def test_consensus_smaller_than_min_match_len(self):
"""
Usually, a match smaller than min_match_length counts as non-match,
but if the whole string is smaller than min_match_length, counts as match.
"""
tester1 = IntervalPartitioner("TTATT", min_match_length=7, alignment=MSA([]))
match, non_match, _ = tester1.get_intervals()
self.assertEqual(match, make_typed_intervals([[0, 4]], Match))
self.assertEqual(non_match, [])
tester2 = IntervalPartitioner("T*ATT", min_match_length=7, alignment=MSA([]))
match, non_match, _ = tester2.get_intervals()
self.assertEqual(match, [])
self.assertEqual(non_match, make_typed_intervals([[0, 4]], NonMatch))
def test_GivenUnorderedIds_SubalignmentStillInSequenceOrder(self):
"""
Sequences given rearranged are still output in input order
"""
result = PrgBuilder.get_sub_alignment_by_list_id(["s3", "s1"], self.alignment)
expected = MSA([self.alignment[0], self.alignment[2]])
self.assertTrue(msas_equal(expected, result))
def test_ambiguous_sequences_in_short_interval_separate_clusters(self):
alignment = MSA([
SeqRecord(Seq("ARAT"), id="s1"),
SeqRecord(Seq("WAAT"), id="s2"),
])
result = kmeans_cluster_seqs_in_interval([0, 3], alignment, 5)
self.assertEqual([["s1"], ["s2"]], result)
def test_get_subalignment_with_interval(self):
result = PrgBuilder.get_sub_alignment_by_list_id(
["s2", "s3"], self.alignment, [0, 2]
)
expected = MSA(
[SeqRecord(Seq("C--"), id="s2"), SeqRecord(Seq("AAT"), id="s3"),]
)
self.assertTrue(msas_equal(expected, result))
def test_TwoIdenticalSequencesClusteredTogether(self):
alignment = MSA([
SeqRecord(Seq("AAAT"), id="s1"),
SeqRecord(Seq("AAAT"), id="s2"),
SeqRecord(Seq("C-CC"), id="s3"),
])
result = kmeans_cluster_seqs_in_interval([0, 3], alignment, 1)
self.assertEqual([["s1", "s2"], ["s3"]], result)
def setUpClass(cls):
cls.alignment = MSA(
[
SeqRecord(Seq("AAAT"), id="s1"),
SeqRecord(Seq("C--C"), id="s2"),
SeqRecord(Seq("AATT"), id="s3"),
SeqRecord(Seq("GNGG"), id="s4"),
]
)
def test_end_in_non_match(self):
tester = IntervalPartitioner(
"**ATT**AAA*C", min_match_length=3, alignment=MSA([])
)
match, non_match, _ = tester.get_intervals()
self.assertEqual(match, make_typed_intervals([[2, 4], [7, 9]], Match))
self.assertEqual(
non_match, make_typed_intervals([[0, 1], [5, 6], [10, 11]], NonMatch)
)
def test_match_non_match_match(self):
tester = IntervalPartitioner("ATT**AAAC", min_match_length=3, alignment=MSA([]))
match, non_match, all_match = tester.get_intervals()
expected_matches = make_typed_intervals([[0, 2], [5, 8]], Match)
expected_non_matches = make_typed_intervals([[3, 4]], NonMatch)
self.assertEqual(match, expected_matches)
self.assertEqual(non_match, expected_non_matches)
# Check interval sorting works
self.assertEqual(
all_match,
[expected_matches[0], expected_non_matches[0], expected_matches[1]],
)
def test_one_long_one_short_sequence_separate_and_ordered_clusters(self):
alignment = MSA([
SeqRecord(Seq("AATTAATTATATAATAAC"), id="s1"),
SeqRecord(Seq("A--------------AAT"), id="s2"),
])
order_1 = kmeans_cluster_seqs_in_interval([0, len(alignment[0])],
alignment, 5)
self.assertEqual(order_1, [["s1"], ["s2"]])
order_2 = kmeans_cluster_seqs_in_interval([0, len(alignment[0])],
alignment[::-1], 5)
self.assertEqual(order_2, [["s2"], ["s1"]])
def test_GivenAllSequencesBelowKmerSize_NoKMeansAndIdenticalSequencesClustered(
self, mockKMeans):
alignment = MSA([
SeqRecord(Seq("AA---AT"), id="s1"),
SeqRecord(Seq("AA---TT"), id="s2"),
SeqRecord(Seq("CA--CAT"), id="s3"),
SeqRecord(Seq("A-A--AT"), id="s4"),
])
result = kmeans_cluster_seqs_in_interval([0, len(alignment[0])],
alignment, 6)
mockKMeans.assert_not_called()
self.assertEqual([["s1", "s4"], ["s2"], ["s3"]], result)
def test_GivenOrderedIds_SubalignmentInSequenceOrder(self):
result = PrgBuilder.get_sub_alignment_by_list_id(["s1", "s3"],
self.alignment)
expected = MSA([self.alignment[0], self.alignment[2]])
self.assertTrue(msas_equal(expected, result))
def test_short_match_counted_as_non_match(self):
tester = IntervalPartitioner("AT***", min_match_length=3, alignment=MSA([]))
match, non_match, _ = tester.get_intervals()
self.assertEqual(match, [])
self.assertEqual(non_match, make_typed_intervals([[0, 4]], NonMatch))
def test_all_match(self):
tester = IntervalPartitioner("ATATAAA", min_match_length=3, alignment=MSA([]))
match, non_match, _ = tester.get_intervals()
self.assertEqual(match, make_typed_intervals([[0, 6]], Match))
self.assertEqual(non_match, [])
def test_one_seq_returns_single_id(self):
alignment = MSA([SeqRecord(Seq("AAAT"), id="s1")])
result = kmeans_cluster_seqs_in_interval([0, 3], alignment, 1)
self.assertTrue(result.no_clustering)