def correctSequences(self, interesting_segments):
# type: (Iterable[Segment]) -> List[Segment]
interesting_segments = list(interesting_segments)
to_correct = []
for seg in interesting_segments:
line = seg.contig # type: NewLine
correct = line.correct_segments.find(seg)
next = line.correct_segments.find(line.suffix(correct.right), 1)
if next is None:
right = len(line)
else:
right = min(len(line), next.left + params.k / 2)
to_correct.append(line.segment(correct.right - params.k / 2,
right))
to_correct = sorted(to_correct,
key=lambda seg:
(basic.Normalize(seg.contig.id), seg.left))
corrected = []
for line_id, it in itertools.groupby(
to_correct, key=lambda seg: basic.Normalize(
seg.contig.id)): # type: NewLine, Iterable[Segment]
it = list(it)
line = None # type: NewLine
forward = SegmentStorage()
backward = SegmentStorage()
for seg in it:
if seg.contig.id != line_id:
backward.add(seg)
line = seg.contig.rc
else:
forward.add(seg)
line = seg.contig
to_polysh = SegmentStorage()
to_polysh.addAll(forward).addAll(backward.rc)
to_polysh.mergeSegments()
line.addListener(to_polysh)
line.addListener(forward)
line.rc.addListener(backward)
sys.stdout.trace("Polishing:", to_polysh)
if (not line.max_extension) and to_polysh[-1].RC().left < 200:
l = to_polysh[-1].right
if self.attemptExtend(line):
to_polysh.add(line.asSegment().suffix(pos=l))
forward.add(line.asSegment().suffix(pos=l))
if (not line.rc.max_extension) and to_polysh[0].left < 200:
l = to_polysh[0].RC().right
if self.attemptExtend(line.rc):
to_polysh.rc.add(line.rc.asSegment().suffix(pos=l))
backward.add(line.rc.asSegment().suffix(pos=l))
to_polysh.mergeSegments()
forward.mergeSegments()
backward.mergeSegments()
line.removeListener(to_polysh)
new_segments = self.polyshSegments(line, to_polysh)
line.removeListener(forward)
line.rc.removeListener(backward)
corrected.extend(forward)
corrected.extend(backward)
line.updateCorrectSegments(line.asSegment())
return corrected
def polyshSegments(self, line, to_polysh):
# type: (NewLine, Iterable[Segment]) -> List[Segment]
segs = SegmentStorage()
corrections = AlignmentStorage()
line.addListener(segs)
segs.addAll(to_polysh)
segs.mergeSegments()
segs.sort()
for seg in segs:
corrections.add(
self.polisher.polishSegment(
seg, list(line.read_alignments.allInter(seg))))
line.correctSequence(list(corrections))
line.removeListener(segs)
return list(segs)
class NewLine(Contig):
def __init__(self, seq, id, extension_handler, rc = None):
# type: (str, str, ExtensionHandler, Optional[NewLine]) -> None
self.extensionHandler = extension_handler
self.seq = seq
self.id = id # type: str
self.circular = False
self.name_printer = None
self.max_extension = False
if rc is None:
self.initial = AlignmentStorage()
self.correct_segments = SegmentStorage()
self.completely_resolved = SegmentStorage()
self.disjointig_alignments = AlignmentStorage()
self.read_alignments = ReadAlignmentStorage()
self.listeners = [self.initial, self.correct_segments, self.completely_resolved, self.disjointig_alignments, self.read_alignments, extension_handler] # type: List[LineListener]
rc = NewLine(basic.RC(seq), basic.Reverse(self.id), extension_handler.rc, self) #type: NewLine
self.rc = rc
self.addListener(ReadAlignmentListener(self))
# self.initial.add(AlignmentPiece.Identical(self.asSegment().asContig().asSegment(), self.asSegment()))
else:
self.initial = rc.initial.rc # type: AlignmentStorage
self.correct_segments = rc.correct_segments.rc # type: SegmentStorage
self.completely_resolved = rc.completely_resolved.rc # type: SegmentStorage
self.disjointig_alignments = rc.disjointig_alignments.rc # type: AlignmentStorage
self.read_alignments = rc.read_alignments.rc # type: ReadAlignmentStorage
self.listeners = [listener.rc for listener in rc.listeners] # type: List[LineListener]
Contig.__init__(self, seq, id, rc)
self.rc = rc #type: NewLine
self.knot = None # type: Knot
def updateCorrectSegments(self, seg, threshold = params.reliable_coverage):
# type: (Segment, int) -> None
segs = AlignmentStorage().addAll(self.read_alignments.allInter(seg)).filterByCoverage(mi=threshold)
self.correct_segments.addAll(segs)
self.correct_segments.mergeSegments()
def addReads(self, alignments):
# type: (Iterable[AlignmentPiece]) -> None
self.read_alignments.addAll(alignments)
self.max_extension = False
def getReadAlignmentsTo(self, seg):
# type: (Segment) -> Iterable[AlignmentPiece]
return self.read_alignments.getAlignmentsTo(seg)
def getPotentialAlignmentsTo(self, seg):
# type: (Segment) -> Generator[AlignmentPiece]
result = []
for alDL in self.disjointig_alignments.getAlignmentsTo(seg):
reduced = alDL.reduce(target=seg)
dt = alDL.seg_from.contig # type: Disjointig
for alRD in dt.getAlignmentsTo(reduced.seg_from):
result.append(alRD.compose(alDL))
result = sorted(result, key = lambda al: (al.seg_from.contig.id, -len(al.seg_from)))
for read, iter in itertools.groupby(result, key = lambda al: al.seg_from.contig):
readRes = []
for al in iter:
found = False
for al1 in readRes:
inter = al.matchingSequence(True).inter(al1.matchingSequence(True))
if len(inter.matches) != 0:
found = True
if not found:
yield al
readRes.append(al)
def getRelevantAlignmentsFor(self, seg):
# type: (Segment) -> Generator[AlignmentPiece]
sys.stdout.trace("Requesting read alignments for", seg)
result = []
if params.debug:
print self.disjointig_alignments
print list(self.disjointig_alignments.allInter(seg))
for alDL in self.disjointig_alignments.allInter(seg):
if len(alDL.seg_to) < params.k:
continue
reduced = alDL.reduce(target=seg)
dt = alDL.seg_from.contig # type: Disjointig
cnt = 0
als = filter(lambda al: al.seg_to.interSize(alDL.seg_from) > 8 * params.k / 10, dt.allInter(reduced.seg_from))
compositions = alDL.massComposeBack(als)
for al in compositions:
if len(al.seg_to) >= params.k:
result.append(al)
cnt += 1
sys.stdout.trace("Request for read alignments for", seg, " collecting finished. Started filtering")
result = sorted(result, key = lambda al: (al.seg_from.contig.id, -len(al.seg_from)))
for read, iter in itertools.groupby(result, key = lambda al: al.seg_from.contig): # type: AlignedRead, Generator[AlignmentPiece]
readRes = []
for al in iter:
found = False
for al1 in readRes:
inter = al.matchingSequence(True).inter(al1.matchingSequence(True))
if len(inter.matches) != 0:
found = True
break
if not found:
if params.debug:
print al
yield al
readRes.append(al)
sys.stdout.trace("Request for read alignments for", seg, "finished")
def position(self, pos):
# type: (int) -> LinePosition
return LinePosition(self, pos)
def extendRight(self, seq, relevant_als = None):
# type: (str, List[AlignmentPiece]) -> None
sys.stdout.trace("Line operation Extend:", self, len(seq), relevant_als)
assert self.knot is None
if relevant_als is None:
relevant_als = []
new_seq = Contig(self.seq + seq, "TMP2_" + self.id)
self.notifyBeforeExtendRight(new_seq, seq)
self.seq = self.seq + seq
self.rc.seq = basic.RC(seq) + self.rc.seq
self.notifyAfterExtendRight(seq, relevant_als)
self.updateCorrectSegments(self.asSegment())
self.max_extension = True
def notifyBeforeExtendRight(self, new_seq, seq):
# type: (Contig, str) -> None
for listener in self.listeners:
listener.fireBeforeExtendRight(self, new_seq, seq)
def notifyAfterExtendRight(self, seq, relevant_als):
# type: (str, Optional[List[AlignmentPiece]]) -> None
for listener in self.listeners:
listener.fireAfterExtendRight(self, seq, relevant_als)
def cutRight(self, pos):
sys.stdout.trace("Line operation Cut:", self, pos)
assert pos > 0 and pos <= len(self)
cut_length = len(self) - pos
if cut_length == 0:
return
new_seq = Contig(self.seq[:pos], "TMP3_" + self.id)
self.notifyBeforeCutRight(new_seq, pos)
self.seq = self.seq[:-cut_length]
self.rc.seq = self.rc.seq[cut_length:]
self.notifyAfterCutRight(pos)
def notifyBeforeCutRight(self, new_seq, pos):
# type: (Contig, int) -> None
for listener in self.listeners:
listener.fireBeforeCutRight(self, new_seq, pos)
def notifyAfterCutRight(self, pos):
# type: (int) -> None
for listener in self.listeners:
listener.fireAfterCutRight(self, pos)
def correctSequence(self, alignments):
# type: (Iterable[AlignmentPiece]) -> None
sys.stdout.trace("Line operation Correct:", alignments)
alignments = [al.cutIdenticalEnds() for al in alignments if al.seg_from.Seq() != al.seg_to.Seq()]
if len(alignments) == 0:
sys.stdout.trace("Skipping trivial correction operation")
return
assert len(alignments) > 0
correction = Correction.constructCorrection(alignments)
self.notifyBeforeCorrect(correction)
old = Contig(self.seq, "old")
self.seq = correction.seq_from.seq
self.rc.seq = basic.RC(self.seq)
correction.changeQT(self, old)
self.notifyAfterCorrect(correction)
def notifyBeforeCorrect(self, alignments):
# type: (Correction) -> None
for listener in self.listeners:
listener.fireBeforeCorrect(alignments)
def notifyAfterCorrect(self, alignments):
# type: (Correction) -> None
for listener in self.listeners:
listener.fireAfterCorrect(self, alignments)
def addReadAlignment(self, al):
# type: (AlignmentPiece) -> AlignmentPiece
self.read_alignments.add(al)
self.max_extension = False
return al
def addListener(self, listener):
self.listeners.append(listener)
self.rc.listeners.append(listener.rc)
def removeListener(self, listener):
self.listeners.remove(listener)
self.rc.listeners.remove(listener.rc)
def save(self, handler):
# type: (TokenWriter) -> None
handler.writeTokenLine(self.id)
handler.writeTokenLine(self.seq)
self.initial.save(handler)
self.correct_segments.save(handler)
self.completely_resolved.save(handler)
self.disjointig_alignments.save(handler)
self.read_alignments.save(handler)
def loadLine(self, handler, disjointigs, reads, contigs):
# type: (TokenReader, DisjointigCollection, ReadCollection, ContigCollection) -> None
self.id = handler.readToken()
self.seq = handler.readToken()
self.rc.id = basic.Reverse(self.id)
n = handler.readInt()
for i in range(n):
handler.readToken()
handler.readToken()
handler.readToken()
seg = Segment.load(handler, self)
handler.readToken()
self.initial.add(AlignmentPiece.Identical(seg.asContig().asSegment(), seg))
# self.add(AlignmentPiece.load(handler, collection_from, collection_to))
self.correct_segments.load(handler, self)
self.completely_resolved.load(handler, self)
self.disjointig_alignments.load(handler, disjointigs, self)
self.read_alignments.load(handler, reads, self)
for al in self.read_alignments:
read = al.seg_from.contig #type: AlignedRead
read.addAlignment(al)
self.max_extension = False
def __str__(self):
if self.name_printer is not None:
return self.name_printer(self)
points = [self.left()]
if len(self.initial) == 0:
points.append("NA")
else:
points.append(self.initial[0].seg_to.left)
points.append(self.initial[-1].seg_to.right)
points.append(self.right())
points = map(str, points)
return "Line:" + str(self.id) + ":" + "[" + ":".join(points) +"]"
def __repr__(self):
points = [self.left()]
points.extend(self.initial)
points.append(self.right())
points = map(str, points)
return "Line:" + str(self.id) + ":" + "[" + ":".join(points) +"]"
def setCircular(self):
self.circular = True
self.rc.circular = True
def cleanReadAlignments(self):
for read in self.read_alignments:
read.seg_from.contig.removeContig(self)
self.read_alignments.clean()
self.max_extension = False
def tie(self, other, gap, gap_seq):
self.knot = Knot(self, other, gap, gap_seq)
other.rc.knot = self.knot.rc
if self == other:
self.setCircular()
def unTie(self):
if self.knot is not None:
self.knot.line_right.rc.knot = None
if self.knot is not None:
self.knot = None