def testCoverageIncludesAll(self):
"""
The coverage function must return an titlesAlignments instance with
all titles if all its titles has sufficient coverage.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(minCoverage=0.0)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result))
def testTitle(self):
"""
Sorting on title must work.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('title')
self.assertEqual([
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
], result)
def testMaxScore_Bits(self):
"""
Sorting on max score must work when scores are bit scores, including a
secondary sort on title.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch('__builtin__.open', mockOpener, create=True):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('maxScore')
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 25
'gi|887699|gb|DQ37780 Cowpox virus 15', # 20
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 20
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 20
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 20
], result)
def testFromThreeSequences(self):
"""
If three sequences with no features are used to create an NJTree
instance, the instance must 1) have a distance matrix that is zero
on the diagonal and ones elsewhere, 2) save the labels, and 3) produce
a simple tree with three children.
"""
sequences = Reads()
sequences.add(AARead('id1', 'A'))
sequences.add(AARead('id2', 'A'))
sequences.add(AARead('id3', 'A'))
labels = ['x', 'y', 'z']
njtree = NJTree.fromSequences(labels, sequences,
landmarks=['AlphaHelix'])
self.assertTrue(np.array_equal(
[
[0, 1, 1],
[1, 0, 1],
[1, 1, 0],
],
njtree.distance))
self.assertIs(labels, njtree.labels)
self.assertEqual(['x:0.5;\n', 'y:0.5;\n', 'z:0.5;\n'],
sorted(str(child) for child in njtree.tree.children))
def testMaxTitlesTwoSortOnLength(self):
"""
The filter function must return the two titles whose sequences are the
longest when maxTitles is 2 and sortOn is 'length'.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json',
'database.fasta')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(maxTitles=2, sortOn='length')
self.assertEqual(
[
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result.keys()))
def testWithScoreBetterThan_EValue(self):
"""
The filter function work correctly when passed a value for
withScoreBetterThan when using e values.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(
reads, 'file.json', 'database.fasta',
scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(withScoreBetterThan=1e-10)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
],
list(result.keys()))
def testLength(self):
"""
Sorting on sequence length must work, including a secondary sort on
title.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch('__builtin__.open', mockOpener, create=True):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('length')
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 38000
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 37000
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 35000
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 35000
'gi|887699|gb|DQ37780 Cowpox virus 15', # 30000
], result)
def testCoverageIncludesSome(self):
"""
The coverage function must return an titlesAlignments instance with
only the expected titles if only some of its titles have sufficient
coverage.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
# To understand why the following produces the result it does,
# you need to look at the HSP coverage in sample_data.py and
# calculate the coverage by hand.
result = titlesAlignments.filter(minCoverage=0.0003)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
],
sorted(result))
def testWithScoreBetterThan_EValue(self):
"""
The filter function work correctly when passed a value for
withScoreBetterThan when using e values.
"""
mockOpener = mockOpen(
read_data=(dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(
reads,
'file.json',
'database.fasta',
scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(withScoreBetterThan=1e-10)
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
], list(result.keys()))
def testExpectedTitleDetails(self):
"""
An instance of TitleAlignments in a TitlesAlignments instance must
have the expected attributes.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
read = Read('id0', 'A' * 70)
reads.add(read)
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
title = 'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99'
titleAlignments = titlesAlignments[title]
self.assertEqual(title, titleAlignments.subjectTitle)
self.assertEqual(37000, titleAlignments.subjectLength)
self.assertEqual(1, len(titleAlignments))
self.assertEqual(read, titleAlignments[0].read)
self.assertEqual(HSP(20), titleAlignments[0].hsps[0])
title = 'gi|887699|gb|DQ37780 Squirrelpox virus 55'
titleAlignments = titlesAlignments[title]
self.assertEqual(title, titleAlignments.subjectTitle)
self.assertEqual(38000, titleAlignments.subjectLength)
self.assertEqual(1, len(titleAlignments))
self.assertEqual(read, titleAlignments[0].read)
self.assertEqual(HSP(25), titleAlignments[0].hsps[0])
def testLengthOne(self):
"""
A FASTA list with just one item gets de-duped to the same one item.
"""
reads = Reads()
reads.add(Read('id', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id', 'GGG')])
def testTitleCollection(self):
"""
A title that occurs in the alignments of multiple reads must have
the data from both reads collected properly.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
read2 = Read('id2', 'A' * 70)
read3 = Read('id3', 'A' * 70)
reads.add(read2)
reads.add(read3)
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
title = 'gi|887699|gb|DQ37780 Cowpox virus 15'
titleAlignments = titlesAlignments[title]
self.assertEqual(title, titleAlignments.subjectTitle)
self.assertEqual(30000, titleAlignments.subjectLength)
self.assertEqual(2, len(titleAlignments))
self.assertEqual(read2, titleAlignments[0].read)
self.assertEqual(HSP(20), titleAlignments[0].hsps[0])
self.assertEqual(read3, titleAlignments[1].read)
self.assertEqual(HSP(20), titleAlignments[1].hsps[0])
def testTabSeparatedSummary(self):
"""
The summary function must return the correct result.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'f.json', 'db')
titlesAlignments = TitlesAlignments(readsAlignments)
summary = titlesAlignments.tabSeparatedSummary(sortOn='title')
expected = (
'0.000297\t'
'20.000000\t'
'20.000000\t'
'1\t'
'1\t'
'37000\t'
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99'
'\n'
'0.000289\t'
'25.000000\t'
'25.000000\t'
'1\t'
'1\t'
'38000\t'
'gi|887699|gb|DQ37780 Squirrelpox virus 55')
self.assertEqual(expected, summary)
def testTitle(self):
"""
Sorting on title must work.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('title')
self.assertEqual([
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
], result)
def testMaxMatchingReads(self):
"""
The filter function must work correctly when passed a value for
maxMatchingReads.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(maxMatchingReads=1)
# Cowpox virus 15 is not in the results as it is matched by two
# reads.
self.assertEqual(
sorted([
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.'
]),
sorted(result))
def testReadSetFilterAllowAnything(self):
"""
The filter function must work correctly when passed a 0.0 value for
minNewReads, i.e. that considers any read set sufficiently novel.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(minNewReads=0.0)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result))
def testTwoByTwoAsDict(self):
"""
If affinityMatrix is called with two reads and the database has two
subjects, and a dict result is requested, the result must be as
expected.
"""
reads = Reads()
reads.add(AARead('id1', 'FRRRFRRRFAAAFRRRFRRRF'))
reads.add(AARead('id2', 'FRRRFRRRFAAAFRRRFRRRF'))
subjects = Reads()
subjects.add(AARead('id3', 'FRRRFRRRFAAAFRRRFRRRF'))
subjects.add(AARead('id4', 'FRRRFRRRFAAAFRRRFRRRF'))
matrix = affinityMatrix(reads, landmarks=['AlphaHelix'],
subjects=subjects, computeDiagonal=True,
returnDict=True)
self.assertEqual(
{
'id1': {
'id3': 1.0,
'id4': 1.0,
},
'id2': {
'id3': 1.0,
'id4': 1.0,
},
},
matrix)
def testFilterWithNoArguments(self):
"""
The filter function must return a TitlesAlignments instance with all
the titles of the original when called with no arguments.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter()
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result.keys()))
def testReadSetFilterAllowAnything(self):
"""
The filter function work correctly when passed a 0.0 value for
minNewReads, i.e. that considers any read set sufficiently novel.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(minNewReads=0.0)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result.keys()))
def testMinMedianScore_EValue(self):
"""
The filter function work correctly when passed a value for
minMedianScore when using e values.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(minMedianScore=1e-9)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result.keys()))
def testCoverageIncludesAll(self):
"""
The coverage function must return an titlesAlignments instance with
all titles if all its titles has sufficient coverage.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(minCoverage=0.0)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result.keys()))
def testCoverageIncludesSome(self):
"""
The coverage function must return an titlesAlignments instance with
only the expected titles if only some of its titles have sufficient
coverage.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
# To understand why the following produces the result it does,
# you need to look at the HSP coverage in sample_data.py and
# calculate the coverage by hand.
result = titlesAlignments.filter(minCoverage=0.0011)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
],
sorted(result.keys()))
def testMaxScore_EValue(self):
"""
Sorting on max score must work when scores are e values, including a
secondary sort on title.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('maxScore')
# self.assertEqual([
# 'gi|887699|gb|DQ37780 Cowpox virus 15', # 1e-6
# 'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 1e-7
# 'gi|887699|gb|DQ37780 Monkeypox virus 456', # 1e-8
# 'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 1e-10
# 'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 1e-11
# ], result)
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 1e-11
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 1e-10
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 1e-8
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 1e-7
'gi|887699|gb|DQ37780 Cowpox virus 15', # 1e-6
], result)
def testTabSeparatedSummary(self):
"""
The summary function must return the correct result.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'f.json')
titlesAlignments = TitlesAlignments(readsAlignments)
summary = titlesAlignments.tabSeparatedSummary(sortOn='title')
expected = (
'0.000297\t'
'20.000000\t'
'20.000000\t'
'1\t'
'1\t'
'37000\t'
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99'
'\n'
'0.000289\t'
'25.000000\t'
'25.000000\t'
'1\t'
'1\t'
'38000\t'
'gi|887699|gb|DQ37780 Squirrelpox virus 55')
self.assertEqual(expected, summary)
def add(self, virusTitle, sampleName):
"""
Add a a virus title, sample name combination and get its FASTA file
name. Write the FASTA file if it does not already exist.
@param virusTitle: A C{str} virus title.
@param sampleName: A C{str} sample name.
@return: A C{str} FASTA file name holding all the reads (without
duplicates) from the sample that matched the proteins in the given
virus.
"""
virusIndex = self._viruses.setdefault(virusTitle, len(self._viruses))
sampleIndex = self._samples.setdefault(sampleName, len(self._samples))
try:
return self._fastaFilenames[(virusIndex, sampleIndex)]
except KeyError:
result = Reads()
for proteinMatch in self._proteinGrouper.virusTitles[
virusTitle][sampleName]:
for read in FastaReads(proteinMatch['fastaFilename'],
checkAlphabet=0):
result.add(read)
saveFilename = join(
proteinMatch['outDir'],
'virus-%d-sample-%d.fasta' % (virusIndex, sampleIndex))
result.filter(removeDuplicates=True).save(saveFilename)
self._fastaFilenames[(virusIndex, sampleIndex)] = saveFilename
return saveFilename
def testFilterWithNoArguments(self):
"""
The filter function must return a TitlesAlignments instance with all
the titles of the original when called with no arguments.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter()
self.assertEqual(
[
'gi|887699|gb|DQ37780 Cowpox virus 15',
'gi|887699|gb|DQ37780 Monkeypox virus 456',
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.',
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result))
def testMaxScore_Bits(self):
"""
Sorting on max score must work when scores are bit scores, including a
secondary sort on title.
"""
mockOpener = mockOpen(
read_data=(dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('maxScore')
self.assertEqual(
[
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 25
'gi|887699|gb|DQ37780 Cowpox virus 15', # 20
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 20
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 20
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 20
],
result)
def testMinMedianScore_EValue(self):
"""
The filter function must work correctly when passed a value for
minMedianScore when using e values.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.filter(minMedianScore=1e-9)
self.assertEqual(
[
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99',
'gi|887699|gb|DQ37780 Squirrelpox virus 55',
],
sorted(result))
def testLength(self):
"""
Sorting on sequence length must work, including a secondary sort on
title.
"""
mockOpener = mockOpen(
read_data=(dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('length')
self.assertEqual(
[
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 38000
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 37000
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 35000
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 35000
'gi|887699|gb|DQ37780 Cowpox virus 15', # 30000
],
result)
def add(self, pathogenName, sampleName):
"""
Add a (pathogen name, sample name) combination and get its FASTA/FASTQ
file name and unique read count. Write the FASTA/FASTQ file if it does
not already exist. Save the unique read count into
C{self._proteinGrouper}.
@param pathogenName: A C{str} pathogen name.
@param sampleName: A C{str} sample name.
@return: A C{str} giving the FASTA/FASTQ file name holding all the
reads (without duplicates, by id) from the sample that matched the
proteins in the given pathogen.
"""
pathogenIndex = self._pathogens.setdefault(pathogenName,
len(self._pathogens))
sampleIndex = self._samples.setdefault(sampleName, len(self._samples))
try:
return self._readsFilenames[(pathogenIndex, sampleIndex)]
except KeyError:
reads = Reads()
for proteinMatch in self._proteinGrouper.pathogenNames[
pathogenName][sampleName]['proteins'].values():
for read in self._readsClass(proteinMatch['readsFilename']):
reads.add(read)
saveFilename = join(
proteinMatch['outDir'], 'pathogen-%d-sample-%d.%s' %
(pathogenIndex, sampleIndex, self._format))
reads.filter(removeDuplicatesById=True)
nReads = reads.save(saveFilename, format_=self._format)
# Save the unique read count into self._proteinGrouper
self._proteinGrouper.pathogenNames[pathogenName][sampleName][
'uniqueReadCount'] = nReads
self._readsFilenames[(pathogenIndex, sampleIndex)] = saveFilename
return saveFilename
def testTitleCollection(self):
"""
A title that occurs in the alignments of multiple reads must have
the data from both reads collected properly.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
read2 = Read('id2', 'A' * 70)
read3 = Read('id3', 'A' * 70)
reads.add(read2)
reads.add(read3)
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
title = 'gi|887699|gb|DQ37780 Cowpox virus 15'
titleAlignments = titlesAlignments[title]
self.assertEqual(title, titleAlignments.subjectTitle)
self.assertEqual(30000, titleAlignments.subjectLength)
self.assertEqual(2, len(titleAlignments))
self.assertEqual(read2, titleAlignments[0].read)
self.assertEqual(HSP(20), titleAlignments[0].hsps[0])
self.assertEqual(read3, titleAlignments[1].read)
self.assertEqual(HSP(20), titleAlignments[1].hsps[0])
def testMaxScore_EValue(self):
"""
Sorting on max score must work when scores are e values, including a
secondary sort on title.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = DiamondReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('maxScore')
# self.assertEqual([
# 'gi|887699|gb|DQ37780 Cowpox virus 15', # 1e-6
# 'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 1e-7
# 'gi|887699|gb|DQ37780 Monkeypox virus 456', # 1e-8
# 'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 1e-10
# 'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 1e-11
# ], result)
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99', # 1e-11
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 1e-10
'gi|887699|gb|DQ37780 Monkeypox virus 456', # 1e-8
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.', # 1e-7
'gi|887699|gb|DQ37780 Cowpox virus 15', # 1e-6
], result)
def testExpectedTitleDetails(self):
"""
An instance of TitleAlignments in a TitlesAlignments instance must
have the expected attributes.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
read = Read('id0', 'A' * 70)
reads.add(read)
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
title = 'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99'
titleAlignments = titlesAlignments[title]
self.assertEqual(title, titleAlignments.subjectTitle)
self.assertEqual(37000, titleAlignments.subjectLength)
self.assertEqual(1, len(titleAlignments))
self.assertEqual(read, titleAlignments[0].read)
self.assertEqual(HSP(20), titleAlignments[0].hsps[0])
title = 'gi|887699|gb|DQ37780 Squirrelpox virus 55'
titleAlignments = titlesAlignments[title]
self.assertEqual(title, titleAlignments.subjectTitle)
self.assertEqual(38000, titleAlignments.subjectLength)
self.assertEqual(1, len(titleAlignments))
self.assertEqual(read, titleAlignments[0].read)
self.assertEqual(HSP(25), titleAlignments[0].hsps[0])
def testLengthOne(self):
"""
A FASTA list with just one item gets de-duped to the same one item.
"""
reads = Reads()
reads.add(Read('id', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id', 'GGG')])
def testRemovalOfIdenticalSequences(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy.
"""
reads = Reads()
reads.add(Read('id', 'GGG'))
reads.add(Read('id', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id', 'GGG')])
def testRemovalOfIdenticalSequences(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy.
"""
reads = Reads()
reads.add(Read('id', 'GGG'))
reads.add(Read('id', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id', 'GGG')])
def testSummary(self):
"""
The summary function must return the correct result.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json',
'database.fasta')
titlesAlignments = TitlesAlignments(readsAlignments)
self.assertEqual(
[
{
'bestScore': 20.0,
'coverage': 0.00031428571428571427,
'hspCount': 1,
'medianScore': 20.0,
'readCount': 1,
'subjectLength': 35000,
'subjectTitle': (
'gi|887699|gb|DQ37780 Monkeypox virus 456'),
},
{
'bestScore': 20.0,
'coverage': 0.00031428571428571427,
'hspCount': 1,
'medianScore': 20.0,
'readCount': 1,
'subjectLength': 35000,
'subjectTitle': (
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.'),
},
{
'bestScore': 20.0,
'coverage': 0.0002972972972972973,
'hspCount': 1,
'medianScore': 20.0,
'readCount': 1,
'subjectLength': 37000,
'subjectTitle': (
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99'),
},
{
'bestScore': 25.0,
'coverage': 0.00028947368421052634,
'hspCount': 1,
'medianScore': 25.0,
'readCount': 1,
'subjectLength': 38000,
'subjectTitle': (
'gi|887699|gb|DQ37780 Squirrelpox virus 55'),
},
],
list(titlesAlignments.summary(sortOn='title')))
def testManuallyAddedReadsLength(self):
"""
A Reads instance with reads added manually must have the correct
length.
"""
reads = Reads()
reads.add(Read('id1', 'AT'))
reads.add(Read('id2', 'AC'))
self.assertEqual(2, len(reads))
def testRemovalOfIdenticalSequencesWithDifferingIds(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy,
including when the read ids differ.
"""
reads = Reads()
reads.add(Read('id1', 'GGG'))
reads.add(Read('id2', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id1', 'GGG')])
def testSummary(self):
"""
The summary function must return the correct result.
"""
mockOpener = mock_open(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n' +
dumps(RECORD1) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
reads.add(Read('id1', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
self.assertEqual(
[
{
'bestScore': 20.0,
'coverage': 0.00031428571428571427,
'hspCount': 1,
'medianScore': 20.0,
'readCount': 1,
'subjectLength': 35000,
'subjectTitle': (
'gi|887699|gb|DQ37780 Monkeypox virus 456'),
},
{
'bestScore': 20.0,
'coverage': 0.00031428571428571427,
'hspCount': 1,
'medianScore': 20.0,
'readCount': 1,
'subjectLength': 35000,
'subjectTitle': (
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.'),
},
{
'bestScore': 20.0,
'coverage': 0.0002972972972972973,
'hspCount': 1,
'medianScore': 20.0,
'readCount': 1,
'subjectLength': 37000,
'subjectTitle': (
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99'),
},
{
'bestScore': 25.0,
'coverage': 0.00028947368421052634,
'hspCount': 1,
'medianScore': 25.0,
'readCount': 1,
'subjectLength': 38000,
'subjectTitle': (
'gi|887699|gb|DQ37780 Squirrelpox virus 55'),
},
],
list(titlesAlignments.summary(sortOn='title')))
def testRemovalOfIdenticalSequencesWithDifferingIds(self):
"""
A list with 2 copies of the same seq is de-duped to have 1 copy,
including when the read ids differ.
"""
reads = Reads()
reads.add(Read('id1', 'GGG'))
reads.add(Read('id2', 'GGG'))
self.assertEqual(list(dedupFasta(reads)), [Read('id1', 'GGG')])
def testAlignmentPanel(self):
"""
The alignmentPanel function must work properly.
"""
findParams = FindParameters(significanceMethod='HashFraction',
binScoreMethod='FeatureAAScore')
reads = Reads()
reads.add(GOLV)
reads.add(AKAV)
alignmentPanel(reads, reads, findParams=findParams, showFigure=False)
def testCorrectNumberOfSequences(self):
"""
The right number of strings must be made (one for each sequence).
"""
reads = Reads()
reads.add(MONKEYPOX)
reads.add(MUMMYPOX)
hashesString = HashesString(reads, 0.0, landmarks=['AlphaHelix'])
result = len(hashesString.hashString)
self.assertEqual(2, result)
def testManuallyAddedReads(self):
"""
A Reads instance with reads added manually must be able to be listed.
"""
reads = Reads()
read1 = Read('id1', 'AT')
read2 = Read('id2', 'AC')
reads.add(read1)
reads.add(read2)
self.assertEqual([read1, read2], list(reads))
def testDefaultLabel(self):
"""
The ClusterAnalysis initializer must assign the default label to any
read without a corresponding label.
"""
reads = Reads()
reads.add(AARead('id', 'MMM'))
ca = ClusterAnalysis(reads, {}, defaultLabel=5,
landmarks=['AlphaHelix'])
self.assertEqual([5], ca.trueLabels)
def testMissingLabelNoDefault(self):
"""
The ClusterAnalysis initializer must raise ValueError if a read is
given without a corresponding label and there is no default label.
"""
reads = Reads()
reads.add(AARead('id', 'MMM'))
error = "Read 'id' has no corresponding label"
six.assertRaisesRegex(self, ValueError, error, ClusterAnalysis, reads,
{}, landmarks=['AlphaHelix'])
def reads(self):
"""
Find the set of reads matching this title.
@return: An instance of C{dark.reads.Reads}.
"""
reads = Reads()
for alignment in self:
reads.add(alignment.read)
return reads
def testOneReadAffinity(self):
"""
The ClusterAnalysis initializer must assign a 1.0 affinity to a single
read.
"""
reads = Reads()
reads.add(AARead('id', 'MMM'))
ca = ClusterAnalysis(reads, {}, defaultLabel=5,
landmarks=['AlphaHelix'])
self.assertEqual([[1.0]], ca.affinity)
def reads(self):
"""
Find the set of reads matching this title.
@return: An instance of C{dark.reads.Reads}.
"""
reads = Reads()
for alignment in self:
reads.add(alignment.read)
return reads
def testFilterOnMaxLength(self):
"""
Filtering on maximal length must work.
"""
reads = Reads()
read1 = Read('id1', 'ATCG')
read2 = Read('id2', 'ACG')
reads.add(read1)
reads.add(read2)
result = reads.filter(maxLength=3)
self.assertEqual([read2], list(result))
def testOneReadClusterCount(self):
"""
The KMeansAnalysis class must find one cluster when given one read,
and set the value of nClusters to 1.
"""
reads = Reads()
reads.add(AARead('id1', 'FRRRFRRRF'))
km = KMeansAnalysis(reads, {}, defaultLabel=0,
landmarks=['AlphaHelix'])
km.cluster(1)
self.assertEqual(1, km.nClusters)
def testOneSequenceSpecificDiagonalValue(self):
"""
If affinityMatrix is called with a single read and a specific
diagonal value, that diagonal value must be in the result.
"""
reads = Reads()
read = AARead('id1', 'AAA')
reads.add(read)
matrix = affinityMatrix(reads, landmarks=['AlphaHelix'],
diagonalValue=2.0)
self.assertEqual([[2.0]], matrix)
def testPlotHistogramLinesMustRun(self):
"""
The plotHistogramLines function must run properly.
"""
findParams = FindParameters(significanceMethod='HashFraction',
binScoreMethod='FeatureAAScore')
reads = Reads()
reads.add(GOLV)
reads.add(AKAV)
reads.add(BUNV)
plotHistogramLines(reads, findParams=findParams)
def testFilterOnLengthNothingMatches(self):
"""
When filtering on length, no reads should be returned if none of them
satisfy the length requirements.
"""
reads = Reads()
read1 = Read('id1', 'ATCG')
read2 = Read('id2', 'ACG')
reads.add(read1)
reads.add(read2)
result = reads.filter(minLength=10, maxLength=15)
self.assertEqual([], list(result))
def testSaveWithUnknownFormat(self):
"""
A Reads instance must raise ValueError if asked to save in an unknown
format.
"""
reads = Reads()
read1 = Read('id1', 'AT', '!!')
read2 = Read('id2', 'AC')
reads.add(read1)
reads.add(read2)
error = "Save format must be either 'fasta' or 'fastq'\\."
self.assertRaisesRegexp(ValueError, error, reads.save, 'file', 'xxx')
def testSaveAsFASTQFailsOnReadWithNoQuality(self):
"""
A Reads instance must raise a ValueError if asked to save in FASTQ
format and there is a read with no quality present.
"""
reads = Reads()
read1 = Read('id1', 'AT', '!!')
read2 = Read('id2', 'AC')
reads.add(read1)
reads.add(read2)
error = "Read 'id2' has no quality information"
self.assertRaisesRegexp(ValueError, error, reads.save, 'file', 'fastq')
def testFilterWithMinLengthEqualToMaxLength(self):
"""
When filtering on length, a read should be returned if its length
equals a passed minimum and maximum length.
"""
reads = Reads()
read1 = Read('id1', 'ATCG')
read2 = Read('id2', 'ACG')
reads.add(read1)
reads.add(read2)
result = reads.filter(minLength=4, maxLength=4)
self.assertEqual([read1], list(result))
def testFilterOnLengthEverythingMatches(self):
"""
When filtering on length, all reads should be returned if they all
satisfy the length requirements.
"""
reads = Reads()
read1 = Read('id1', 'ATCG')
read2 = Read('id2', 'ACG')
reads.add(read1)
reads.add(read2)
result = reads.filter(minLength=2, maxLength=5)
self.assertEqual([read1, read2], list(result))
def testSaveToFileDescriptor(self):
"""
A Reads instance must save to a file-like object if not passed a string
filename.
"""
reads = Reads()
read1 = Read('id1', 'AT')
read2 = Read('id2', 'AC')
reads.add(read1)
reads.add(read2)
fp = StringIO()
reads.save(fp)
self.assertEqual('>id1\nAT\n>id2\nAC\n', fp.getvalue())
def testMaxTitlesNegative(self):
"""
The filter function must raise a ValueError if maxTitles is less than
zero.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD0) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id0', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
error = '^maxTitles \(-1\) cannot be negative\.$'
six.assertRaisesRegex(self, ValueError, error,
titlesAlignments.filter, maxTitles=-1)
