def allSingleBaseMutations(templateSequence, positions=None):
"""
Same as ``uniqueSingleBaseMutations``, but no filtering as to
whether the mutated sequences are unique.
"""
allBases = "ACGT"
positions = positions or xrange(0, len(templateSequence))
for tplStart in positions:
tplBase = templateSequence[tplStart]
# snvs
for subsBase in allBases:
if subsBase != tplBase:
yield cc.Mutation_Substitution(tplStart, subsBase)
# Insertions
for insBase in allBases:
yield cc.Mutation_Insertion(tplStart, insBase)
# Deletion
yield cc.Mutation_Deletion(tplStart, 1)
def uniqueSingleBaseMutations(templateSequence, positions=None):
"""
Return an iterator over all single-base mutations of a
templateSequence that result in unique mutated sequences.
"""
allBases = "ACGT"
positions = positions or xrange(0, len(templateSequence))
for tplStart in positions:
tplBase = templateSequence[tplStart]
prevTplBase = templateSequence[tplStart-1] if (tplStart > 0) else None
# snvs
for subsBase in allBases:
if subsBase != tplBase:
yield cc.Mutation_Substitution(tplStart, subsBase)
# Insertions---only allowing insertions that are not cognate
# with the previous base.
for insBase in allBases:
if insBase != prevTplBase:
yield cc.Mutation_Insertion(tplStart, insBase)
# Deletion--only allowed if refBase does not match previous tpl base
if tplBase != prevTplBase:
yield cc.Mutation_Deletion(tplStart, 1)