def align_to_named_seq(self, seqs):
"""returns alignment to named seq"""
if self._moltype and self._moltype != seqs.moltype:
seqs = seqs.to_moltype(self._moltype)
ref_seq = seqs.get_seq(self._ref_name)
aligned = None
kwargs = self._kwargs.copy()
no_ref_gap = None
for i in range(seqs.num_seqs):
seq = seqs.seqs[i]
if seq.name == self._ref_name:
continue
result = global_pairwise(ref_seq, seq, **kwargs)
if no_ref_gap is None:
no_ref_gap = _GapInRef(result.moltype, seqs.moltype.gap)
# as we're going to be using a pairwise distance that excludes gaps
# eliminating positions with deletions in the reference
result = result.filtered(no_ref_gap)
aligned = result if aligned is None else aligned.add_from_ref_aln(result)
# default to ArrayAlign
new = aligned.to_type(array_align=True, moltype=self._moltype)
return new
def align_to_named_seq(self, seqs):
"""returns alignment to named seq"""
seqs = seqs.to_moltype(self._moltype)
ref_seq = seqs.get_seq(self._ref_name)
aligned = None
kwargs = self._kwargs.copy()
def gap_in_ref(gap_char):
gap_char = gap_char[0]
def array_ref_gap(x):
r = x.flatten()[0] != gap_char
return r
def standard_ref_gap(x):
r = x[0] != gap_char
return r
func = {"-": standard_ref_gap}.get(gap_char, array_ref_gap)
return func
no_ref_gap = None
for i in range(seqs.num_seqs):
seq = seqs.seqs[i]
if seq.name == self._ref_name:
continue
result = global_pairwise(ref_seq, seq, **kwargs)
if no_ref_gap is None:
gap = result.moltype.alphabet.to_indices(seqs.moltype.gap)
no_ref_gap = gap_in_ref(gap)
# as we're going to be using a pairwise distance that excludes gaps
# eliminating positions with deletions in the reference
result = result.filtered(no_ref_gap)
if aligned is None:
aligned = result.to_type(array_align=False)
continue
aligned = aligned.add_from_ref_aln(
result.to_type(array_align=False))
new = ArrayAlignment(aligned.to_dict(),
moltype=seqs.moltype,
info=seqs.info)
return new
def align_to_named_seq(self, seqs):
"""returns alignment to named seq"""
if self._moltype and self._moltype != seqs.moltype:
seqs = seqs.to_moltype(self._moltype)
ref_seq = seqs.get_seq(self._ref_name)
kwargs = self._kwargs.copy()
pwise = []
for seq in seqs.seqs:
if seq.name == self._ref_name:
continue
aln = global_pairwise(ref_seq, seq,
**kwargs).to_type(array_align=False)
pwise.append(((seq.name, aln)))
return pairwise_to_multiple(pwise,
ref_seq,
self._moltype,
info=seqs.info)
