def test_region_subject_to_query_no_endgaps(self):
a = AlignedPair(
("a", "ABCDEF"),
("b", "HIJKLM"))
# In an alignment with no gaps, the query sequence coordinates should
# always match the subject sequence coordinates
r = AlignedRegion.from_subject(a, 0, 3)
self.assertEqual(r.in_alignment(), (0, 3))
rq = AlignedRegion.from_query(a, 0, 3)
self.assertEqual(r.in_alignment(), (0, 3))
r = AlignedRegion.from_subject(a, 1, 5)
self.assertEqual(r.in_alignment(), (1, 5))
rq = AlignedRegion.from_query(a, 1, 5)
self.assertEqual(r.in_alignment(), (1, 5))
r = AlignedRegion.from_subject(a)
self.assertEqual(r.in_alignment(), (0, 6))
rq = AlignedRegion.from_query(a)
self.assertEqual(r.in_alignment(), (0, 6))
def test_from_query_with_endgaps(self):
a = AlignedPair(
("a", "--ABC-EF---"),
("b", "HIJKLMNOPQR"))
r = AlignedRegion.from_query(a, 1, 4)
self.assertEqual(r.start_idx, 3)
self.assertEqual(r.end_idx, 7)
self.assertEqual(r.in_query(), (1, 4))
self.assertEqual(r.in_subject(), (3, 7))
self.assertEqual(r.query_offset(), 0)
self.assertEqual(r.subject_offset(), 0)
def test_from_query_region_crazy(self):
a = AlignedPair(
("a", "-A-BC-EF---"),
# |||| (1, 5)
("b", "--HI-JK-LMN"))
r = AlignedRegion.from_query(a, 0, 3)
self.assertEqual(r.in_alignment(), (1, 5))
self.assertEqual(r.in_query(), (0, 3))
self.assertEqual(r.in_subject(), (0, 2))
self.assertEqual(r.query_offset(), 0)
self.assertEqual(r.subject_offset(), 0)
def test_from_query_no_endgaps(self):
a = AlignedPair(
("a", "ABCDEF"),
("b", "HIJKLM"))
r = AlignedRegion.from_query(a, 2, 5)
self.assertEqual(r.start_idx, 2)
self.assertEqual(r.end_idx, 5)
self.assertEqual(r.in_query(), (2, 5))
self.assertEqual(r.in_subject(), (2, 5))
self.assertEqual(r.query_offset(), 0)
self.assertEqual(r.subject_offset(), 0)