def estimate(args):
"""
%prog estimate gaps.bed all.spans.bed all.mates
Estimate gap sizes based on mate positions and library insert sizes.
"""
from collections import defaultdict
from jcvi.formats.bed import intersectBed_wao
from jcvi.formats.posmap import MatesFile
p = OptionParser(estimate.__doc__)
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())
gapsbed, spansbed, matesfile = args
mf = MatesFile(matesfile)
bed = Bed(gapsbed)
order = bed.order
gap2mate = defaultdict(set)
mate2gap = defaultdict(set)
for a, b in intersectBed_wao(gapsbed, spansbed):
gapsize = a.span
if gapsize != 100:
continue
gapname = a.accn
if b is None:
gap2mate[gapname] = set()
continue
matename = b.accn
gap2mate[gapname].add(matename)
mate2gap[matename].add(gapname)
omgapsbed = "gaps.linkage.bed"
fw = open(omgapsbed, "w")
for gapname, mates in sorted(gap2mate.items()):
i, b = order[gapname]
nmates = len(mates)
if nmates < opts.minlinks:
print("{0}\t{1}".format(b, nmates), file=fw)
continue
print(gapname, mates)
fw.close()
def estimate(args):
"""
%prog estimate gaps.bed all.spans.bed all.mates
Estimate gap sizes based on mate positions and library insert sizes.
"""
from collections import defaultdict
from jcvi.formats.bed import intersectBed_wao
from jcvi.formats.posmap import MatesFile
p = OptionParser(estimate.__doc__)
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())
gapsbed, spansbed, matesfile = args
mf = MatesFile(matesfile)
bed = Bed(gapsbed)
order = bed.order
gap2mate = defaultdict(set)
mate2gap = defaultdict(set)
for a, b in intersectBed_wao(gapsbed, spansbed):
gapsize = a.span
if gapsize != 100:
continue
gapname = a.accn
if b is None:
gap2mate[gapname] = set()
continue
matename = b.accn
gap2mate[gapname].add(matename)
mate2gap[matename].add(gapname)
omgapsbed = "gaps.linkage.bed"
fw = open(omgapsbed, "w")
for gapname, mates in sorted(gap2mate.items()):
i, b = order[gapname]
nmates = len(mates)
if nmates < opts.minlinks:
print >> fw, "{0}\t{1}".format(b, nmates)
continue
print gapname, mates
fw.close()
def validate(args):
"""
%prog validate diploid.napus.fractionation cds.bed
Check whether [S] intervals overlap with CDS.
"""
from jcvi.formats.bed import intersectBed_wao
p = OptionParser(validate.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
fractionation, cdsbed = args
fp = open(fractionation)
sbed = "S.bed"
fw = open(sbed, "w")
for row in fp:
a, b, c = row.split()
if not c.startswith("[S]"):
continue
tag, (seqid, start, end) = get_tag(c, None)
print >> fw, "\t".join(str(x) for x in (seqid, start - 1, end, b))
fw.close()
pairs = {}
for a, b in intersectBed_wao(sbed, cdsbed):
if b is None:
continue
pairs[a.accn] = b.accn
validated = fractionation + ".validated"
fw = open(validated, "w")
fp.seek(0)
fixed = 0
for row in fp:
a, b, c = row.split()
if b in pairs:
assert c.startswith("[S]")
c = pairs[b]
fixed += 1
print >> fw, "\t".join((a, b, c))
logging.debug("Fixed {0} [S] cases in `{1}`.".format(fixed, validated))
fw.close()
def validate(args):
"""
%prog validate diploid.napus.fractionation cds.bed
Check whether [S] intervals overlap with CDS.
"""
from jcvi.formats.bed import intersectBed_wao
p = OptionParser(validate.__doc__)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
fractionation, cdsbed = args
fp = open(fractionation)
sbed = "S.bed"
fw = open(sbed, "w")
for row in fp:
a, b, c = row.split()
if not c.startswith("[S]"):
continue
tag, (seqid, start, end) = get_tag(c, None)
print >> fw, "\t".join(str(x) for x in (seqid, start - 1, end, b))
fw.close()
pairs = {}
for a, b in intersectBed_wao(sbed, cdsbed):
if b is None:
continue
pairs[a.accn] = b.accn
validated = fractionation + ".validated"
fw = open(validated, "w")
fp.seek(0)
fixed = 0
for row in fp:
a, b, c = row.split()
if b in pairs:
assert c.startswith("[S]")
c = pairs[b]
fixed += 1
print >> fw, "\t".join((a, b, c))
logging.debug("Fixed {0} [S] cases in `{1}`.".format(fixed, validated))
fw.close()
def gffselect(args):
"""
%prog gffselect gmaplocation.bed expectedlocation.bed translated.ids tag
Try to match up the expected location and gmap locations for particular
genes. translated.ids was generated by fasta.translate --ids. tag must be
one of "complete|pseudogene|partial".
"""
from jcvi.formats.bed import intersectBed_wao
p = OptionParser(gffselect.__doc__)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
gmapped, expected, idsfile, tag = args
data = get_tags(idsfile)
completeness = dict((a.replace("mrna", "path"), c) \
for (a, b, c) in data)
seen = set()
idsfile = expected.rsplit(".", 1)[0] + ".ids"
fw = open(idsfile, "w")
cnt = 0
for a, b in intersectBed_wao(expected, gmapped):
if b is None:
continue
aname, bbname = a.accn, b.accn
bname = bbname.split(".")[0]
if completeness[bbname] != tag:
continue
if aname == bname:
if bname in seen:
continue
seen.add(bname)
print >> fw, bbname
cnt += 1
fw.close()
logging.debug("Total {0} records written to `{1}`.".format(cnt, idsfile))
def gffselect(args):
"""
%prog gffselect gmaplocation.bed expectedlocation.bed translated.ids tag
Try to match up the expected location and gmap locations for particular
genes. translated.ids was generated by fasta.translate --ids. tag must be
one of "complete|pseudogene|partial".
"""
from jcvi.formats.bed import intersectBed_wao
p = OptionParser(gffselect.__doc__)
opts, args = p.parse_args(args)
if len(args) != 4:
sys.exit(not p.print_help())
gmapped, expected, idsfile, tag = args
data = get_tags(idsfile)
completeness = dict((a.replace("mrna", "path"), c) \
for (a, b, c) in data)
seen = set()
idsfile = expected.rsplit(".", 1)[0] + ".ids"
fw = open(idsfile, "w")
cnt = 0
for a, b in intersectBed_wao(expected, gmapped):
if b is None:
continue
aname, bbname = a.accn, b.accn
bname = bbname.split(".")[0]
if completeness[bbname] != tag:
continue
if aname == bname:
if bname in seen:
continue
seen.add(bname)
print >> fw, bbname
cnt += 1
fw.close()
logging.debug("Total {0} records written to `{1}`.".format(cnt, idsfile))
