def test_Align2_reversed(self):
"""Tests the Align method, reversing query and ref from above."""
aligner = ssw.Aligner()
filter_ = ssw.Filter()
aligner.set_reference_sequence(QUERY)
alignment = aligner.align(REF, filter_)
self.assertEqual(21, alignment.sw_score)
self.assertEqual(8, alignment.query_begin)
self.assertEqual(21, alignment.query_end)
self.assertEqual(0, alignment.ref_begin)
self.assertEqual(14, alignment.ref_end)
self.assertEqual(2, alignment.mismatches)
self.assertEqual('8S4=1X4=1D5=17S', alignment.cigar_string)
def test_Align(self):
"""Tests the Align method."""
aligner = ssw.Aligner()
filter_ = ssw.Filter()
length = aligner.set_reference_sequence(REF)
self.assertEqual(len(REF), length)
alignment = aligner.align(QUERY, filter_)
self.assertEqual(21, alignment.sw_score)
self.assertEqual(8, alignment.sw_score_next_best)
self.assertEqual(8, alignment.ref_begin)
self.assertEqual(21, alignment.ref_end)
self.assertEqual(0, alignment.query_begin)
self.assertEqual(14, alignment.query_end)
self.assertEqual(4, alignment.ref_end_next_best)
self.assertEqual(2, alignment.mismatches)
self.assertEqual('4=1X4=1I5=', alignment.cigar_string)
def __init__(self, query_seq, match, mismatch, gap_open_penalty,
gap_extend_penalty):
"""Creates a new LibSSWPairwiseAligner, aligning against query_seq.
Arguments:
query_seq: str, the string we'll align our targets against.
match: int > 0, alignment match score.
mismatch: int > 0, alignment mismatch score.
gap_open_penalty: int > 0, alignment gap_open penalty score.
gap_extend_penalty: int > 0, alignment gap_extension penalty score.
"""
self.filter = libssw.Filter()
self.aligner = libssw.Aligner.construct(
match_score=match,
mismatch_penalty=mismatch,
gap_opening_penalty=gap_open_penalty,
gap_extending_penalty=gap_extend_penalty)
self.query = query_seq
def test_longer(self):
"""Test longer strings, so the second-best alignment is considered."""
ref = 'TTTTGGGGGGGGGGGGG'
query = 'TTATTGGGGGGGGGGGGG'
match = 4
mismatch = 2
gap_extend_penalty = 2
gap_open_penalty = 4
aligner = ssw.Aligner.construct(
match_score=match,
mismatch_penalty=mismatch,
gap_opening_penalty=gap_open_penalty,
gap_extending_penalty=gap_extend_penalty)
filter_ = ssw.Filter()
length = aligner.set_reference_sequence(ref)
self.assertEqual(len(ref), length)
alignment = aligner.align(query, filter_)
p(alignment)
self.assertEqual('2=1I15=', alignment.cigar_string)
def test_short(self):
"""Test very short strings."""
ref = 'tttt'
query = 'ttAtt'
match = 4
mismatch = 2
gap_extend_penalty = 2
gap_open_penalty = 4
aligner = ssw.Aligner.construct(
match_score=match,
mismatch_penalty=mismatch,
gap_opening_penalty=gap_open_penalty,
gap_extending_penalty=gap_extend_penalty)
filter_ = ssw.Filter()
length = aligner.set_reference_sequence(ref)
self.assertEqual(len(ref), length)
alignment = aligner.align(query, filter_)
p(alignment)
self.assertEqual('2=1I2=', alignment.cigar_string)
