def testAaSequencesChangesTranslationErrorIgnore(self):
"""
Check that no error is printed when checking AA sequences and
onError='ignore' and that the expected result is returned.
"""
features = Features(
{
'orf1ab': {
'name': 'ORF1ab polyprotein',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
err = StringIO()
testCount, errorCount, result = genome.checkFeature(
'orf1ab', 'A100000A', nt=False, onError='ignore', errFp=err)
self.assertEqual('', err.getvalue())
self.assertEqual(1, testCount)
self.assertEqual(1, errorCount)
self.assertEqual((False, None, False, None), result['A100000A'])
def testNtSequencesChangesIndexErrorIgnore(self):
"""
If we check on nucleotide sequences with an out-of-range
check, no error should be printed if we pass onError='ignore'
and the expected error result must be returned.
"""
features = Features(
{
'spike': {
'name': 'spike',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
err = StringIO()
testCount, errorCount, result = genome.checkFeature(
'spike', 'A100000A', nt=True, onError='ignore', errFp=err)
self.assertEqual('', err.getvalue())
self.assertEqual(1, testCount)
self.assertEqual(1, errorCount)
self.assertEqual((False, None, False, None), result['A100000A'])
def testNtSequencesChangesString(self):
"""
It must be possible to retrieve aligned nucleotide sequences
and check on changes using a string specification.
"""
features = Features(
{
'spike': {
'name': 'spike',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
# Note: 1-based locations.
testCount, errorCount, result = genome.checkFeature(
'spike', 'A1A T2A A3T T4T', True)
self.assertEqual(4, testCount)
self.assertEqual(3, errorCount)
self.assertEqual((True, 'A', True, 'A'), result['A1A'])
self.assertEqual((True, 'T', False, 'T'), result['T2A'])
self.assertEqual((False, 'T', True, 'T'), result['A3T'])
self.assertEqual((False, 'C', False, 'C'), result['T4T'])
def testPassingRefence(self):
"""
It must be possible to pass a reference
"""
reference = DNARead('refId', 'ATTC')
features = Features({}, reference)
self.assertIs(reference, features.reference)
def testNtSequencesChangesTuple(self):
"""
It must be possible to retrieve aligned nucleotide sequences
and check on changes using a tuple specification.
"""
features = Features(
{
'spike': {
'name': 'spike',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
# Note: 0-based offsets.
testCount, errorCount, result = genome.checkFeature(
'spike',
(('A', 0, 'A'), ('T', 1, 'A'), ('A', 2, 'T'), ('T', 3, 'T')), True)
self.assertEqual(4, testCount)
self.assertEqual(3, errorCount)
self.assertEqual((True, 'A', True, 'A'), result[('A', 0, 'A')])
self.assertEqual((True, 'T', False, 'T'), result[('T', 1, 'A')])
self.assertEqual((False, 'T', True, 'T'), result[('A', 2, 'T')])
self.assertEqual((False, 'C', False, 'C'), result[('T', 3, 'T')])
def testKnownFeatures(self):
"""
Only known feature names are allowed.
"""
features = Features()
for variant in VARIANTS:
for featureName in VARIANTS[variant]['changes']:
self.assertIsInstance(features[featureName], dict)
def main(args):
"""
Describe SARS-CoV-2 annotations.
@param args: A C{Namespace} instance as returned by argparse with
values for command-line options.
"""
features = Features(args.gbFile)
print(f'Features for {features.reference.id}:')
for featureName, feature in sorted(features.items()):
print(f'{featureName}:')
print(' start:', feature['start'])
print(' stop:', feature['stop'])
print(' length:', feature['stop'] - feature['start'])
try:
print(' product:', feature['product'])
except KeyError:
pass
try:
print(' function:', feature['function'])
except KeyError:
pass
sequence = feature['sequence']
print(f' sequence (len {len(sequence):5d} nt):',
(sequence[:args.maxLen] +
'...') if len(sequence) > args.maxLen else sequence)
try:
translation = feature['translation']
except KeyError:
# Some features (e.g., UTR, stem loops) do not have a translation.
pass
else:
print(f' translation (len {len(translation):5d} aa):',
(translation[:args.maxLen] +
'...') if len(translation) > args.maxLen else translation)
def testPassingDict(self):
"""
It must be possible to initialize a Features instance via a dict.
"""
value = {
'name': 'spike',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
}
features = Features({'spike': value})
self.assertIn('spike', features)
self.assertEqual(value, features['spike'])
def testNtSequencesGenomeGap(self):
"""
The genome must be able to have a gap relative to the reference.
"""
referenceSequence = 'TGGCGTGGA' + ('T' * 20) + 'CAAATCGG'
genomeFeature = 'TGGA' + ('T' * 19) + 'CAAATCGG'
genomeSequence = 'CCCGGTGGCG' + genomeFeature + 'CCCCCCC'
features = Features(
{
'spike': {
'name': 'spike',
'sequence': referenceSequence,
'start': 5,
'stop': len(referenceSequence),
},
},
DNARead('refId', referenceSequence))
genome = SARS2Genome(DNARead('genId', genomeSequence), features)
# The genome offset is initialized to None and isn't set until
# after ntSequences is called.
# self.assertEqual(None, alignment.genomeOffset)
referenceNt, genomeNt = genome.ntSequences('spike')
# self.assertEqual(5, alignment.genomeOffset)
self.assertEqual(referenceSequence[5:], referenceNt.sequence)
self.assertEqual('refId (spike)', referenceNt.id)
expected = 'TGGA-' + ('T' * 19) + 'CAAATCGG'
self.assertEqual(expected, genomeNt.sequence)
self.assertEqual('genId (spike)', genomeNt.id)
testCount, errorCount, result = genome.checkFeature(
'spike', 'T5-', True)
self.assertEqual(1, testCount)
self.assertEqual(0, errorCount)
self.assertEqual((True, 'T', True, '-'), result['T5-'])
def testAaSequencesTranslationNoSlipperySequenceRaise(self):
"""
The aaSequences function must raise if it can't translate an
'ORF1ab polyprotein' sequence due to a missing slippery sequence.
"""
features = Features(
{
'ORF1ab polyprotein': {
'name': 'ORF1ab polyprotein',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
error = r'^No slippery sequence found\.$'
self.assertRaisesRegex(NoSlipperySequenceError, error,
genome.aaSequences, 'ORF1ab polyprotein')
def testNtSequencesChangesIndexErrorPrint(self):
"""
If we check on nucleotide sequences with an out-of-range
check, an error must be printed if we pass onError='print'
and the expected error result must be returned.
"""
features = Features(
{
'spike': {
'name': 'spike',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
err = StringIO()
# Two lines of error output are printed.
error = (
r"Index 99999 out of range trying to access feature "
r"'spike' of length 4 sequence 'refId (spike)' via "
r"expected change specification 'A100000A'."
"\n"
r"Index 99999 out of range trying to access feature "
r"'spike' of length 4 sequence 'genId (spike)' via "
r"expected change specification 'A100000A'."
"\n"
)
testCount, errorCount, result = genome.checkFeature(
'spike', 'A100000A', nt=True, onError='print', errFp=err)
self.assertEqual(error, err.getvalue())
self.assertEqual(1, testCount)
self.assertEqual(1, errorCount)
self.assertEqual((False, None, False, None), result['A100000A'])
def testAaSequencesChangesTranslationErrorRaise(self):
"""
Check that a TranslationError is raised when checking AA
sequences.
"""
features = Features(
{
'orf1ab': {
'name': 'ORF1ab polyprotein',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
error = r"^No slippery sequence found\.$"
self.assertRaisesRegex(
NoSlipperySequenceError, error, genome.checkFeature,
'orf1ab', 'A100000A', False)
def testNtSequencesChangesIndexErrorRaise(self):
"""
If we check on nucleotide sequences with an out-of-range
check, an IndexError must be raised.
"""
features = Features(
{
'spike': {
'name': 'spike',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
error = (r"^Index 99999 out of range trying to access feature "
r"'spike' of length 4 sequence 'refId \(spike\)' via "
r"expected change specification 'A100000A'\.$")
self.assertRaisesRegex(IndexError, error, genome.checkFeature,
'spike', 'A100000A', True)
def testNtSequencesGenomeSNP(self):
"""
The genome must be able to have a SNP relative to the reference.
"""
referenceSequence = 'TGGCGTGGA' + ('T' * 20) + 'CAAATCGG'
genomeFeature = 'TGGCGTGGA' + ('T' * 9) + 'A' + ('T' * 10) + 'CAAATCGG'
genomeSequence = 'CCCGG' + genomeFeature + 'CCCCCCC'
features = Features(
{
'spike': {
'name': 'spike',
'sequence': referenceSequence,
'start': 0,
'stop': len(referenceSequence),
},
},
DNARead('refId', referenceSequence))
genome = SARS2Genome(DNARead('genId', genomeSequence), features)
referenceNt, genomeNt = genome.ntSequences('spike')
expected = 'TGGCGTGGA' + ('T' * 9) + 'A' + ('T' * 10) + 'CAAATCGG'
self.assertEqual(expected, genomeNt.sequence)
self.assertEqual('genId (spike)', genomeNt.id)
self.assertEqual(referenceSequence, referenceNt.sequence)
self.assertEqual('refId (spike)', referenceNt.id)
testCount, errorCount, result = genome.checkFeature(
'spike', 'T19A', True)
self.assertEqual(1, testCount)
self.assertEqual(0, errorCount)
self.assertEqual((True, 'T', True, 'A'), result['T19A'])
def testNtSequences(self):
"""
It must be possible to retrieve aligned nucleotide sequences.
"""
features = Features(
{
'spike': {
'name': 'spike',
'sequence': 'ATTC',
'start': 0,
'stop': 4,
},
},
DNARead('refId', 'ATTC'))
genome = SARS2Genome(DNARead('genId', 'GGATTCGG'), features)
referenceNt, genomeNt = genome.ntSequences('spike')
self.assertEqual('ATTC', genomeNt.sequence)
self.assertEqual('genId (spike)', genomeNt.id)
self.assertEqual('ATTC', referenceNt.sequence)
self.assertEqual('refId (spike)', referenceNt.id)
from unittest import TestCase
from dark.reads import DNARead
from sars2seq.features import Features
_FEATURES = Features()
class TestFeatures(TestCase):
"""
Test the Features class.
"""
def testGetFeatures(self):
"""
The getitem method must return a dict.
"""
self.assertIsInstance(_FEATURES['spike'], dict)
def testUnknownFeature(self):
"""
If an unknown feature is asked for, a KeyError must be raised.
"""
self.assertRaisesRegex(KeyError, "^'xx'$", _FEATURES.__getitem__, 'xx')
def testPassingDict(self):
"""
It must be possible to initialize a Features instance via a dict.
"""
value = {
'name': 'spike',
def main(args):
"""
Describe a SARS-CoV-2 genome.
@param args: A C{Namespace} instance as returned by argparse with
values for command-line options.
"""
outDir = args.outDir
if outDir:
if not exists(outDir):
os.makedirs(outDir)
features = Features(args.gbFile)
if args.feature:
if args.canonicalNames:
wantedFeatures = map(features.canonicalName, args.feature)
else:
wantedFeatures = args.feature
else:
if args.noFeatures:
wantedFeatures = []
else:
wantedFeatures = sorted(features)
namedMatches = defaultdict(list)
foundSets = defaultdict(list)
reads = list(FastaReads(args.genome))
print('SEQUENCE SHORT NAMES\n')
maxLen = 0
nameSummary = []
for read in reads:
shortId = read.id.split()[0]
if len(shortId) > maxLen:
maxLen = len(shortId)
nameSummary.append((shortId, read.id))
read.id = shortId
for shortId, longId in nameSummary:
print(f'{shortId:{maxLen}s} = {longId}')
print('\nPER-SEQUENCE RESULTS\n')
for read in reads:
genome = SARS2Genome(read, features)
if args.checkVariant:
with genomeFilePointer(read, args, '-variant-summary.txt') as fp:
nCount = genome.genome.sequence.count('N')
genomeLen = len(genome.genome)
nonNCount = genomeLen - nCount
coverage = nonNCount / genomeLen
print(f'{read.id} (coverage {nonNCount}/{genomeLen} = '
f'{coverage * 100.0:.2f} %)', file=fp)
theseNamedMatches, theseFoundSets = printVariantSummary(
genome, fp, args)
for match, ids in theseNamedMatches.items():
namedMatches[match].extend(ids)
for match, ids in theseFoundSets.items():
foundSets[match].extend(ids)
print(file=fp)
for i, featureName in enumerate(wantedFeatures):
with featureFilePointers(read, featureName, args) as fps:
processFeature(featureName, features, genome, fps, i, args)
print('\nSUMMARY\n')
if namedMatches:
print('Named change sets:')
for changeSet in sorted(CHANGE_SETS):
desc = ', '.join(sorted(CHANGE_SETS[changeSet], key=key))
print(f' {changeSet}: {desc}')
print()
print('Known variant combinations matched (count):')
for match in sorted(namedMatches):
print(f' {match} ({len(namedMatches[match])}):')
for name in sorted(namedMatches[match]):
print(f' {name}')
if foundSets:
print()
if foundSets:
print('Sets of changes found (count):')
for match in sorted(foundSets):
desc = ', '.join(sorted(match, key=key))
print(f' {desc} ({len(foundSets[match])}):')
for name in sorted(foundSets[match]):
print(f' {name}')
def main(args):
"""
Describe a SARS-CoV-2 genome.
@param args: A C{Namespace} instance as returned by argparse with
values for command-line options.
@return: An C{int} exit status.
"""
outDir = args.outDir
if outDir:
if not exists(outDir):
os.makedirs(outDir)
features = Features(args.gbFile)
if args.feature:
if args.canonicalNames:
wantedFeatures = map(features.canonicalName, args.feature)
else:
wantedFeatures = args.feature
else:
if args.noFeatures:
wantedFeatures = []
else:
wantedFeatures = sorted(features)
if not (args.checkVariant or wantedFeatures):
print('No action specified - I have nothing to do!', file=sys.stderr)
return 1
count = ignoredDueToCoverageCount = 0
for count, read in enumerate(FastaReads(args.genome), start=1):
if args.minReferenceCoverage is not None:
coverage = ((len(read) - read.sequence.upper().count('N')) /
len(features.reference))
if coverage < args.minReferenceCoverage:
ignoredDueToCoverageCount += 1
print(
f'Genome {read.id!r} ignored due to low '
f'({coverage * 100.0:.2f}%) coverage of the reference.',
file=sys.stderr)
continue
genome = SARS2Genome(read, features)
if args.checkVariant:
with genomeFilePointer(read, args, '-variant-summary.txt') as fp:
print(read.id, file=fp)
printVariantSummary(genome, fp, args)
for i, featureName in enumerate(wantedFeatures):
with featureFilePointers(read, featureName, args) as fps:
processFeature(featureName, genome, fps, i, args)
print(f'Examined {count} genomes.')
if args.minReferenceCoverage is not None:
print(f'Ignored {ignoredDueToCoverageCount} genomes due to low '
f'coverage.')
return 0
from unittest import TestCase
from os.path import dirname, join
from .fasta import getSequence
import sars2seq
from sars2seq.checker import Checker, AAChecker, NTChecker
from sars2seq.features import Features
from sars2seq.genome import SARS2Genome
DATA_DIR = join(dirname(dirname(sars2seq.__file__)), 'data')
REF_GB = join(DATA_DIR, 'NC_045512.2.gb')
FEATURES = Features(REF_GB)
class Test_EPI_ISL_601443(TestCase):
"""
Test the EPI_ISL_601433 sequence. This is the variant of concern
(VOC 202012/01) referred to in https://www.gov.uk/government/publications/
investigation-of-novel-sars-cov-2-variant-variant-of-concern-20201201
"""
genomeRead = getSequence(join(DATA_DIR, 'EPI_ISL_601443.fasta'))
genome = SARS2Genome(genomeRead, FEATURES)
def testIndexError(self):
"""
If an check on a non-existent index is attempted, an IndexError must
be raised.
"""
checker = Checker('spike', 'N500001Y', False)