gb.accn
continue
large += 1
large_genes += blocksize
ranges = [(x.start, x.end) for x in beds]
rmin, rmax = range_minmax(ranges)
rmin -= flank
rmax += flank
name = "-".join((beds[0].accn, beds[-1].accn))
print >> fw, "\t".join(str(x) for x in (chr, rmin - 1, rmax, name))
fw.close()
fwe.close()
extrabed = mergeBed(extrabed, d=flank, nms=True)
fastaFromBed(extrabed, oldassembly, name=True)
summary([extrabed])
logging.debug("Singleton blocks : {0}".format(singletons))
logging.debug("Large blocks : {0} ({1} genes)".format(large, large_genes))
def annotate(args):
"""
%prog annotate agpfile gaps.linkage.bed assembly.fasta
Annotate AGP file with linkage info of `paired-end` or `map`.
File `gaps.linkage.bed` is generated by assembly.gaps.estimate().
"""
from jcvi.formats.agp import AGP, bed, tidy
p = OptionParser(annotate.__doc__)
p.add_option("--minsize", default=200,
help="Smallest component size [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
agpfile, linkagebed, assemblyfasta = args
linkagebed = Bed(linkagebed)
spannedgaps = set()
for b in linkagebed:
score = int(b.score)
if score == 0:
spannedgaps.add((b.accn, b.start, b.end))
agp = AGP(agpfile)
newagpfile = agpfile.rsplit(".", 1)[0] + ".linkage.agp"
newagp = open(newagpfile, "w")
contig_id = 0
minsize = opts.minsize
for a in agp:
if not a.is_gap:
cs = a.component_span
if cs < minsize:
a.is_gap = True
a.component_type = "N"
a.gap_length = cs
a.gap_type = "scaffold"
a.linkage = "yes"
a.linkage_evidence = []
else:
contig_id += 1
a.component_id = "contig{0:04d}".format(contig_id)
a.component_beg = 1
a.component_end = cs
a.component_type = "W"
print >> newagp, a
continue
gapinfo = (a.object, a.object_beg, a.object_end)
gaplen = a.gap_length
if gaplen == 100 and gapinfo not in spannedgaps:
a.component_type = "U"
tag = "map"
else:
tag = "paired-ends"
a.linkage_evidence.append(tag)
print >> newagp, a
newagp.close()
logging.debug("Annotated AGP written to `{0}`.".format(newagpfile))
contigbed = assemblyfasta.rsplit(".", 1)[0] + ".contigs.bed"
bedfile = bed([newagpfile, "--nogaps", "--outfile=" + contigbed])
contigfasta = fastaFromBed(bedfile, assemblyfasta, name=True, stranded=True)
tidy([newagpfile, contigfasta])
def install(args):
"""
%prog install patchers.bed patchers.fasta backbone.fasta alt.fasta
Install patches into backbone, using sequences from alternative assembly.
The patches sequences are generated via jcvi.assembly.patch.fill().
The output is a bedfile that can be converted to AGP using
jcvi.formats.agp.frombed().
"""
from jcvi.apps.base import blast
from jcvi.formats.blast import BlastSlow
from jcvi.formats.fasta import SeqIO
from jcvi.utils.iter import roundrobin
p = OptionParser(install.__doc__)
p.add_option(
"--rclip",
default=1,
type="int",
help="Pair ID is derived from rstrip N chars [default: %default]")
p.add_option(
"--maxsize",
default=1000000,
type="int",
help="Maximum size of patchers to be replaced [default: %default]")
p.add_option("--prefix",
help="Prefix of the new object [default: %default]")
p.add_option(
"--strict",
default=False,
action="store_true",
help="Only update if replacement has no gaps [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
pbed, pfasta, bbfasta, altfasta = args
Max = opts.maxsize # Max DNA size to replace gap
rclip = opts.rclip
prefix = opts.prefix
blastfile = blast([altfasta, pfasta, "--wordsize=100", "--pctid=99"])
order = Bed(pbed).order
beforebed, afterbed = "before.bed", "after.bed"
fwa = open(beforebed, "w")
fwb = open(afterbed, "w")
key1 = lambda x: x.query
key2 = lambda x: x.query[:-rclip] if rclip else key1
data = BlastSlow(blastfile)
for pe, lines in groupby(data, key=key2):
lines = list(lines)
if len(lines) != 2:
continue
a, b = lines
aquery, bquery = a.query, b.query
asubject, bsubject = a.subject, b.subject
if asubject != bsubject:
continue
astrand, bstrand = a.orientation, b.orientation
assert aquery[-1] == 'L' and bquery[-1] == 'R', str((aquery, bquery))
ai, ax = order[aquery]
bi, bx = order[bquery]
qstart, qstop = ax.start + a.qstart - 1, bx.start + b.qstop - 1
if astrand == '+' and bstrand == '+':
sstart, sstop = a.sstart, b.sstop
elif astrand == '-' and bstrand == '-':
sstart, sstop = b.sstart, a.sstop
else:
continue
if sstart > sstop:
continue
if sstop > sstart + Max:
continue
name = aquery[:-1] + "LR"
print >> fwa, "\t".join(str(x) for x in \
(ax.seqid, qstart - 1, qstop, name, 1000, "+"))
print >> fwb, "\t".join(str(x) for x in \
(asubject, sstart - 1, sstop, name, 1000, astrand))
fwa.close()
fwb.close()
beforefasta = fastaFromBed(beforebed, bbfasta, name=True, stranded=True)
afterfasta = fastaFromBed(afterbed, altfasta, name=True, stranded=True)
# Exclude the replacements that contain more Ns than before
ah = SeqIO.parse(beforefasta, "fasta")
bh = SeqIO.parse(afterfasta, "fasta")
count_Ns = lambda x: x.seq.count('n') + x.seq.count('N')
exclude = set()
for arec, brec in zip(ah, bh):
an = count_Ns(arec)
bn = count_Ns(brec)
if opts.strict:
if bn == 0:
continue
elif bn < an:
continue
id = arec.id
exclude.add(id)
logging.debug("Ignore {0} updates because of decreasing quality."\
.format(len(exclude)))
abed = Bed(beforebed, sorted=False)
bbed = Bed(afterbed, sorted=False)
abed = [x for x in abed if x.accn not in exclude]
bbed = [x for x in bbed if x.accn not in exclude]
abedfile = "before.filtered.bed"
bbedfile = "after.filtered.bed"
afbed = Bed()
afbed.extend(abed)
bfbed = Bed()
bfbed.extend(bbed)
afbed.print_to_file(abedfile)
bfbed.print_to_file(bbedfile)
# Shuffle the two bedfiles together
sz = Sizes(bbfasta)
sizes = sz.mapping
shuffled = "shuffled.bed"
border = bfbed.order
all = []
afbed.sort(key=afbed.nullkey)
totalids = len(sizes)
import math
pad = int(math.log10(totalids)) + 1
cj = 0
seen = set()
accn = lambda x: "{0}{1:0{2}d}".format(prefix, x, pad)
for seqid, aa in afbed.sub_beds():
cj += 1
abeds, bbeds, beds = [], [], []
size = sizes[seqid]
ranges = [(x.seqid, x.start, x.end) for x in aa]
cranges = range_interleave(ranges, sizes={seqid: size})
for seqid, start, end in cranges:
bedline = "\t".join(str(x) for x in (seqid, start - 1, end))
abeds.append(BedLine(bedline))
for a in aa:
gapid = a.accn
bi, b = border[gapid]
bbeds.append(b)
a = abeds[0] if abeds else []
assert abs(len(abeds) - len(bbeds)) <= 1
if (not a) or a.start > 1:
abeds, bbeds = bbeds, abeds
beds = list(roundrobin(abeds, bbeds))
if prefix:
for b in beds:
b.accn = accn(cj)
all.extend(beds)
seen.add(seqid)
# Singletons
for seqid, size in sz.iter_sizes():
if seqid in seen:
continue
bedline = "\t".join(str(x) for x in (seqid, 0, size, accn(cj)))
b = BedLine(bedline)
cj += 1
if prefix:
b.accn = accn(cj)
all.append(b)
shuffledbed = Bed()
shuffledbed.extend(all)
shuffledbed.print_to_file(shuffled)
