def test6970G72VCorrectLocation(self):
"""
The 69-70 deletion with a substitution leading to G72V must be
aligned correctly.
"""
seq = 'CATGCTAT------CTCTGTGACC'
self.assertEqual('HAI--SVT', translateSpike(seq))
def testPlus2GapCorrectLocation(self):
"""
A sequence with an out of frame gap (G--) must be in the correct
location.
"""
seq = 'TTGG---TTTATTACCAC'
self.assertEqual('LV-YYH', translateSpike(seq))
def test6970S71FCorrectLocation(self):
"""
The 69-70 deletion with a substitution leading to S71F must be
aligned correctly.
"""
seq = 'CATGCTAT------CTTTGGGACC'
self.assertEqual('HAI--FGT', translateSpike(seq))
def testInFrameGapAmbiguousCorrectLocation(self):
"""
A sequence with an in frame gap and an ambiguity must be translated
correcty.
"""
seq = 'TTG---GTTTANTACCAC'
self.assertEqual('L-VXYH', translateSpike(seq))
def testB16172_156_157GapCorrectLocation(self):
"""
The gap at 156/157 in B.1.617.2 must be in the correct location.
"""
seq = 'GAAAGTG------GAGTTTATTCTAGT'
self.assertEqual('ESG--VYSS', translateSpike(seq))
def testPlus1GapAdjacentAmbiguityCorrectLocation(self):
"""
A sequence with an out of frame gap (TT-) must be translated correctly.
"""
seq = 'TT---NGTTTATTACCAC'
self.assertEqual('X-VYYH', translateSpike(seq))
def testInFrameGapCorrectLocation(self):
"""
A sequence with an in frame gap must be in the correct location.
"""
seq = 'TTG---GTTTATTACCAC'
self.assertEqual('L-VYYH', translateSpike(seq))
def testPlus2GapCorrectLength(self):
"""
A sequence with an out of frame gap (A--) must have the correct length.
"""
seq = 'TTGG---TTTATTACCAC'
self.assertEqual(len(seq) / 3, len(translateSpike(seq)))
def testInFrameGapCorrectLength(self):
"""
A sequence with an in frame gap must have the correct length.
"""
seq = 'TTG---GTTTATTACCAC'
self.assertEqual(len(seq) / 3, len(translateSpike(seq)))
def testNoGapsCorrectSequence(self):
"""
A sequence with no gaps must be translated correctly.
"""
seq = 'TTGGTTGTTTATTACCAC'
self.assertEqual(Seq(seq).translate(), translateSpike(seq))
def aaSequences(self, featureName):
"""
Match the genome and the reference at the amino acid level.
@param featureName: A C{str} feature name.
@raise TranslationError: or one of its sub-classes (see translate.py)
if a feature nucleotide sequence cannot be translated.
@return: A 2-C{tuple} of C{dark.reads.AARead} instances, holding
the amino acids for the feature as located in the reference
genome and then the corresponding amino acids from the genome being
examined.
"""
try:
return self._cache['aa'][featureName]
except KeyError:
pass
referenceNt, genomeNt = self.ntSequences(featureName)
assert len(referenceNt) == len(genomeNt)
feature = self.features[featureName]
name = feature['name']
gapCount = genomeNt.sequence.count('-')
if (name == 'surface glycoprotein' and gapCount > 0
and gapCount % 3 == 0):
referenceAaAligned = AARead(
self.features.reference.id + f' ({name})',
translateSpike(referenceNt.sequence))
genomeAaAligned = AARead(self.genome.id + f' ({name})',
translateSpike(genomeNt.sequence))
if not len(referenceAaAligned) == len(genomeAaAligned):
raise TranslatedReferenceAndGenomeLengthError(
'Genome and reference AA sequences have different lengths.'
)
else:
referenceAa = AARead(
self.features.reference.id + f' ({name})',
feature.get('translation', translate(feature['sequence'],
name)))
genomeAa = AARead(
self.genome.id + f' ({name})',
translate(genomeNt.sequence.replace('-', ''), name))
referenceAaAligned, genomeAaAligned = mafft(Reads(
[referenceAa, genomeAa]),
options=MAFFT_OPTIONS)
if DEBUG:
print(f'AA MATCH {name}:')
print(f'ref nt aligned {len(referenceNt.sequence)}:',
referenceNt.sequence[SLICE])
print(f'gen nt aligned {len(genomeNt.sequence)}:',
genomeNt.sequence[SLICE])
print(f'ref aa {len(referenceAa.sequence)}:',
referenceAa.sequence[SLICE])
print(f'gen aa {len(genomeAa.sequence)}:',
genomeAa.sequence[SLICE])
print(f'ref aa aligned {len(referenceAaAligned.sequence)}:',
referenceAaAligned.sequence[SLICE])
print(f'gen aa aligned {len(genomeAaAligned.sequence)}:',
genomeAaAligned.sequence[SLICE])
self._cache['aa'][featureName] = referenceAaAligned, genomeAaAligned
return referenceAaAligned, genomeAaAligned
