def testMedianScore_Bits(self):
"""
Sorting on median score must work when scores are bit scores,
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' + dumps(RECORD4) + '\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))
reads.add(Read('id4', 'A' * 70))
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('medianScore')
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 25
'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
'gi|887699|gb|DQ37780 Cowpox virus 15', # 20
], 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 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 testMedianScore_EValue(self):
"""
Sorting on median 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' + dumps(RECORD4) + '\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))
reads.add(Read('id4', 'A' * 70))
readsAlignments = BlastReadsAlignments(
reads, 'file.json', scoreClass=LowerIsBetterScore)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('medianScore')
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', # worst :-)
], 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('__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 testMedianScore_Bits(self):
"""
Sorting on median 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' + dumps(RECORD4) + '\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))
reads.add(Read('id4', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('medianScore')
self.assertEqual([
'gi|887699|gb|DQ37780 Squirrelpox virus 55', # 25
'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
'gi|887699|gb|DQ37780 Cowpox virus 15', # 20
], result)
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 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_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 testEmpty(self):
"""
Sorting when there are no titles must return the empty list.
"""
mockOpener = mockOpen(read_data=PARAMS)
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('title')
self.assertEqual([], result)
def testEmpty(self):
"""
Sorting when there are no titles must return the empty list.
"""
mockOpener = mock_open(read_data=dumps(PARAMS) + '\n')
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('title')
self.assertEqual([], result)
def testEmpty(self):
"""
Sorting when there are no titles must return the empty list.
"""
mockOpener = mockOpen(read_data=dumps(PARAMS) + '\n')
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
readsAlignments = BlastReadsAlignments(reads, 'file.json')
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('title')
self.assertEqual([], result)
def testReadCount(self):
"""
Sorting on read count must work, including a secondary sort on title.
"""
mockOpener = mockOpen(read_data=(PARAMS + RECORD0 + RECORD1 + RECORD2 +
RECORD3))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('readCount')
self.assertEqual([
COWPOX.id, # 2
CATPOX.id, # 1
MONKEYPOX.id, # 1
MUMMYPOX.id, # 1
SQUIRRELPOX.id, # 1
], result)
def testLength(self):
"""
Sorting on sequence length must work.
"""
mockOpener = mockOpen(read_data=(PARAMS + RECORD0 + RECORD1 + RECORD2 +
RECORD3))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('length')
self.assertEqual([
MUMMYPOX.id, # 48
MONKEYPOX.id, # 47
SQUIRRELPOX.id, # 41
CATPOX.id, # 34
COWPOX.id, # 14
], result)
def testTitle(self):
"""
Sorting on title must work.
"""
mockOpener = mockOpen(read_data=(PARAMS + RECORD0 + RECORD1 + RECORD2 +
RECORD3))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('title')
self.assertEqual([
CATPOX.id,
COWPOX.id,
MONKEYPOX.id,
MUMMYPOX.id,
SQUIRRELPOX.id,
], result)
def testMaxScore(self):
"""
Sorting on max score must work, including a secondary sort on title.
"""
mockOpener = mockOpen(read_data=(PARAMS + RECORD0 + RECORD1 + RECORD2 +
RECORD3))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
titlesAlignments = TitlesAlignments(readsAlignments)
result = titlesAlignments.sortTitles('maxScore')
self.assertEqual([
SQUIRRELPOX.id, # 1.0
COWPOX.id, # 0.75
MONKEYPOX.id, # 0.6
CATPOX.id, # 0.5
MUMMYPOX.id, # 0.4
], result)
oneAlignmentPerRead=args.oneAlignmentPerRead,
maxHspsPerHit=args.maxHspsPerHit,
scoreCutoff=args.scoreCutoff,
whitelist=set(args.whitelist) if args.whitelist else None,
blacklist=set(args.blacklist) if args.blacklist else None,
titleRegex=args.titleRegex,
negativeTitleRegex=args.negativeTitleRegex,
truncateTitlesAfter=args.truncateTitlesAfter,
taxonomy=args.taxonomy)
titlesAlignments = TitlesAlignments(readsAlignments).filter(
minMatchingReads=args.minMatchingReads,
minMedianScore=args.minMedianScore,
withScoreBetterThan=args.withScoreBetterThan,
minNewReads=args.minNewReads)
nTitles = len(titlesAlignments)
print('Found %d interesting title%s.' % (nTitles,
'' if nTitles == 1 else 's'))
if args.earlyExit:
print('Matched titles (sorted by best score, descending):')
print('\n'.join(titlesAlignments.sortTitles('maxScore')))
sys.exit(0)
alignmentPanel(titlesAlignments, sortOn=args.sortOn, interactive=True,
outputDir=args.outputDir,
idList=parseColors(args.color) if args.color else None,
equalizeXAxes=args.equalizeXAxes, xRange=args.xRange,
logLinearXAxis=args.logLinearXAxis, logBase=args.logBase)
