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 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 findOrDie(s):
"""
Look up an amino acid.
@param s: A C{str} amino acid specifier. This may be a full name,
a 3-letter abbreviation or a 1-letter abbreviation. Case is ignored.
@return: An C{AminoAcid} instance, if one can be found. Else exit.
"""
aa = find(s)
if aa:
return aa
else:
print("Unknown amino acid or codon: %s" % s, file=sys.stderr)
print("Valid arguments are: %s." % list(CODONS.keys()), file=sys.stderr)
sys.exit(1)
def findOrDie(s):
"""
Look up an amino acid.
@param s: A C{str} amino acid specifier. This may be a full name,
a 3-letter abbreviation or a 1-letter abbreviation. Case is ignored.
@return: An C{AminoAcid} instance, if one can be found. Else exit.
"""
aa = find(s)
if aa:
return aa
else:
print('Unknown amino acid or codon: %s' % s, file=sys.stderr)
print('Valid arguments are: %s.' % list(CODONS.keys()),
file=sys.stderr)
sys.exit(1)
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()))
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 testCorrectAAs(self):
"""
The CODONS dict must have the correct AA keys.
"""
self.assertEqual(AA_LETTERS, sorted(CODONS.keys()))
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))
#!/usr/bin/env python
import sys
from Bio import SeqIO
from os.path import exists
from dark.aa import CODONS
START_CODON = 'ATG'
STOP_CODONS = {'TAA', 'TAG', 'TGA'}
CODON_TO_AA = {}
START_AA = 'M'
STOP_AA = '*'
for aa, codons in CODONS.items():
for codon in codons:
CODON_TO_AA[codon] = aa
for codon in STOP_CODONS:
CODON_TO_AA[codon] = STOP_AA
_rcTable = str.maketrans('ACGT', 'TGCA')
def revcomp(s):
"""
Reverse complement a nucleotide string.
"""
return s.translate(_rcTable)[::-1]
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 testCorrectAAs(self):
"""
The CODONS dict must have the correct AA keys.
"""
self.assertEqual(AA_LETTERS, sorted(CODONS.keys()))