def testEmpty(self):
"""
If passed an empty readsAlignments, titleCounts must return an
empty dictionary.
"""
mockOpener = mockOpen(read_data=PARAMS)
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
self.assertEqual({}, titleCounts(readsAlignments))
def testEmpty(self):
"""
If passed an empty readsAlignments, titleCounts must return an
empty dictionary.
"""
mockOpener = mockOpen(read_data=dumps(PARAMS) + '\n')
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
readsAlignments = BlastReadsAlignments(reads, 'file.json')
self.assertEqual({}, titleCounts(readsAlignments))
def testEmpty(self):
"""
If passed an empty readsAlignments, titleCounts must return an
empty dictionary.
"""
mockOpener = mock_open(read_data=dumps(PARAMS) + '\n')
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
readsAlignments = DiamondReadsAlignments(reads, 'file.json')
self.assertEqual({}, titleCounts(readsAlignments))
def testDuplicatedTitle(self):
"""
If alignments for reads have a common title, the count on that title
must be correct.
"""
mockOpener = mockOpen(read_data=(PARAMS + RECORD2 + RECORD3))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
self.assertEqual(
{
COWPOX.id: 2,
},
titleCounts(readsAlignments))
def testDuplicatedTitle(self):
"""
If alignments for reads have a common title, the count on that title
must be correct.
"""
mockOpener = mockOpen(read_data=(dumps(PARAMS) + '\n' +
dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
self.assertEqual({
'gi|887699|gb|DQ37780 Cowpox virus 15': 2,
}, titleCounts(readsAlignments))
def testThreeRecords(self):
"""
If alignments for three reads are passed to titleCounts, it must
return the correct title counts.
"""
mockOpener = mockOpen(read_data=(PARAMS + RECORD0 + RECORD1 + RECORD2))
with patch.object(builtins, 'open', mockOpener):
readsAlignments = LightReadsAlignments('file.json', DB)
self.assertEqual(
{
SQUIRRELPOX.id: 1,
MUMMYPOX.id: 1,
COWPOX.id: 1,
MONKEYPOX.id: 1,
CATPOX.id: 1
},
titleCounts(readsAlignments))
def testDuplicatedTitle(self):
"""
If alignments for reads have a common title, the count on that title
must be correct.
"""
mockOpener = mockOpen(read_data=(
dumps(PARAMS) + '\n' + dumps(RECORD2) + '\n' +
dumps(RECORD3) + '\n'))
with patch.object(builtins, 'open', mockOpener):
reads = Reads()
reads.add(Read('id2', 'A' * 70))
reads.add(Read('id3', 'A' * 70))
readsAlignments = BlastReadsAlignments(reads, 'file.json')
self.assertEqual(
{
'gi|887699|gb|DQ37780 Cowpox virus 15': 2,
},
titleCounts(readsAlignments))
def testThreeRecords(self):
"""
If alignments for three reads are passed to titleCounts, it must
return the correct title counts.
"""
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')
self.assertEqual(
{
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99': 1,
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.': 1,
'gi|887699|gb|DQ37780 Cowpox virus 15': 1,
'gi|887699|gb|DQ37780 Monkeypox virus 456': 1,
'gi|887699|gb|DQ37780 Squirrelpox virus 55': 1
}, titleCounts(readsAlignments))
def testThreeRecords(self):
"""
If alignments for three reads are passed to titleCounts, it must
return the correct title counts.
"""
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')
self.assertEqual(
{
'gi|887699|gb|DQ37780 Squirrelpox virus 1296/99': 1,
'gi|887699|gb|DQ37780 Mummypox virus 3000 B.C.': 1,
'gi|887699|gb|DQ37780 Cowpox virus 15': 1,
'gi|887699|gb|DQ37780 Monkeypox virus 456': 1,
'gi|887699|gb|DQ37780 Squirrelpox virus 55': 1
},
titleCounts(readsAlignments))
