def test_get_table(self):
"""Test get_table method."""
# Negative tests:
for table_id in [-1, "hello"]:
self.assertIsNone(table.get_table(table_id))
# Positive tests:
for table_id, dna in itertools.product([45372, "45372", "Abies alba"],
[True, False]):
self.__test_table(table.get_table(table_id, dna=dna), dna=dna)
def test_sample(self):
"""Test sample method."""
codon_table = table.get_table("Escherichia coli")
amino_acid = "L"
# Get codon usage for amino acid:
aa_codons = codon_table[amino_acid]
# Apply sample a number of times:
sampled = [utils.sample(codon_table, amino_acid) for _ in range(10000)]
# Test:
self._test(sampled, aa_codons)
def test_codon_optimise(self):
"""Test codon optimise method."""
# TODO: update in future to codon optimise random amino acid sequence,
# then translate back to original amino acid sequence.
# (Will need Biopython, but don't want to add extra dependency.
codon_table = table.get_table(9606)
amino_acid = "S"
# Get codon usage for amino acid:
aa_codons = codon_table[amino_acid]
# Generate amino acid sequence and codon optimise:
aa_seq = "".join([amino_acid] * 100000)
dna_seq = utils.optimise(codon_table, aa_seq)
# Extract codons from DNA sequence:
codons = [dna_seq[i : i + 3] for i in range(0, len(dna_seq), 3)]
# Test:
self._test(codons, aa_codons)