def loadFromFasta(self,
handler,
save_names=False,
int_ids=False,
filter=lambda rec: True):
# type: (BinaryIO, bool, bool, Callable[[NamedSequence], bool]) -> DisjointigCollection
recs = list(SeqIO.parse_fasta(handler))
if save_names:
for rec in recs:
assert rec.id not in self.items.keys() and basic.Reverse(
rec.id) not in self.items.keys()
for rec in recs:
if not filter(rec):
continue
if save_names:
number = basic.parseNegativeNumber(rec.id)
if number is not None:
self.cnt = max(self.cnt, int(abs(number)) + 1)
if int_ids:
self.addNew(rec.seq, str(number))
else:
self.addNew(rec.seq)
else:
self.addNew(rec.seq)
return self
def EACL(aligner, cl_params, contigs, disjointigs, dot_plot, extender, lines, reads, save_handler):
cnt = 0
stop = False
while not stop:
stop = True
if cl_params.focus is None:
keys = list(lines.items.keys())
else:
keys = cl_params.focus
for line_id in keys:
if line_id not in lines.items:
if cl_params.focus is None:
continue
else:
for key in lines.items.keys():
if str(basic.parseNegativeNumber(basic.parseLineName(key)[-1])) == line_id and lines[key].knot is None:
line_id = key
break
if line_id not in lines.items.keys():
continue
line = lines[line_id]
sys.stdout.info("Investigating", line)
extended = extender.processLine(line)
if extended > 0:
cnt += 1
stop = False
if cnt > 10:
cnt = 0
if save_handler is not None:
printState(lines)
sys.stdout.trace( "Saving current state")
writer = save_handler.getWriter()
sys.stdout.trace( "Save details:", writer.info)
saveAll(writer, cl_params, aligner, contigs, reads, disjointigs, lines, dot_plot)
def parse(self, edge_ids=None):
# type: (Optional[Dict[int, List[str]]]) -> Generator[Tuple[int, int, int, int, EdgeInfo]]
for s in self.dot.readlines():
if s.find("->") == -1:
continue
v_from = basic.parseNumber(s)
v_to = basic.parseNumber(s, s.find("->"))
eid = basic.parseNegativeNumber(s, s.find("id"))
len = basic.parseNegativeNumber(s, s.find("\\l"))
cov = basic.parseNumber(s, s.find("k "))
unique = (s.find("black") != -1)
src = (s.find("dir = both") != -1)
if edge_ids is None or eid in edge_ids:
if edge_ids is not None:
if "sink" in edge_ids[eid]:
v_to = "sink"
if "source" in edge_ids[eid]:
v_from = "source"
yield eid, v_from, v_to, cov, EdgeInfo(s, unique, cov, len,
src)