:param transformer: The MutationTransformer that takes in the original sequence
and applies the SNP mutations. Mutation structures will vary
with each transformer.
"""
xf = transformer
e = None
try:
sequences = xf.sequence_variants(original, mutations, combination_width, strand)
except ReturnWithCaveats, e:
rc = e
sequences = e.return_value
sequences = [seq for seq in sequences if seq.positive_strand_sequence != original.positive_strand_sequence]
if original.strand == strand:
sequences.insert(0, TransformedGenomeSequence.from_sequence(original))
else:
sequences.insert(0, TransformedGenomeSequence.from_sequence(original.reverse_complement()))
if e:
raise ReturnWithCaveats(e.explanations, sequences)
else:
return sequences
def find_in_sequence(fragment, sequence):
regex = base_regexp_expand(fragment, overlap=True)
return __find_in_sequence_regex(regex, sequence, overlapped=True)
def __find_in_sequence_regex(regex, sequence, overlapped=True):
seq_matches = []
def duplicate(cls, sequence, name=None):
return TransformedGenomeSequence.from_sequence(sequence, name=name)
