def testOpenFile(self):
"""
When an open file pointer is passed to asHandle, that same file
pointer must be returned.
"""
with patch.object(builtins, 'open', mock_open()):
fp = open('file')
with asHandle(fp) as newfp:
self.assertIs(fp, newfp)
def testStr(self):
"""
When a string filename is passed to asHandle, it must be possible to
read the correct data from the fp that is returned.
"""
mockOpener = mock_open(read_data='xxx')
with patch.object(builtins, 'open', mockOpener):
with asHandle('file') as fp:
self.assertEqual('xxx', fp.read())
def testStr(self):
"""
When a string filename is passed to asHandle, it must be possible to
read the correct data from the fp that is returned.
"""
mockOpener = mockOpen(read_data='xxx')
with patch.object(builtins, 'open', mockOpener):
with asHandle('file') as fp:
self.assertEqual('xxx', fp.read())
def save(self, filename):
"""
Write SAM output to a file.
@param filename: A C{str} filename or an already-open file handle.
"""
with asHandle(filename) as fp:
self._writer.save(fp, tmpfp=self._tf)
self._tf.close()
self._tf = self._writer = None
def testOpenFile(self):
"""
When an open file pointer is passed to asHandle, that same file
pointer must be returned.
"""
mockOpener = mockOpen()
with patch.object(builtins, 'open', mockOpener):
fp = open('file')
with asHandle(fp) as newfp:
self.assertIs(fp, newfp)
def testGzip(self):
"""
When a string '*.gz' filename is passed to asHandle, it must be
possible to read the correct data from the fp that is returned.
"""
result = BytesIO(b'xxx')
with patch.object(gzip, 'GzipFile') as mockMethod:
mockMethod.return_value = result
with asHandle('file.gz') as fp:
self.assertEqual('xxx', fp.read())
def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
as an instance of the desired read class.
"""
for _file in self._files:
with asHandle(_file) as fp:
# Use FastqGeneralIterator because it provides access to
# the unconverted quality string (i.e., it doesn't try to
# figure out the numeric quality values, which we don't
# care about at this point).
for sequenceId, sequence, quality in FastqGeneralIterator(fp):
yield self.readClass(sequenceId, sequence, quality)
def iter(self):
"""
Iterate over the sequences in self.file_, yielding each as an
instance of the desired read class.
@raise ValueError: If the input file has an odd number of records or
if any sequence has a different length than its predicted
secondary structure.
"""
checkAlphabet = self._checkAlphabet
upperCase = self._upperCase
count = 0
for _file in self._files:
with asHandle(_file) as fp:
records = SeqIO.parse(fp, 'fasta')
while True:
try:
record = next(records)
except StopIteration:
break
count += 1
try:
structureRecord = next(records)
except StopIteration:
raise ValueError('Structure file %r has an odd number '
'of records.' % _file)
if len(structureRecord) != len(record):
raise ValueError(
'Sequence %r length (%d) is not equal to '
'structure %r length (%d) in input file %r.' % (
record.description, len(record),
structureRecord.description,
len(structureRecord), _file))
if upperCase:
read = self._readClass(
record.description,
str(record.seq.upper()),
str(structureRecord.seq.upper()))
else:
read = self._readClass(record.description,
str(record.seq),
str(structureRecord.seq))
if checkAlphabet is None or count < checkAlphabet:
read.checkAlphabet(count=None)
yield read
def testGzip(self):
"""
When a string '*.gz' filename is passed to asHandle, it must be
possible to read the correct data from the fp that is returned.
"""
if six.PY3:
self.skipTest('Mocking gzip.GzipFile disabled under Python 3')
# This test should be better. It should actually create some gzip
# compressed data and make sure that it's decompressed
# properly. But Python mocking makes me so confused...
result = File('xxx')
with patch.object(gzip, 'GzipFile') as mockMethod:
mockMethod.return_value = result
with asHandle('file.gz') as fp:
self.assertEqual('xxx', fp.read())
def testGzip(self):
"""
When a string '*.gz' filename is passed to asHandle, it must be
possible to read the correct data from the fp that is returned.
"""
if six.PY3:
self.skipTest('Mocking gzip.GzipFile disabled under Python 3')
# This test should be better. It should actually create some gzip
# compressed data and make sure that it's decompressed
# properly. But Python mocking makes me so confused...
result = StringIO('xxx')
with patch.object(gzip, 'GzipFile') as mockMethod:
mockMethod.return_value = result
with asHandle('file.gz') as fp:
self.assertEqual('xxx', fp.read())
def iter(self):
"""
Iterate over the sequences in self.file_, yielding each as an
instance of the desired read class.
@raise ValueError: If the input file has an odd number of records or
if any sequence has a different length than its predicted
secondary structure.
"""
upperCase = self._upperCase
for _file in self._files:
with asHandle(_file) as fp:
records = SeqIO.parse(fp, 'fasta')
while True:
try:
record = next(records)
except StopIteration:
break
try:
structureRecord = next(records)
except StopIteration:
raise ValueError('Structure file %r has an odd number '
'of records.' % _file)
if len(structureRecord) != len(record):
raise ValueError(
'Sequence %r length (%d) is not equal to '
'structure %r length (%d) in input file %r.' % (
record.description, len(record),
structureRecord.description,
len(structureRecord), _file))
if upperCase:
read = self._readClass(
record.description,
str(record.seq.upper()),
str(structureRecord.seq.upper()))
else:
read = self._readClass(record.description,
str(record.seq),
str(structureRecord.seq))
yield read
def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
as an instance of the desired read class.
"""
checkAlphabet = self._checkAlphabet
count = 0
for _file in self._files:
with asHandle(_file) as fp:
for seq in SeqIO.parse(fp, 'fasta'):
if self._upperCase:
read = self._readClass(seq.description,
str(seq.seq.upper()))
else:
read = self._readClass(seq.description, str(seq.seq))
if checkAlphabet is None or count < checkAlphabet:
read.checkAlphabet(count=None)
yield read
count += 1
def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
as an instance of the desired read class.
"""
checkAlphabet = self._checkAlphabet
count = 0
for _file in self._files:
with asHandle(_file) as fp:
for seq in SeqIO.parse(fp, 'fasta'):
if self._upperCase:
read = self._readClass(seq.description,
str(seq.seq.upper()))
else:
read = self._readClass(seq.description, str(seq.seq))
if checkAlphabet is None or count < checkAlphabet:
read.checkAlphabet(count=None)
yield read
count += 1
def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
as an instance of the desired read class.
"""
count = 0
for _file in self._files:
with asHandle(_file) as fp:
# Duplicate some code here so as not to test
# self._upperCase in the loop.
if self._upperCase:
for seq in SeqIO.parse(fp, 'fasta'):
read = self._readClass(seq.description,
str(seq.seq.upper()))
yield read
count += 1
else:
for seq in SeqIO.parse(fp, 'fasta'):
read = self._readClass(seq.description, str(seq.seq))
yield read
count += 1
def iter(self):
"""
Iterate over the sequences in the files in self.files_, yielding each
as an instance of the desired read class.
"""
count = 0
for _file in self._files:
with asHandle(_file) as fp:
# Duplicate some code here so as not to test
# self._upperCase in the loop.
if self._upperCase:
for seq in SeqIO.parse(fp, 'fasta'):
read = self._readClass(seq.description,
str(seq.seq.upper()))
yield read
count += 1
else:
for seq in SeqIO.parse(fp, 'fasta'):
read = self._readClass(seq.description, str(seq.seq))
yield read
count += 1
