def testInitializedRead(self):
"""
It must be possible to read from a StringIO instance that is
initialized on creation.
"""
s = StringIO('hey')
self.assertEqual('hey', s.getvalue())
def testInitializedRead(self):
"""
It must be possible to read from a StringIO instance that is
initialized on creation.
"""
s = StringIO('hey')
self.assertEqual('hey', s.getvalue())
def testWriteRead(self):
"""
It must be possible to write and read to/from a StringIO instance as
normal.
"""
s = StringIO()
s.write('hey')
self.assertEqual('hey', s.getvalue())
def testWriteRead(self):
"""
It must be possible to write and read to/from a StringIO instance as
normal.
"""
s = StringIO()
s.write('hey')
self.assertEqual('hey', s.getvalue())
def testOpenNotCalledOnRepeatedCall(self):
"""
If a repeated call to pathogenSampleFiles.add is made with the same
arguments, no file should be read because the original result value is
cached.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('out/0.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n')
elif self.count == 1:
self.test.assertEqual('out/pathogen-0-sample-0.fasta',
filename)
self.count += 1
return self.manager
else:
self.test.fail(
'We are only supposed to be called twice. '
'Filename: %r, Args: %r, Keyword args: %r.' %
(filename, args, kwargs))
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
)
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
pg = ProteinGrouper()
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
sideEffect = Open(self, manager()).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
self.assertEqual('>id1\nACTG\n', fastaIO.getvalue())
# Repeated call. The side effect open will fail if open is
# called at this point.
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
def testIdenticalReadsRemoved(self):
"""
If two proteins in the same pathogen are matched by the same read, the
de-duplicated FASTA for the pathogen must have only one copy of the
duplicated read.
"""
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.expectedFilenames = {'out/0.fasta', 'out/1.fasta',
'out/pathogen-0-sample-0.fasta'}
def sideEffect(self, filename, *args, **kwargs):
try:
self.expectedFilenames.remove(filename)
except KeyError:
self.test.fail(
'Open called with unexpected filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
else:
if filename == 'out/0.fasta':
return StringIO('>id1\nACTG\n')
elif filename == 'out/1.fasta':
return StringIO('>id1\nACTG\n>id2\nCAGT\n')
else:
return self.manager
fp = StringIO(
'0.63 41.3 44.2 9 9 12 gi|327410| protein 77 [Lausannevirus]\n'
'0.77 46.6 48.1 5 6 74 gi|327409| ubiquitin [Lausannevirus]\n'
)
fastaIO = StringIO()
@contextmanager
def manager():
yield fastaIO
pg = ProteinGrouper()
pg.addFile('filename-1', fp)
pathogenSampleFiles = PathogenSampleFiles(pg)
opener = Open(self, manager())
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = opener.sideEffect
filename = pathogenSampleFiles.add('Lausannevirus', 'filename-1')
self.assertEqual('out/pathogen-0-sample-0.fasta', filename)
self.assertEqual('>id1\nACTG\n>id2\nCAGT\n', fastaIO.getvalue())
# Make sure all expected filenames were seen by the mocked open.
self.assertEqual(set(), opener.expectedFilenames)
def testWritePathogenIndex(self):
"""
The writePatogenIndex function must write a file with the expected
content.
"""
pathogenSampleFiles = PathogenSampleFiles(None)
pathogenSampleFiles._pathogens = {
'virus b': 4,
'virus a': 3,
'virus c': 9,
}
fp = StringIO()
pathogenSampleFiles.writePathogenIndex(fp)
self.assertEqual('3 virus a\n4 virus b\n9 virus c\n', fp.getvalue())
def testWriteSampleIndex(self):
"""
The writeSampleIndex function must write a file with the expected
content.
"""
pathogenSampleFiles = PathogenSampleFiles(None)
pathogenSampleFiles._samples = {
'NEO11': 500,
'NEO33': 24,
'NEO66': 333,
}
fp = StringIO()
pathogenSampleFiles.writeSampleIndex(fp)
self.assertEqual('24 NEO33\n333 NEO66\n500 NEO11\n', fp.getvalue())
def testTwoReads(self):
"""
It must be possible to access a FASTA file with two reads like a dict.
"""
pyfaidxIndex = StringIO()
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return BytesIO(b'>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 1:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 2:
self.count += 1
return self.manager
elif self.count == 3:
self.count += 1
return StringIO(pyfaidxIndex.getvalue())
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
@contextmanager
def manager():
yield pyfaidxIndex
sideEffect = Open(self, manager()).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
reads = FastaFaiReads('filename.fasta')
self.assertEqual(DNARead('id1', 'ACTG'), reads['id1'])
self.assertEqual(DNARead('id2', 'AACCTTGG'), reads['id2'])
# Check that the fai index was built correctly.
self.assertEqual(pyfaidxIndex.getvalue(),
'id1\t4\t5\t4\t5\nid2\t8\t15\t8\t9\n')
def testTwoReads(self):
"""
It must be possible to access a FASTA file with two reads like a dict.
"""
pyfaidxIndex = StringIO()
class Open(object):
def __init__(self, test, manager):
self.test = test
self.manager = manager
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return BytesIO(b'>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 1:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 2:
self.count += 1
return self.manager
elif self.count == 3:
self.count += 1
return StringIO(pyfaidxIndex.getvalue())
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
@contextmanager
def manager():
yield pyfaidxIndex
sideEffect = Open(self, manager()).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
reads = FastaFaiReads('filename.fasta')
self.assertEqual(DNARead('id1', 'ACTG'), reads['id1'])
self.assertEqual(DNARead('id2', 'AACCTTGG'), reads['id2'])
# Check that the fai index was built correctly.
self.assertEqual(pyfaidxIndex.getvalue(),
'id1\t4\t5\t4\t5\nid2\t8\t15\t8\t9\n')
