def _get_mutations(seqs, standard):
mutations = []
for seq in seqs:
aln = global_alignment(seq, target=standard,
matrix='blosum62', gap_open=-15, gap_extend=-1)
mutations.extend(_parse_mutations(aln))
return mutations
def realign_germline(self, antibody, query_start=None, query_end=None):
'''
Due to restrictions on the available scoring parameters in BLASTn, incorrect truncation
of the v-gene alignment can occur. This function re-aligns the query sequence with
the identified germline variable gene using more appropriate alignment parameters.
Args:
oriented_input (str): the raw input sequence, correctly oriented
query_start (int): 5' position in `oriented_input` at which the sequence
should be truncated prior to alignment with the germline sequence.
query_end (int): 3' position in `oriented_input` at which the seqeunce
should be truncated prior to alignment with the germline sequence
'''
oriented_input = antibody.oriented_input
germline_seq = self._get_germline_sequence_for_realignment()
aln_params = self._realignment_scoring_params(self.gene_type)
# if the alignment start/end positions have been annotated by the assigner,
# force re-alignment using those parameters
if all([
x is not None for x in [
self.query_start, self.query_end, self.germline_start,
self.germline_end
]
]):
query = oriented_input.sequence[self.query_start:self.query_end]
germline = germline_seq[self.germline_start:self.germline_end]
alignment = global_alignment(query, germline, **aln_params)
# use local alignment to determine alignment start/end positions if
# they haven't already been determined by the assigner
else:
query = oriented_input.sequence[query_start:query_end]
alignment = local_alignment(query, germline_seq, **aln_params)
if alignment:
self._process_realignment(antibody, alignment, query_start)
else:
antibody.log('GERMLINE REALIGNMENT ERROR')
antibody.log('REALIGNMENT QUERY SEQUENCE:', query)
antibody.log('QUERY START:', query_start)
antibody.log('QUERN END:', query_end)
def _align_to_reference(self):
aln = global_alignment(self.sequence, self.reference, aa=True)
self._aligned = aln.aligned_query
self._aligned_reference = aln.aligned_target