def makeConsensusSequence(self):
min_confscore = self.settings.getMinConfScore()
# Get the raw sequences and align the forward/reverse traces if we have both.
if self.numseqs == 2:
align = PairwiseAlignment()
align.setSequences(self.seqtraces[0].getBaseCalls(),
self.seqtraces[1].getBaseCalls())
align.doAlignment()
self.alignedseqs[0], self.alignedseqs[
1] = align.getAlignedSequences()
self.seqindexes[0], self.seqindexes[
1] = align.getAlignedSeqIndexes()
else:
self.alignedseqs[0] = self.seqtraces[0].getBaseCalls()
self.seqindexes[0] = range(0, len(self.alignedseqs[0]))
# If we have primers, align them to the alignment or single sequence.
haveprimers = (self.settings.getForwardPrimer() != ''
and self.settings.getReversePrimer() != '')
if haveprimers:
if self.numseqs == 1:
self.alignPrimerToSequence()
else:
self.alignPrimersToAlignment()
# Build the consensus sequence.
if self.numseqs == 1:
self.makeSingleConsensus(min_confscore)
else:
if self.settings.getConsensusAlgorithm() == 'Bayesian':
self.makeBayesianConsensus(min_confscore)
else:
self.makeLegacyConsensus(min_confscore)
# Do sequence trimming, if requested.
if self.settings.getTrimConsensus():
if self.settings.getTrimPrimers() and haveprimers:
if self.numseqs == 1:
self.trimPrimerFromSequence()
else:
self.trimPrimersFromAlignment()
if self.settings.getTrimEndGaps():
self.trimEndGaps()
if self.settings.getDoQualityTrim():
winsize, basecnt = self.settings.getQualityTrimParams()
self.trimConsensus(winsize, basecnt)
def makeConsensusSequence(self):
min_confscore = self.settings.getMinConfScore()
# Get the raw sequences and align the forward/reverse traces if we have both.
if self.numseqs == 2:
align = PairwiseAlignment()
align.setSequences(self.seqtraces[0].getBaseCalls(), self.seqtraces[1].getBaseCalls())
align.doAlignment()
self.alignedseqs[0], self.alignedseqs[1] = align.getAlignedSequences()
self.seqindexes[0], self.seqindexes[1] = align.getAlignedSeqIndexes()
else:
self.alignedseqs[0] = self.seqtraces[0].getBaseCalls()
self.seqindexes[0] = range(0, len(self.alignedseqs[0]))
# If we have primers, align them to the alignment or single sequence.
haveprimers = (self.settings.getForwardPrimer() != '' and self.settings.getReversePrimer() != '')
if haveprimers:
if self.numseqs == 1:
self.alignPrimerToSequence()
else:
self.alignPrimersToAlignment()
# Build the consensus sequence.
if self.numseqs == 1:
self.makeSingleConsensus(min_confscore)
else:
if self.settings.getConsensusAlgorithm() == 'Bayesian':
self.makeBayesianConsensus(min_confscore)
else:
self.makeLegacyConsensus(min_confscore)
# Do sequence trimming, if requested.
if self.settings.getTrimConsensus():
if self.settings.getTrimPrimers() and haveprimers:
if self.numseqs == 1:
self.trimPrimerFromSequence()
else:
self.trimPrimersFromAlignment()
if self.settings.getTrimEndGaps():
self.trimEndGaps()
if self.settings.getDoQualityTrim():
winsize, basecnt = self.settings.getQualityTrimParams()
self.trimConsensus(winsize, basecnt)
def alignPrimerToSequence(self):
"""
Aligns a primer sequence to the base calls of a single trace file.
Also adjusts the alignment and alignment indices to accomodate
the alignment with the primer, if extra gaps are needed. An
alignment-length string containing the aligned primer in the
appropriate location is saved as self.alignedprimers.
"""
if self.numseqs == 2:
return
# Figure out if we're working on a reverse trace and get the
# appropriate primer sequence to search for.
isreverse = self.seqtraces[0].isReverseComplemented()
if isreverse:
primer = self.settings.getForwardPrimer()
else:
primer = sequencetrace.reverseCompSequence(
self.settings.getReversePrimer())
if primer == '':
return
# Align the primer sequence to the trace sequence. Using a harsher gap
# penalty (-12 instead of -6) seems to improve the chances of getting the
# primer to align in the correct location.
align = PairwiseAlignment()
align.setGapPenalty(-12)
align.setSequences(primer, self.alignedseqs[0])
align.doAlignment()
praligned, seqaligned = align.getAlignedSequences()
# Use the new alignment for the trace sequence and index list.
self.alignedseqs[0] = seqaligned
self.seqindexes[0] = align.getAlignedSeqIndexes()[1]
# Replace starting and ending gap characters in the aligned primer
# sequences with spaces.
praligned = self.trimAlignedPrimerEnds(praligned)
self.alignedprimers = praligned
def alignPrimerToSequence(self):
"""
Aligns a primer sequence to the base calls of a single trace file.
Also adjusts the alignment and alignment indices to accomodate
the alignment with the primer, if extra gaps are needed. An
alignment-length string containing the aligned primer in the
appropriate location is saved as self.alignedprimers.
"""
if self.numseqs == 2:
return
# Figure out if we're working on a reverse trace and get the
# appropriate primer sequence to search for.
isreverse = self.seqtraces[0].isReverseComplemented()
if isreverse:
primer = self.settings.getForwardPrimer()
else:
primer = sequencetrace.reverseCompSequence(self.settings.getReversePrimer())
if primer == '':
return
# Align the primer sequence to the trace sequence. Using a harsher gap
# penalty (-12 instead of -6) seems to improve the chances of getting the
# primer to align in the correct location.
align = PairwiseAlignment()
align.setGapPenalty(-12)
align.setSequences(primer, self.alignedseqs[0])
align.doAlignment()
praligned, seqaligned = align.getAlignedSequences()
# Use the new alignment for the trace sequence and index list.
self.alignedseqs[0] = seqaligned
self.seqindexes[0] = align.getAlignedSeqIndexes()[1]
# Replace starting and ending gap characters in the aligned primer
# sequences with spaces.
praligned = self.trimAlignedPrimerEnds(praligned)
self.alignedprimers = praligned
