def testNoQuality(self):
"""
A FASTA file read must not have any quality information.
"""
data = '\n'.join(['>id1', 'ACGT'])
mockOpener = mockOpen(read_data=data)
with patch('__builtin__.open', mockOpener, create=True):
reads = list(FastaReads('filename.fasta'))
self.assertEqual(None, reads[0].quality)
def testOneRead(self):
"""
A FASTA file with one read must be read properly.
"""
data = '\n'.join(['>id1', 'ACGT'])
mockOpener = mockOpen(read_data=data)
with patch('__builtin__.open', mockOpener, create=True):
reads = list(FastaReads('filename.fasta'))
self.assertEqual([Read('id1', 'ACGT')], reads)
def testTwoReads(self):
"""
A FASTA file with two reads must be read properly and its
sequences must be returned in the correct order.
"""
data = '\n'.join(['>id1', 'ACGT', '>id2', 'TGCA'])
mockOpener = mockOpen(read_data=data)
with patch('__builtin__.open', mockOpener, create=True):
reads = list(FastaReads('filename.fasta'))
self.assertEqual(2, len(reads))
self.assertEqual([Read('id1', 'ACGT'), Read('id2', 'TGCA')], reads)
def testSaveAsFASTA(self):
"""
A Reads instance must be able to save in FASTA format.
"""
reads = Reads()
read1 = Read('id1', 'AT')
read2 = Read('id2', 'AC')
reads.add(read1)
reads.add(read2)
mockOpener = mockOpen()
with patch('__builtin__.open', mockOpener, create=True):
reads.save('filename', 'fasta')
handle = mockOpener()
self.assertEqual([call('>id1\nAT\n'), call('>id2\nAC\n')],
handle.write.call_args_list)
def testSaveWithUppercaseFormat(self):
"""
A Reads instance must save correctly when the format string is
given in upper case.
"""
reads = Reads()
read1 = Read('id1', 'AT')
read2 = Read('id2', 'AC')
reads.add(read1)
reads.add(read2)
mockOpener = mockOpen()
with patch('__builtin__.open', mockOpener, create=True):
reads.save('filename', 'FASTA')
handle = mockOpener()
self.assertEqual([call('>id1\nAT\n'), call('>id2\nAC\n')],
handle.write.call_args_list)
def testEmpty(self):
"""An empty FASTA file results in an empty iterator."""
mockOpener = mockOpen()
with patch('__builtin__.open', mockOpener, create=True):
reads = FastaReads('filename.fasta')
self.assertEqual([], list(reads))