def path_to_agp(g, path, object, sizes, status):
lines = []
for (a, ao), (b, bo) in pairwise(path):
ao = get_orientation(ao, status)
e = g.get_edge(a.v, b.v)
cline = AGPLine.cline(object, a.v, sizes, ao)
gline = AGPLine.gline(object, e.length)
lines.append(cline)
lines.append(gline)
# Do not forget the last one
z, zo = path[-1]
zo = get_orientation(zo, status)
cline = AGPLine.cline(object, z.v, sizes, zo)
lines.append(cline)
return lines
def path_to_agp(g, path, object, sizes, status):
lines = []
for (a, ao), (b, bo) in pairwise(path):
ao = get_orientation(ao, status)
e = g.get_edge(a.v, b.v)
cline = AGPLine.cline(object, a.v, sizes, ao)
gline = AGPLine.gline(object, e.length)
lines.append(cline)
lines.append(gline)
# Do not forget the last one
z, zo = path[-1]
zo = get_orientation(zo, status)
cline = AGPLine.cline(object, z.v, sizes, zo)
lines.append(cline)
return lines
def write_agp(self, filename):
sizes = self.sz
agp = []
for scaffold, lines in self.iter_scaffold():
for a, b in pairwise(lines):
cline = AGPLine.cline(scaffold, a.tig, sizes, a.oo)
gline = AGPLine.gline(scaffold, a.gaps)
agp.append(cline)
agp.append(gline)
a = lines[-1]
cline = AGPLine.cline(scaffold, a.tig, sizes, a.oo)
agp.append(cline)
fw = open(filename, "w")
for a in agp:
print >> fw, a
fw.close()
reindex([filename, "--inplace"])
return filename
def write_agp(self, filename):
sizes = self.sz
agp = []
for scaffold, lines in self.iter_scaffold():
for a, b in pairwise(lines):
cline = AGPLine.cline(scaffold, a.tig, sizes, a.oo)
gline = AGPLine.gline(scaffold, a.gaps)
agp.append(cline)
agp.append(gline)
a = lines[-1]
cline = AGPLine.cline(scaffold, a.tig, sizes, a.oo)
agp.append(cline)
fw = open(filename, "w")
for a in agp:
print >> fw, a
fw.close()
reindex([filename, "--inplace"])
return filename
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 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])