def testFilterRandomSubsetOfOneFromTenReads(self):
"""
It must be possible to select a random subset of one read from a set
of ten reads, where the read count is provided to C{filter} via the
C{trueLength} argument.
"""
data = '\n'.join(['>id', 'ACGT'] * 10)
with patch.object(builtins, 'open', mock_open(read_data=data)):
reads = FastaReads('filename.fasta')
result = list(reads.filter(randomSubset=1, trueLength=10))
self.assertEqual(1, len(result))
def testFilterRandomSubsetOfZeroFromZeroReads(self):
"""
It must be possible to select a random subset of zero reads from a set
of zero reads, where the read count is provided to C{filter} via the
C{trueLength} argument.
"""
data = ''
with patch.object(builtins, 'open', mock_open(read_data=data)):
reads = FastaReads('filename.fasta')
result = list(reads.filter(randomSubset=0, trueLength=0))
self.assertEqual([], result)
def testFilterRandomSubsetOfOneFromTenReads(self):
"""
It must be possible to select a random subset of one read from a set
of ten reads, where the read count is provided to C{filter} via the
C{trueLength} argument.
"""
data = '\n'.join(['>id', 'ACGT'] * 10)
mockOpener = mockOpen(read_data=data)
with patch.object(builtins, 'open', mockOpener):
reads = FastaReads('filename.fasta')
result = list(reads.filter(randomSubset=1, trueLength=10))
self.assertEqual(1, len(result))
def testFilterRandomSubsetOfZeroFromZeroReads(self):
"""
It must be possible to select a random subset of zero reads from a set
of zero reads, where the read count is provided to C{filter} via the
C{trueLength} argument.
"""
data = ''
mockOpener = mockOpen(read_data=data)
with patch.object(builtins, 'open', mockOpener):
reads = FastaReads('filename.fasta')
result = list(reads.filter(randomSubset=0, trueLength=0))
self.assertEqual([], result)
def testFilterRandomSubsetOfTwoFromTwoReads(self):
"""
It must be possible to select a random subset of two reads from a set
of two reads, where the read count is provided to C{filter} via the
C{trueLength} argument.
"""
data = '\n'.join(['>id1', 'ACGT', '>id2', 'TGCA'])
with patch.object(builtins, 'open', mock_open(read_data=data)):
reads = FastaReads('filename.fasta')
result = list(reads.filter(randomSubset=2, trueLength=2))
self.assertEqual(
[Read('id1', 'ACGT'), Read('id2', 'TGCA')], result)
def testFilterRandomSubsetOfTwoFromTwoReads(self):
"""
It must be possible to select a random subset of two reads from a set
of two reads, where the read count is provided to C{filter} via the
C{trueLength} argument.
"""
data = '\n'.join(['>id1', 'ACGT', '>id2', 'TGCA'])
mockOpener = mockOpen(read_data=data)
with patch.object(builtins, 'open', mockOpener):
reads = FastaReads('filename.fasta')
result = list(reads.filter(randomSubset=2, trueLength=2))
self.assertEqual([Read('id1', 'ACGT'), Read('id2', 'TGCA')],
result)
