def testGapAndMatch(self):
"""
Two sequences containing matches and gaps must compare as
expected.
"""
read1 = AARead('id1', 'GALHN-')
read2 = AARead('id2', 'GALHNA')
match = compareAaReads(read1, read2)
self.assertEqual(
'''\
Matches: 5/6 (83.33%)
Mismatches: 1/6 (16.67%)
Not involving gaps (i.e., conflicts): 0
Involving a gap in one sequence: 1/6 (16.67%)
Involving a gap in both sequences: 0
Id: id1
Length: 6
Gaps: 1/6 (16.67%)
Gap locations (1-based): 6
Id: id2
Length: 6
Gaps: 0''',
matchToString(match, read1, read2)
)
def testOffsets(self):
"""
If a set of wanted offsets is passed, the result must be restricted to
just those offsets.
"""
self.assertEqual(
{
'match': {
'matchCount': 1,
'gapMismatchCount': 0,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 1,
},
'read1': {
'extraCount': 0,
'gapOffsets': [],
},
'read2': {
'extraCount': 0,
'gapOffsets': [],
},
},
compareAaReads(AARead('id1', 'GAL-L'),
AARead('id2', 'G-LHN'),
offsets=set([0, 4])))
def testNonDefaultGapChars(self):
"""
We must be able to specify the gap characters.
"""
for gap in '+$':
self.assertEqual(
{
'match': {
'matchCount': 3,
'gapMismatchCount': 2,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 0,
},
'read1': {
'extraCount': 0,
'gapOffsets': [2],
},
'read2': {
'extraCount': 0,
'gapOffsets': [0],
},
},
compareAaReads(AARead('id1', 'GA%sHN' % gap),
AARead('id2', '%sALHN' % gap),
gapChars='+$'))
def processFeature(featureName, features, genome, fps, featureNumber, args):
"""
Process a feature from a genome.
@param featureName: A C{str} feature name.
@param features: A C{Features} instance.
@param genome: A C{SARS2Genome} instance.
@param fps: A C{dict} of file pointers for the various output streams.
@param featureNumber: The C{int} 0-based count of the features requested.
This will be zero for the first feature, 1 for the second, etc.
@param args: A C{Namespace} instance as returned by argparse with
values for command-line options.
"""
result = genome.feature(featureName)
feature = features.getFeature(featureName)
referenceNt, genomeNt = result.ntSequences()
referenceAa, genomeAa = result.aaSequences()
newlineNeeded = False
if args.printNtMatch:
fp = fps['nt-match']
if featureNumber:
print(file=fp)
print(f'Feature: {featureName} nucleotide match', file=fp)
print(f' Reference nt location {feature["start"] + 1}, genome nt '
f'location {result.genomeOffset + 1}', file=fp)
match = compareDNAReads(referenceNt, genomeNt)
print(dnaMatchToString(match, referenceNt, genomeNt,
matchAmbiguous=False, indent=' '), file=fp)
printDiffs(referenceNt, genomeNt, True, feature['start'], fp,
indent=' ')
newlineNeeded = True
if args.printAaMatch:
fp = fps['aa-match']
if newlineNeeded or featureNumber:
print(file=fp)
print(f'Feature: {featureName} amino acid match', file=fp)
match = compareAaReads(referenceAa, genomeAa)
print(aaMatchToString(match, referenceAa, genomeAa, indent=' '),
file=fp)
printDiffs(referenceAa, genomeAa, False, feature['start'], fp,
indent=' ')
if args.printNtSequence:
noGaps = Read(genomeNt.id, genomeNt.sequence.replace('-', ''))
Reads([noGaps]).save(fps['nt-sequence'])
if args.printAaSequence:
noGaps = Read(genomeAa.id, genomeAa.sequence.replace('-', ''))
Reads([noGaps]).save(fps['aa-sequence'])
if args.printNtAlignment:
Reads([genomeNt, referenceNt]).save(fps['nt-align'])
if args.printAaAlignment:
Reads([genomeAa, referenceAa]).save(fps['aa-align'])
def testGapInSecond(self):
"""
A gap in the second sequence must be dealt with correctly.
"""
self.assertEqual(
{
'match': {
'matchCount': 3,
'gapMismatchCount': 2,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 0,
},
'read1': {
'extraCount': 0,
'gapOffsets': [],
},
'read2': {
'extraCount': 0,
'gapOffsets': [1, 2],
},
}, compareAaReads(AARead('id1', 'GALHN'), AARead('id2', 'G--HN')))
def testGapInFirst(self):
"""
A gap in the first sequence must be dealt with correctly.
"""
self.assertEqual(
{
'match': {
'matchCount': 4,
'gapMismatchCount': 1,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 0,
},
'read1': {
'extraCount': 0,
'gapOffsets': [3],
},
'read2': {
'extraCount': 0,
'gapOffsets': [],
},
}, compareAaReads(AARead('id1', 'GAL-N'), AARead('id2', 'GALHN')))
def testExactMatch(self):
"""
Two sequences that match exactly must compare as expected.
"""
self.assertEqual(
{
'match': {
'matchCount': 5,
'gapMismatchCount': 0,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 0,
},
'read1': {
'extraCount': 0,
'gapOffsets': [],
},
'read2': {
'extraCount': 0,
'gapOffsets': [],
},
}, compareAaReads(AARead('id1', 'GALHN'), AARead('id2', 'GALHN')))
def testEmptySequences(self):
"""
Two empty sequences must compare as expected.
"""
self.assertEqual(
{
'match': {
'matchCount': 0,
'gapMismatchCount': 0,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 0,
},
'read1': {
'extraCount': 0,
'gapOffsets': [],
},
'read2': {
'extraCount': 0,
'gapOffsets': [],
},
}, compareAaReads(AARead('id1', ''), AARead('id2', '')))
def testGapGap(self):
"""
Coinciding gaps in the sequences must be dealt with correctly
"""
self.assertEqual(
{
'match': {
'matchCount': 2,
'gapMismatchCount': 2,
'gapGapMismatchCount': 1,
'nonGapMismatchCount': 0,
},
'read1': {
'extraCount': 0,
'gapOffsets': [2, 3],
},
'read2': {
'extraCount': 0,
'gapOffsets': [1, 2],
},
}, compareAaReads(AARead('id1', 'GA--N'), AARead('id2', 'G--HN')))
def testMismatch(self):
"""
If the sequences have mismatched bases, their count
must be given correctly in the nonGapMismatchCount.
"""
self.assertEqual(
{
'match': {
'matchCount': 3,
'gapMismatchCount': 0,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 2,
},
'read1': {
'extraCount': 0,
'gapOffsets': [],
},
'read2': {
'extraCount': 0,
'gapOffsets': [],
},
}, compareAaReads(AARead('id1', 'GALYY'), AARead('id2', 'GALHN')))
def testNoOffsets(self):
"""
If an empty set of wanted offsets is passed, the result must be empty.
"""
self.assertEqual(
{
'match': {
'matchCount': 0,
'gapMismatchCount': 0,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 0,
},
'read1': {
'extraCount': 0,
'gapOffsets': [],
},
'read2': {
'extraCount': 0,
'gapOffsets': [],
},
},
compareAaReads(AARead('id1', 'GAL-N'),
AARead('id2', 'G-LHN'), offsets=set()))
def testExtraInSecond(self):
"""
If the second sequence has extra bases, they must be indicated in the
extraCount.
"""
self.assertEqual(
{
'match': {
'matchCount': 5,
'gapMismatchCount': 0,
'gapGapMismatchCount': 0,
'nonGapMismatchCount': 0,
},
'read1': {
'extraCount': 0,
'gapOffsets': [],
},
'read2': {
'extraCount': 2,
'gapOffsets': [],
},
}, compareAaReads(AARead('id1', 'GALHN'), AARead('id2',
'GALHNHN')))
if args.alignmentFile:
assert reads.save(args.alignmentFile) == 2
offsets = (parseRangeString(args.sites, convertToZeroBased=True)
if args.sites else None)
read1, read2 = reads
len1, len2 = map(len, reads)
identicalLengths = len1 == len2
# Sanity check.
if args.align:
assert identicalLengths
match = compareAaReads(read1, read2, offsets=offsets)
x = 'Post-alignment, sequence' if args.align else 'Sequence'
if identicalLengths:
print('%s lengths are identical: %s' % (x, len1))
else:
print('%s lengths: %d, %d (difference %d)' % (x, len1, len2,
abs(len1 - len2)))
print(matchToString(match, read1, read2, offsets=offsets))
if args.showDiffs:
# Print all sites where the sequences differ.
width = int(log10(max(len1, len2))) + 1
headerPrinted = False
for site, (a, b) in enumerate(zip(read1.sequence, read2.sequence),
if args.alignmentFile:
assert reads.save(args.alignmentFile) == 2
offsets = (parseRangeString(args.sites, convertToZeroBased=True)
if args.sites else None)
read1, read2 = reads
len1, len2 = map(len, reads)
identicalLengths = len1 == len2
# Sanity check.
if args.align:
assert identicalLengths
match = compareAaReads(read1, read2, offsets=offsets)
x = 'Post-alignment, sequence' if args.align else 'Sequence'
if identicalLengths:
print('%s lengths are identical: %s' % (x, len1))
else:
print('%s lengths: %d, %d (difference %d)' %
(x, len1, len2, abs(len1 - len2)))
print(matchToString(match, read1, read2, offsets=offsets))
if args.showDiffs:
# Print all sites where the sequences differ.
width = int(log10(max(len1, len2))) + 1
headerPrinted = False
for site, (a, b) in enumerate(zip(read1.sequence, read2.sequence),
def processFeature(featureName, genome, fps, featureNumber, args):
"""
Process a feature from a genome.
@param featureName: A C{str} feature name.
@param genome: A C{SARS2Genome} instance.
@param fps: A C{dict} of file pointers for the various output streams.
@param featureNumber: The C{int} 0-based count of the features requested.
This will be zero for the first feature, 1 for the second, etc.
@param args: A C{Namespace} instance as returned by argparse with
values for command-line options.
"""
referenceNt, genomeNt = genome.ntSequences(featureName)
feature = genome.features[featureName]
if args.printAaMatch or args.printAaSequence or args.printAaAlignment:
try:
referenceAa, genomeAa = genome.aaSequences(featureName)
except TranslationError as e:
if args.onError == 'raise':
raise
elif args.onError == 'print':
print(
f'Could not translate feature {featureName} in genome '
f'{genome.genome.id}: {e}',
file=sys.stderr)
referenceAa = genomeAa = None
newlineNeeded = False
if args.printNtMatch:
fp = fps['nt-match']
if featureNumber:
print(file=fp)
print(f'Feature: {featureName} nucleotide match', file=fp)
print(f' Reference nt location {feature["start"] + 1}', file=fp)
match = compareDNAReads(referenceNt, genomeNt)
print(dnaMatchToString(match,
referenceNt,
genomeNt,
matchAmbiguous=False,
indent=' '),
file=fp)
printDiffs(referenceNt,
genomeNt,
True,
feature['start'],
fp,
indent=' ')
newlineNeeded = True
if args.printAaMatch and genomeAa:
fp = fps['aa-match']
if newlineNeeded or featureNumber:
print(file=fp)
print(f'Feature: {featureName} amino acid match', file=fp)
match = compareAaReads(referenceAa, genomeAa)
print(aaMatchToString(match, referenceAa, genomeAa, indent=' '),
file=fp)
printDiffs(referenceAa,
genomeAa,
False,
feature['start'],
fp,
indent=' ')
if args.printNtSequence:
noGaps = Read(genomeNt.id, genomeNt.sequence.replace('-', ''))
Reads([noGaps]).save(fps['nt-sequence'])
if args.printAaSequence and genomeAa:
noGaps = Read(genomeAa.id, genomeAa.sequence.replace('-', ''))
Reads([noGaps]).save(fps['aa-sequence'])
if args.printNtAlignment:
Reads([genomeNt, referenceNt]).save(fps['nt-align'])
if args.printAaAlignment and genomeAa:
Reads([genomeAa, referenceAa]).save(fps['aa-align'])
