def test_assemble(self):
sequences = ['ABCD', 'BCDE', 'CDEF', 'ABCDE', 'DEFG']
c = assemble(
sequences, 3, min_edge_trim_weight=1, remap_min_exact_match=1
)
self.assertEqual(1, len(c))
self.assertEqual('ABCDEFG', c[0].seq)
self.assertEqual(5, c[0].remap_score())
def test_deterministic_assembly(self):
contig_sequences = set()
for i in range(20):
random.shuffle(self.seq)
contigs = assemble(self.seq,
111,
min_edge_trim_weight=3,
assembly_max_paths=8,
assembly_min_uniq=0.1,
min_complexity=0.1)
self.assertEqual(1, len(contigs))
contig_sequences.add(contigs[0].seq)
self.assertEqual(1, len(contig_sequences))
def test_deterministic_assembly(self, assembly_sequences):
contig_sequences = set()
for i in range(20):
random.shuffle(assembly_sequences)
contigs = assemble(
assembly_sequences,
111,
min_edge_trim_weight=3,
assembly_max_paths=8,
assembly_min_uniq=0.1,
min_complexity=0.1,
)
assert len(contigs) == 1
contig_sequences.add(contigs[0].seq)
assert len(contig_sequences) == 1
def test_repeat_region_assembly(self):
rep = 'ABCDEF'
seqs = kmers(rep + rep, len(rep))
contigs = assemble(seqs, len(rep) - 1, remap_min_exact_match=1)
self.assertEqual(0, len(contigs))
def test_assemble_empty_list(self):
self.assertEqual([], assemble([], 1))
def test_assemble_empty_list(self):
assert assemble([], 1) == []
def test_assemble(self):
sequences = ['ABCD', 'BCDE', 'CDEF', 'ABCDE', 'DEFG']
c = assemble(sequences, 3, min_edge_trim_weight=1, remap_min_exact_match=1)
assert len(c) == 1
assert c[0].seq == 'ABCDEFG'
assert c[0].remap_score() == 5