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BUG: nondeterministic inclusion of sequences in extract-reads #210

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BUG: nondeterministic inclusion of sequences in extract-reads #210

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7 changes: 4 additions & 3 deletions q2_feature_classifier/_cutter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ def _seq_to_regex(seq):
for base in str(seq):
if base in skbio.DNA.degenerate_chars:
result.append('[{0}]'.format(
''.join(skbio.DNA.degenerate_map[base])))
''.join(sorted(skbio.DNA.degenerate_map[base]))))
else:
result.append(base)

Expand All @@ -39,15 +39,16 @@ def _primers_to_regex(f_primer, r_primer):

def _local_aln(primer, sequence):
best_score = None
for one_primer in primer.expand_degenerates():
for one_primer in sorted([str(s) for s in primer.expand_degenerates()]):
# `sequence` may contain degenerates. These will usually be N
# characters, which SSW will score as zero. Although undocumented, SSW
# will treat other degenerate characters as a mismatch. We acknowledge
# that this approach is a heuristic to finding an optimal alignment and
# may be revisited in the future if there's an aligner that explicitly
# handles degenerates.
this_aln = \
skbio.alignment.local_pairwise_align_ssw(one_primer, sequence)
skbio.alignment.local_pairwise_align_ssw(skbio.DNA(one_primer),
sequence)
score = this_aln[1]
if best_score is None or score > best_score:
best_score = score
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