def posmap(args):
"""
%prog posmap frgscf.sorted scf.fasta scfID
Perform QC on the selected scfID, generate multiple BED files for plotting.
"""
p = OptionParser(posmap.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(p.print_help())
frgscffile, fastafile, scf = args
# fasta
cmd = "faOneRecord {0} {1}".format(fastafile, scf)
scffastafile = scf + ".fasta"
if not op.exists(scffastafile):
sh(cmd, outfile=scffastafile)
# sizes
sizesfile = scffastafile + ".sizes"
sizes = Sizes(scffastafile).mapping
scfsize = sizes[scf]
logging.debug("`{0}` has length of {1}.".format(scf, scfsize))
# gaps.bed
gapsbedfile = scf + ".gaps.bed"
if not op.exists(gapsbedfile):
args = [scffastafile, "--bed", "--mingap=100"]
gaps(args)
# reads frgscf posmap
posmapfile = scf + ".posmap"
if not op.exists(posmapfile):
args = [frgscffile, scf]
query(args)
# reads bed
bedfile = scf + ".bed"
if not op.exists(bedfile):
args = [posmapfile]
bed(args)
# reads bedpe
bedpefile = scf + ".bedpe"
pairsbedfile = scf + ".pairs.bed"
if not (op.exists(bedpefile) and op.exists(pairsbedfile)):
bed_to_bedpe(bedfile, bedpefile, pairsbedfile=pairsbedfile, ca=True)
# base coverage
basecoverage = Coverage(bedfile, sizesfile)
pecoverage = Coverage(pairsbedfile, sizesfile)
def posmap(args):
"""
%prog posmap frgscf.sorted scf.fasta scfID
Perform QC on the selected scfID, generate multiple BED files for plotting.
"""
p = OptionParser(posmap.__doc__)
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(p.print_help())
frgscffile, fastafile, scf = args
# fasta
cmd = "faOneRecord {0} {1}".format(fastafile, scf)
scffastafile = scf + ".fasta"
if not op.exists(scffastafile):
sh(cmd, outfile=scffastafile)
# sizes
sizesfile = scffastafile + ".sizes"
sizes = Sizes(scffastafile).mapping
scfsize = sizes[scf]
logging.debug("`{0}` has length of {1}.".format(scf, scfsize))
# gaps.bed
gapsbedfile = scf + ".gaps.bed"
if not op.exists(gapsbedfile):
args = [scffastafile, "--bed", "--mingap=100"]
gaps(args)
# reads frgscf posmap
posmapfile = scf + ".posmap"
if not op.exists(posmapfile):
args = [frgscffile, scf]
query(args)
# reads bed
bedfile = scf + ".bed"
if not op.exists(bedfile):
args = [posmapfile]
bed(args)
# reads bedpe
bedpefile = scf + ".bedpe"
pairsbedfile = scf + ".pairs.bed"
if not (op.exists(bedpefile) and op.exists(pairsbedfile)):
bed_to_bedpe(bedfile, bedpefile, pairsbedfile=pairsbedfile, ca=True)
# base coverage
Coverage(bedfile, sizesfile)
Coverage(pairsbedfile, sizesfile)
def dedup(args):
"""
%prog dedup scaffolds.fasta
Remove redundant contigs with CD-HIT. This is run prior to
assembly.sspace.embed().
"""
from jcvi.formats.fasta import gaps
from jcvi.apps.cdhit import deduplicate, ids
p = OptionParser(dedup.__doc__)
p.set_align(pctid=GoodPct)
p.set_mingap(default=10)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
scaffolds, = args
mingap = opts.mingap
splitfile, oagpfile, cagpfile = gaps(
[scaffolds, "--split", "--mingap={0}".format(mingap)])
dd = splitfile + ".cdhit"
clstrfile = dd + ".clstr"
idsfile = dd + ".ids"
if need_update(splitfile, clstrfile):
deduplicate([splitfile, "--pctid={0}".format(opts.pctid)])
if need_update(clstrfile, idsfile):
ids([clstrfile])
agp = AGP(cagpfile)
reps = set(x.split()[-1] for x in open(idsfile))
pf = scaffolds.rsplit(".", 1)[0]
dedupagp = pf + ".dedup.agp"
fw = open(dedupagp, "w")
ndropped = ndroppedbases = 0
for a in agp:
if not a.is_gap and a.component_id not in reps:
span = a.component_span
logging.debug("Drop component {0} ({1})".\
format(a.component_id, span))
ndropped += 1
ndroppedbases += span
continue
print >> fw, a
fw.close()
logging.debug("Dropped components: {0}, Dropped bases: {1}".\
format(ndropped, ndroppedbases))
logging.debug("Deduplicated file written to `{0}`.".format(dedupagp))
tidyagp = tidy([dedupagp, splitfile])
dedupfasta = pf + ".dedup.fasta"
build([tidyagp, dd, dedupfasta])
return dedupfasta
def dedup(args):
"""
%prog dedup scaffolds.fasta
Remove redundant contigs with CD-HIT. This is run prior to
assembly.sspace.embed().
"""
from jcvi.formats.fasta import gaps
from jcvi.apps.cdhit import deduplicate, ids
p = OptionParser(dedup.__doc__)
p.set_align(pctid=GoodPct)
p.set_mingap(default=10)
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
scaffolds, = args
mingap = opts.mingap
splitfile, oagpfile, cagpfile = gaps([scaffolds, "--split", "--mingap={0}".format(mingap)])
dd = splitfile + ".cdhit"
clstrfile = dd + ".clstr"
idsfile = dd + ".ids"
if need_update(splitfile, clstrfile):
deduplicate([splitfile, "--pctid={0}".format(opts.pctid)])
if need_update(clstrfile, idsfile):
ids([clstrfile])
agp = AGP(cagpfile)
reps = set(x.split()[-1] for x in open(idsfile))
pf = scaffolds.rsplit(".", 1)[0]
dedupagp = pf + ".dedup.agp"
fw = open(dedupagp, "w")
ndropped = ndroppedbases = 0
for a in agp:
if not a.is_gap and a.component_id not in reps:
span = a.component_span
logging.debug("Drop component {0} ({1})".\
format(a.component_id, span))
ndropped += 1
ndroppedbases += span
continue
print >> fw, a
fw.close()
logging.debug("Dropped components: {0}, Dropped bases: {1}".\
format(ndropped, ndroppedbases))
logging.debug("Deduplicated file written to `{0}`.".format(dedupagp))
tidyagp = tidy([dedupagp, splitfile])
dedupfasta = pf + ".dedup.fasta"
build([tidyagp, dd, dedupfasta])
return dedupfasta
def run_gapsplit(infile=None, outfile=None):
gaps([infile, "--split"])
return outfile
def embed(args):
"""
%prog embed evidencefile scaffolds.fasta contigs.fasta
Use SSPACE evidencefile to scaffold contigs into existing scaffold
structure, as in `scaffolds.fasta`. Contigs.fasta were used by SSPACE
directly to scaffold.
Rules:
1. Only update existing structure by embedding contigs small enough to fit.
2. Promote singleton contigs only if they are big (>= min_length).
"""
p = OptionParser(embed.__doc__)
p.set_mingap(default=10)
p.add_option("--min_length", default=200, type="int", help="Minimum length to consider [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
evidencefile, scaffolds, contigs = args
min_length = opts.min_length
splitfasta, oagp, cagp = gaps([scaffolds, "--split", "--mingap={0}".format(opts.mingap)])
agp = AGP(cagp)
p = agp.graph
ef = EvidenceFile(evidencefile, contigs)
sizes = ef.sz
q = ef.graph
logging.debug("Reference graph: {0}".format(p))
logging.debug("Patch graph: {0}".format(q))
newagp = deepcopy(agp)
seen = set()
deleted = set()
for a in agp:
if a.is_gap:
continue
name = a.component_id
object = a.object
if name in deleted:
print >>sys.stderr, "* Skip {0}, already embedded".format(name)
continue
seen.add(name)
target_name, tag = get_target(p, name)
path = q.get_path(name, target_name, tag=tag)
path_size = sum([sizes[x.v] for x, t in path]) if path else None
status = NO_UPDATE
# Heuristic, the patch must not be too long
if path and path_size > min_length and len(path) > 3:
path = None
if not path:
print >>sys.stderr, name, target_name, path, path_size, status
continue
backward = False
for x, t in path:
if x.v in seen:
print >>sys.stderr, "* Does not allow backward" " patch on {0}".format(x.v)
backward = True
break
if backward:
continue
# Build the path plus the ends
vv = q.get_node(name)
path.appendleft((vv, tag))
if tag == ">":
path.reverse()
status = INSERT_BEFORE
elif target_name is None:
status = INSERT_AFTER
else:
target = q.get_node(target_name)
path.append((target, tag))
status = INSERT_BETWEEN
print >>sys.stderr, name, target_name, path, path_size, status
# Trim the ends off from the constructed AGPLines
lines = path_to_agp(q, path, object, sizes, status)
if status == INSERT_BEFORE:
lines = lines[:-1]
td = newagp.insert_lines(name, lines, delete=True, verbose=True)
elif status == INSERT_AFTER:
lines = lines[1:]
td = newagp.insert_lines(name, lines, after=True, delete=True, verbose=True)
else:
lines = lines[1:-1]
td = newagp.update_between(name, target_name, lines, delete=True, verbose=True)
deleted |= td
seen |= td
# Recruite big singleton contigs
CUTOFF = opts.min_length
for ctg, size in sizes.items():
if ctg in seen:
continue
if size < CUTOFF:
continue
newagp.append(AGPLine.cline(ctg, ctg, sizes, "?"))
# Write a new AGP file
newagpfile = "embedded.agp"
newagp.print_to_file(newagpfile, index=True)
tidy([newagpfile, contigs])
def run_gapsplit(infile=None, outfile=None):
gaps([infile, "--split"])
return outfile
def embed(args):
"""
%prog embed evidencefile scaffolds.fasta contigs.fasta
Use SSPACE evidencefile to scaffold contigs into existing scaffold
structure, as in `scaffolds.fasta`. Contigs.fasta were used by SSPACE
directly to scaffold.
Rules:
1. Only update existing structure by embedding contigs small enough to fit.
2. Promote singleton contigs only if they are big (>= min_length).
"""
p = OptionParser(embed.__doc__)
p.set_mingap(default=10)
p.add_option("--min_length", default=200, type="int",
help="Minimum length to consider [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 3:
sys.exit(not p.print_help())
evidencefile, scaffolds, contigs = args
min_length = opts.min_length
splitfasta, oagp, cagp = gaps([scaffolds, "--split",
"--mingap={0}".format(opts.mingap)])
agp = AGP(cagp)
p = agp.graph
ef = EvidenceFile(evidencefile, contigs)
sizes = ef.sz
q = ef.graph
logging.debug("Reference graph: {0}".format(p))
logging.debug("Patch graph: {0}".format(q))
newagp = deepcopy(agp)
seen = set()
deleted = set()
for a in agp:
if a.is_gap:
continue
name = a.component_id
object = a.object
if name in deleted:
print >> sys.stderr, "* Skip {0}, already embedded".format(name)
continue
seen.add(name)
target_name, tag = get_target(p, name)
path = q.get_path(name, target_name, tag=tag)
path_size = sum([sizes[x.v] for x, t in path]) if path else None
status = NO_UPDATE
# Heuristic, the patch must not be too long
if path and path_size > min_length and len(path) > 3:
path = None
if not path:
print >> sys.stderr, name, target_name, path, path_size, status
continue
backward = False
for x, t in path:
if x.v in seen:
print >> sys.stderr, "* Does not allow backward" \
" patch on {0}".format(x.v)
backward = True
break
if backward:
continue
# Build the path plus the ends
vv = q.get_node(name)
path.appendleft((vv, tag))
if tag == ">":
path.reverse()
status = INSERT_BEFORE
elif target_name is None:
status = INSERT_AFTER
else:
target = q.get_node(target_name)
path.append((target, tag))
status = INSERT_BETWEEN
print >> sys.stderr, name, target_name, path, path_size, status
# Trim the ends off from the constructed AGPLines
lines = path_to_agp(q, path, object, sizes, status)
if status == INSERT_BEFORE:
lines = lines[:-1]
td = newagp.insert_lines(name, lines, \
delete=True, verbose=True)
elif status == INSERT_AFTER:
lines = lines[1:]
td = newagp.insert_lines(name, lines, after=True, \
delete=True, verbose=True)
else:
lines = lines[1:-1]
td = newagp.update_between(name, target_name, lines, \
delete=True, verbose=True)
deleted |= td
seen |= td
# Recruite big singleton contigs
CUTOFF = opts.min_length
for ctg, size in sizes.items():
if ctg in seen:
continue
if size < CUTOFF:
continue
newagp.append(AGPLine.cline(ctg, ctg, sizes, "?"))
# Write a new AGP file
newagpfile = "embedded.agp"
newagp.print_to_file(newagpfile, index=True)
tidy([newagpfile, contigs])