def testCodonContent(self):
"""
Codons must only contain the letters A, T, G, C.
"""
for codons in CODONS.values():
for codon in codons:
self.assertTrue(all(letter in 'ACGT' for letter in codon))
def testStopCodonsNotInCodonTable(self):
"""
The stop codons must not be in the main table.
"""
for stop in STOP_CODONS:
for codons in CODONS.values():
self.assertNotIn(stop, codons)
def testStopCodonsNotInCodonTable(self):
"""
The stop codons must not be in the main table.
"""
for stop in STOP_CODONS:
for codons in CODONS.values():
self.assertNotIn(stop, codons)
def testCodonContent(self):
"""
Codons must only contain the letters A, T, G, C.
"""
for codons in CODONS.values():
for codon in codons:
self.assertTrue(all(letter in 'ACGT' for letter in codon))
def testCodonsAreNotAbbrev3s(self):
"""
No codon can be the same as an amino acid 3-letter abbreviation (or
else our find function may not be unambiguous in what it returns).
"""
for codons in CODONS.values():
self.assertFalse(
any(codon.title() in ABBREV3_TO_ABBREV1 for codon in codons))
def testCodonsAreNotAbbrev3s(self):
"""
No codon can be the same as an amino acid 3-letter abbreviation (or
else our find function may not be unambiguous in what it returns).
"""
for codons in CODONS.values():
self.assertFalse(
any(codon.title() in ABBREV3_TO_ABBREV1 for codon in codons))
def testDistinct(self):
"""
All nucleotide triples must be distinct.
"""
seen = set()
for codons in CODONS.values():
for codon in codons:
seen.add(codon)
self.assertEqual(61, len(seen))
def testDistinct(self):
"""
All nucleotide triples must be distinct.
"""
seen = set()
for codons in CODONS.values():
for codon in codons:
seen.add(codon)
self.assertEqual(61, len(seen))
def testAllCodonsPresent(self):
"""
All possible codons must be present, as either coding for an AA
or as a stop codon.
"""
combinations = set(''.join(x) for x in product('ACGT', 'ACGT', 'ACGT'))
for codons in CODONS.values():
for codon in codons:
combinations.remove(codon)
# Just the stop codons should be left.
self.assertEqual(set(STOP_CODONS), combinations)
def testAllCodonsPresent(self):
"""
All possible codons must be present, as either coding for an AA
or as a stop codon.
"""
combinations = set(
''.join(x) for x in product('ACGT', 'ACGT', 'ACGT'))
for codons in CODONS.values():
for codon in codons:
combinations.remove(codon)
# Just the stop codons should be left.
self.assertEqual(set(STOP_CODONS), combinations)
def testCodonLength(self):
"""
All codons must be three bases long.
"""
for codons in CODONS.values():
self.assertTrue(all(len(codon) == 3 for codon in codons))
def testNumberCodons(self):
"""
The table must contain 61 codons. This is 4^3 - 3. I.e., all possible
combinations of 3 bases minus the three stop codons.
"""
self.assertEqual(61, sum(len(codons) for codons in CODONS.values()))
def testCodonLength(self):
"""
All codons must be three bases long.
"""
for codons in CODONS.values():
self.assertTrue(all(len(codon) == 3 for codon in codons))
def testNumberCodons(self):
"""
The table must contain 61 codons. This is 4^3 - 3. I.e., all possible
combinations of 3 bases minus the three stop codons.
"""
self.assertEqual(61, sum(len(codons) for codons in CODONS.values()))
def testNumberCodons(self):
"""
The table must contain the right number of codons.
"""
self.assertEqual(44, sum(len(codons) for codons in CODONS.values()))
def testNumberCodons(self):
"""
The table must contain the right number of codons.
"""
self.assertEqual(44, sum(len(codons) for codons in CODONS.values()))
