def test_drop_similar_different_lengths(self):
c1 = Contig(
'atcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatcgatcgatatgggcatcagc',
2)
c2 = Contig(
'atcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatcgatcgatagggcatcagc',
1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(1, len(result))
self.assertEqual(c1.seq, result[0].seq)
def test_drop_similar_different_lengths(self):
c1 = Contig(
'atcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatcgatcgatatgggcatcagc',
2,
)
c2 = Contig(
'atcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatatcgatcgatcgatcgatcgatcgatagggcatcagc',
1,
)
result = filter_contigs([c2, c1], 0.10)
assert len(result) == 1
assert result[0].seq == c1.seq
def test_retain_disimilar_different_lengths(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 2)
c2 = Contig('atcgatcgatcgatcgatcgatcccgtgatatagggcatcagc', 1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(2, len(result))
def test_retain_disimilar(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 2)
c2 = Contig('atcgadatcgatcgatcgatctgtdstcgatatagggca', 1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(2, len(result))
def test_drop_alt_allele_by_score(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 2)
c2 = Contig('atcgatcgatcgatcgatctatcgatatagggcatcagc', 1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(1, len(result))
self.assertEqual(c1.seq, result[0].seq)
def test_drop_reverse_complement(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 1)
c2 = Contig('gctgatgccctatatcgatcgatcgatcgatcgatcgat', 1)
result = filter_contigs([c2, c1], 0.10)
self.assertEqual(1, len(result))
self.assertEqual(c1.seq, result[0].seq)
def test_drop_alt_allele_by_score(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 2)
c2 = Contig('atcgatcgatcgatcgatctatcgatatagggcatcagc', 1)
result = filter_contigs([c2, c1], 0.10)
assert len(result) == 1
assert result[0].seq == c1.seq
def test_drop_reverse_complement(self):
c1 = Contig('atcgatcgatcgatcgatcgatcgatatagggcatcagc', 1)
c2 = Contig('gctgatgccctatatcgatcgatcgatcgatcgatcgat', 1)
result = filter_contigs([c2, c1], 0.10)
assert len(result) == 1
assert result[0].seq == c1.seq
