def mask(args):
"""
%prog mask fastafile
Mask the contaminants. By default, this will compare against UniVec_Core and
Ecoli.fasta. Merge the contaminant results, and use `maskFastaFromBed`. Can
perform FASTA tidy if requested.
"""
p = OptionParser(mask.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
assert op.exists(fastafile)
outfastafile = fastafile.rsplit(".", 1)[0] + ".masked.fasta"
vecbedfile = blast([fastafile])
ecoliurl = \
"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/NC_000913.fna"
ecolifile = download(ecoliurl, filename="Ecoli.fasta")
assert op.exists(ecolifile)
ecolibedfile = blast([fastafile, "--db={0}".format(ecolifile)])
cmd = "cat {0} {1}".format(vecbedfile, ecolibedfile)
cmd += " | mergeBed -nms -d 100 -i stdin"
cmd += " | maskFastaFromBed -fi {0} -bed stdin -fo {1}".\
format(fastafile, outfastafile)
sh(cmd)
tidy([outfastafile])
def mask(args):
"""
%prog mask fastafile
Mask the contaminants. By default, this will compare against UniVec_Core and
Ecoli.fasta. Merge the contaminant results, and use `maskFastaFromBed`. Can
perform FASTA tidy if requested.
"""
p = OptionParser(mask.__doc__)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastafile, = args
assert op.exists(fastafile)
outfastafile = fastafile.rsplit(".", 1)[0] + ".masked.fasta"
vecbedfile = blast([fastafile])
ecoliurl = \
"ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/NC_000913.fna"
ecolifile = download(ecoliurl, filename="Ecoli.fasta")
assert op.exists(ecolifile)
ecolibedfile = blast([fastafile, "--db={0}".format(ecolifile)])
cmd = "cat {0} {1}".format(vecbedfile, ecolibedfile)
cmd += " | mergeBed -nms -d 100 -i stdin"
cmd += " | maskFastaFromBed -fi {0} -bed stdin -fo {1}".\
format(fastafile, outfastafile)
sh(cmd)
tidy([outfastafile])
def mask(args):
"""
%prog mask fastafile
Mask the contaminants. By default, this will compare against UniVec_Core and
Ecoli.fasta. Merge the contaminant results, and use `maskFastaFromBed`. Can
perform FASTA tidy if requested.
"""
p = OptionParser(mask.__doc__)
p.add_option(
"--db",
default=ECOLI_URL,
help=
"Contaminant db other than Ecoli K12, will download if file starts with http://, https://, or ftp://",
)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
(fastafile, ) = args
db = opts.db
assert op.exists(fastafile)
outfastafile = fastafile.rsplit(".", 1)[0] + ".masked.fasta"
vecbedfile = blast([fastafile])
ecolifile = (download(db, filename="Ecoli.fasta", handle_gzip=True)
if is_internet_file(db) else db)
assert op.exists(ecolifile)
ecolibedfile = blast([fastafile, "--db={0}".format(ecolifile)])
cmd = "cat {0} {1}".format(vecbedfile, ecolibedfile)
cmd += " | sort -k1,1 -k2,2n"
cmd += " | mergeBed -c 4 -o distinct -d 100 -i stdin"
cmd += " | maskFastaFromBed -fi {0} -bed stdin -fo {1}".format(
fastafile, outfastafile)
sh(cmd)
return tidy([outfastafile])
def scaffold(args):
"""
%prog scaffold ctgfasta agpfile
Build scaffolds based on ordering in the AGP file.
"""
from jcvi.formats.agp import bed, order_to_agp, build
from jcvi.formats.bed import Bed
p = OptionParser(scaffold.__doc__)
p.add_option("--prefix",
default=False,
action="store_true",
help="Keep IDs with same prefix together [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
ctgfasta, agpfile = args
sizes = Sizes(ctgfasta).mapping
pf = ctgfasta.rsplit(".", 1)[0]
phasefile = pf + ".phases"
fwphase = open(phasefile, "w")
newagpfile = pf + ".new.agp"
fwagp = open(newagpfile, "w")
scaffoldbuckets = defaultdict(list)
bedfile = bed([agpfile, "--nogaps", "--outfile=tmp"])
bb = Bed(bedfile)
for s, partialorder in bb.sub_beds():
name = partialorder[0].accn
bname = name.rsplit("_", 1)[0] if opts.prefix else s
scaffoldbuckets[bname].append([(b.accn, b.strand)
for b in partialorder])
# Now the buckets contain a mixture of singletons and partially resolved
# scaffolds. Print the scaffolds first then remaining singletons.
for bname, scaffolds in sorted(scaffoldbuckets.items()):
ctgorder = []
singletons = set()
for scaf in sorted(scaffolds):
for node, orientation in scaf:
ctgorder.append((node, orientation))
if len(scaf) == 1:
singletons.add(node)
nscaffolds = len(scaffolds)
nsingletons = len(singletons)
if nsingletons == 1 and nscaffolds == 0:
phase = 3
elif nsingletons == 0 and nscaffolds == 1:
phase = 2
else:
phase = 1
msg = "{0}: Scaffolds={1} Singletons={2} Phase={3}".\
format(bname, nscaffolds, nsingletons, phase)
print >> sys.stderr, msg
print >> fwphase, "\t".join((bname, str(phase)))
order_to_agp(bname, ctgorder, sizes, fwagp)
fwagp.close()
os.remove(bedfile)
fastafile = "final.fasta"
build([newagpfile, ctgfasta, fastafile])
tidy([fastafile])
def scaffold(args):
"""
%prog scaffold ctgfasta agpfile
Build scaffolds based on ordering in the AGP file.
"""
from jcvi.formats.agp import bed, order_to_agp, build
from jcvi.formats.bed import Bed
p = OptionParser(scaffold.__doc__)
p.add_option("--prefix", default=False, action="store_true",
help="Keep IDs with same prefix together [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
ctgfasta, agpfile = args
sizes = Sizes(ctgfasta).mapping
pf = ctgfasta.rsplit(".", 1)[0]
phasefile = pf + ".phases"
fwphase = open(phasefile, "w")
newagpfile = pf + ".new.agp"
fwagp = open(newagpfile, "w")
scaffoldbuckets = defaultdict(list)
bedfile = bed([agpfile, "--nogaps", "--outfile=tmp"])
bb = Bed(bedfile)
for s, partialorder in bb.sub_beds():
name = partialorder[0].accn
bname = name.rsplit("_", 1)[0] if opts.prefix else s
scaffoldbuckets[bname].append([(b.accn, b.strand) for b in partialorder])
# Now the buckets contain a mixture of singletons and partially resolved
# scaffolds. Print the scaffolds first then remaining singletons.
for bname, scaffolds in sorted(scaffoldbuckets.items()):
ctgorder = []
singletons = set()
for scaf in sorted(scaffolds):
for node, orientation in scaf:
ctgorder.append((node, orientation))
if len(scaf) == 1:
singletons.add(node)
nscaffolds = len(scaffolds)
nsingletons = len(singletons)
if nsingletons == 1 and nscaffolds == 0:
phase = 3
elif nsingletons == 0 and nscaffolds == 1:
phase = 2
else:
phase = 1
msg = "{0}: Scaffolds={1} Singletons={2} Phase={3}".\
format(bname, nscaffolds, nsingletons, phase)
print >> sys.stderr, msg
print >> fwphase, "\t".join((bname, str(phase)))
order_to_agp(bname, ctgorder, sizes, fwagp)
fwagp.close()
os.remove(bedfile)
fastafile = "final.fasta"
build([newagpfile, ctgfasta, fastafile])
tidy([fastafile])
