def testDictLookupGzipDataWithBGZsuffix(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected read when the index file is in BGZF format and has a .bgz
suffix.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count <= 1:
self.test.assertEqual('filename.fasta.bgz', filename)
self.count += 1
writerIO = BytesIO()
writer = bgzf.BgzfWriter(fileobj=writerIO)
writer.write(b'>id0\nAC\n')
writer.flush()
fileobj = BytesIO(writerIO.getvalue())
fileobj.mode = 'rb'
return bgzf.BgzfReader(fileobj=fileobj)
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(bgzf, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename.fasta.bgz')
self.assertEqual(DNARead('id0', 'AC'), index['id0'])
index.close()
def testDictLookupWithTwoFiles(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected reads when sequences are added from two files.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0 or self.count == 2 or self.count == 3:
self.test.assertEqual('filename1.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 1 or self.count == 4:
self.test.assertEqual('filename2.fasta', filename)
self.count += 1
return StringIO('>seq3\nAAACCC\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename1.fasta')
index.addFile('filename2.fasta')
self.assertEqual(DNARead('id1', 'ACTG'), index['id1'])
self.assertEqual(DNARead('id2', 'AACCTTGG'), index['id2'])
self.assertEqual(DNARead('seq3', 'AAACCC'), index['seq3'])
index.close()
def testDictLookupSpecificReadClass(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected read type.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0 or self.count == 1:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nMM\n>id2\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:', readClass=AARead)
index.addFile('filename.fasta')
result = index['id1']
self.assertTrue(isinstance(result, AARead))
self.assertEqual(AARead('id1', 'MM'), result)
index.close()
def testDictLookupWithFastaDirectory(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected read, obtained from the expected file name, when a FASTA base
directory is specified.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('/tmp/f.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\r\nCCCC\nGGG\n>id2\nAACCTG\n')
if self.count == 1:
self.test.assertEqual(
os.path.join('/usr/local/fasta', 'f.fasta'), filename)
self.count += 1
return StringIO('>id1\nACTG\r\nCCCC\nGGG\n>id2\nAACCTG\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:', fastaDirectory='/usr/local/fasta')
index.addFile('/tmp/f.fasta')
self.assertEqual(DNARead('id1', 'ACTGCCCCGGG'), index['id1'])
index.close()
def testFindWithTwoFiles(self):
""""
The _find method must return the expected filename and offset when
sequences are added from two files.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename1.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 1:
self.test.assertEqual('filename2.fasta', filename)
self.count += 1
return StringIO('>sequence3\nAAACCC\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename1.fasta')
index.addFile('filename2.fasta')
self.assertEqual(('filename1.fasta', 5), index._find('id1'))
self.assertEqual(('filename1.fasta', 15), index._find('id2'))
self.assertEqual(('filename2.fasta', 11), index._find('sequence3'))
index.close()
def testAddDuplicateFile(self):
""""
If a filename is passed to addFile more than once, a ValueError must
be raised.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
self.assertEqual(2, index.addFile('filename.fasta'))
error = "^Duplicate file name: 'filename\\.fasta'$"
assertRaisesRegex(self, ValueError, error, index._addFilename,
'filename.fasta')
index.close()
def testDictLookupSequenceMiddleOfThree(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected read when the sequence spans multiple lines and is the middle
one of three sequences in the input file.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0 or self.count == 1:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO(
'>id1\nACTG\nCCCC\n>id2\nAACCTG\nAAA\n>id3\nAAA\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename.fasta')
self.assertEqual(DNARead('id2', 'AACCTGAAA'), index['id2'])
index.close()
def testDictLookupWithTwoFiles(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected reads when sequences are added from two files.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0 or self.count == 2 or self.count == 3:
self.test.assertEqual('filename1.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 1 or self.count == 4:
self.test.assertEqual('filename2.fasta', filename)
self.count += 1
return StringIO('>seq3\nAAACCC\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename1.fasta')
index.addFile('filename2.fasta')
self.assertEqual(DNARead('id1', 'ACTG'), index['id1'])
self.assertEqual(DNARead('id2', 'AACCTTGG'), index['id2'])
self.assertEqual(DNARead('seq3', 'AAACCC'), index['seq3'])
index.close()
def testDictLookupWithFastaDirectory(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected read, obtained from the expected file name, when a FASTA base
directory is specified.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('/tmp/f.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\r\nCCCC\nGGG\n>id2\nAACCTG\n')
if self.count == 1:
self.test.assertEqual(
os.path.join('/usr/local/fasta', 'f.fasta'), filename)
self.count += 1
return StringIO('>id1\nACTG\r\nCCCC\nGGG\n>id2\nAACCTG\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:', fastaDirectory='/usr/local/fasta')
index.addFile('/tmp/f.fasta')
self.assertEqual(DNARead('id1', 'ACTGCCCCGGG'), index['id1'])
index.close()
def testAddDuplicateFile(self):
""""
If a filename is passed to addFile more than once, a ValueError must
be raised.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
self.assertEqual(2, index.addFile('filename.fasta'))
error = "^Duplicate file name: 'filename.fasta'$"
self.assertRaisesRegexp(ValueError, error, index._addFilename,
'filename.fasta')
index.close()
def testAddOneFile(self):
""""
Test the creation of an index with sequences added from one file.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
self.assertEqual(2, index.addFile('filename.fasta'))
index.close()
def testAddFilesWithDuplicateSequence(self):
""""
If a sequence id occurs in more than one FASTA file, a ValueError must
be raised.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename1.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 1:
self.test.assertEqual('filename2.fasta', filename)
self.count += 1
return StringIO('>id2\nAAACCC\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename1.fasta')
error = ("^FASTA sequence id 'id2', found in file "
"'filename2\.fasta', was previously added from file "
"'filename1\.fasta'\.$")
self.assertRaisesRegexp(ValueError, error, index.addFile,
'filename2.fasta')
index.close()
def testDictLookupSequenceCrossesNewlines(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected read when the sequence spans multiple lines of the input file,
including lines ending in \n and \r\n.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0 or self.count == 1:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\r\nCCCC\nGGG\n>id2\nAACCTG\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename.fasta')
self.assertEqual(DNARead('id1', 'ACTGCCCCGGG'), index['id1'])
index.close()
def testDictLookupSpecificReadClass(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected read type.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0 or self.count == 1:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nMM\n>id2\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:', readClass=AARead)
index.addFile('filename.fasta')
result = index['id1']
self.assertTrue(isinstance(result, AARead))
self.assertEqual(AARead('id1', 'MM'), result)
index.close()
def testDictLookupGzipDataWithBGZsuffix(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected read when the index file is in BGZF format and has a .bgz
suffix.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count <= 1:
self.test.assertEqual('filename.fasta.bgz', filename)
self.count += 1
writerIO = BytesIO()
writer = bgzf.BgzfWriter(fileobj=writerIO)
writer.write(b'>id0\nAC\n')
writer.flush()
fileobj = BytesIO(writerIO.getvalue())
fileobj.mode = 'rb'
return bgzf.BgzfReader(fileobj=fileobj)
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(bgzf, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename.fasta.bgz')
self.assertEqual(DNARead('id0', 'AC'), index['id0'])
index.close()
def testAddFilesWithDuplicateSequence(self):
""""
If a sequence id occurs in more than one FASTA file, a ValueError must
be raised.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename1.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 1:
self.test.assertEqual('filename2.fasta', filename)
self.count += 1
return StringIO('>id2\nAAACCC\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename1.fasta')
error = ("^FASTA sequence id 'id2', found in file "
"'filename2\\.fasta', was previously added from file "
"'filename1\\.fasta'\\.$")
assertRaisesRegex(self, ValueError, error, index.addFile,
'filename2.fasta')
index.close()
def testFindWithTwoFiles(self):
""""
The _find method must return the expected filename and offset when
sequences are added from two files.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename1.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
elif self.count == 1:
self.test.assertEqual('filename2.fasta', filename)
self.count += 1
return StringIO('>sequence3\nAAACCC\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename1.fasta')
index.addFile('filename2.fasta')
self.assertEqual(('filename1.fasta', 5), index._find('id1'))
self.assertEqual(('filename1.fasta', 15), index._find('id2'))
self.assertEqual(('filename2.fasta', 11), index._find('sequence3'))
index.close()
def testAddOneFile(self):
""""
Test the creation of an index with sequences added from one file.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count == 0:
self.test.assertEqual('filename.fasta', filename)
self.count += 1
return StringIO('>id1\nACTG\n>id2\nAACCTTGG\n')
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(builtins, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
self.assertEqual(2, index.addFile('filename.fasta'))
index.close()
def testGetFileNumber(self):
""""
The internal _getFileNumber method must return the expected result.
"""
index = SqliteIndex(':memory:')
self.assertEqual(1, index._addFilename('filename.fasta'))
self.assertEqual(1, index._getFileNumber('filename.fasta'))
index.close()
def testGetNonexistentFileNumber(self):
""""
If the internal _getFileNumber method is called with a file whose name
has not been added, it must return None.
"""
index = SqliteIndex(':memory:')
self.assertEqual(None, index._getFileNumber('filename.fasta'))
index.close()
def testAddFilename(self):
""""
Test the internal _addFilename method.
"""
index = SqliteIndex(':memory:')
self.assertEqual(1, index._addFilename('filename1.fasta'))
self.assertEqual(2, index._addFilename('filename2.fasta'))
index.close()
def testGetFileNumber(self):
""""
The internal _getFileNumber method must return the expected result.
"""
index = SqliteIndex(':memory:')
self.assertEqual(1, index._addFilename('filename.fasta'))
self.assertEqual(1, index._getFileNumber('filename.fasta'))
index.close()
def testGetNonexistentFileNumber(self):
""""
If the internal _getFileNumber method is called with a file whose name
has not been added, it must return None.
"""
index = SqliteIndex(':memory:')
self.assertEqual(None, index._getFileNumber('filename.fasta'))
index.close()
def testAddFilename(self):
""""
Test the internal _addFilename method.
"""
index = SqliteIndex(':memory:')
self.assertEqual(1, index._addFilename('filename1.fasta'))
self.assertEqual(2, index._addFilename('filename2.fasta'))
index.close()
def testDictLookupGzipData(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected reads when sequences span multiple lines of the input file,
and include lines ending in \n and \r\n and have been compressed with
bgzip, including when sequences are more than 64K bytes into the input
file.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count <= 4:
self.test.assertEqual('filename.fasta.gz', filename)
self.count += 1
writerIO = BytesIO()
writer = bgzf.BgzfWriter(fileobj=writerIO)
writer.write(
b'>id0\nAC\n' +
b'>id1\n' + (b'A' * 70000) + b'\n' +
b'>id2\r\nACTG\r\nCCCC\r\nGGG\r\n' +
b'>id3\nAACCTG\n')
writer.flush()
fileobj = BytesIO(writerIO.getvalue())
fileobj.mode = 'rb'
return bgzf.BgzfReader(fileobj=fileobj)
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(bgzf, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename.fasta.gz')
self.assertEqual(DNARead('id0', 'AC'), index['id0'])
self.assertEqual(DNARead('id1', 'A' * 70000), index['id1'])
self.assertEqual(DNARead('id2', 'ACTGCCCCGGG'), index['id2'])
self.assertEqual(DNARead('id3', 'AACCTG'), index['id3'])
index.close()
def testDictLookupGzipData(self):
""""
The __getitem__ method (i.e., dictionary-like lookup) must return the
expected reads when sequences span multiple lines of the input file,
and include lines ending in \n and \r\n and have been compressed with
bgzip, including when sequences are more than 64K bytes into the input
file.
"""
class Open(object):
def __init__(self, test):
self.test = test
self.count = 0
def sideEffect(self, filename, *args, **kwargs):
if self.count <= 4:
self.test.assertEqual('filename.fasta.gz', filename)
self.count += 1
writerIO = BytesIO()
writer = bgzf.BgzfWriter(fileobj=writerIO)
writer.write(b'>id0\nAC\n' + b'>id1\n' + (b'A' * 70000) +
b'\n' + b'>id2\r\nACTG\r\nCCCC\r\nGGG\r\n' +
b'>id3\nAACCTG\n')
writer.flush()
fileobj = BytesIO(writerIO.getvalue())
fileobj.mode = 'rb'
return bgzf.BgzfReader(fileobj=fileobj)
else:
self.test.fail(
'Open called too many times. Filename: %r, Args: %r, '
'Keyword args: %r.' % (filename, args, kwargs))
sideEffect = Open(self).sideEffect
with patch.object(bgzf, 'open') as mockMethod:
mockMethod.side_effect = sideEffect
index = SqliteIndex(':memory:')
index.addFile('filename.fasta.gz')
self.assertEqual(DNARead('id0', 'AC'), index['id0'])
self.assertEqual(DNARead('id1', 'A' * 70000), index['id1'])
self.assertEqual(DNARead('id2', 'ACTGCCCCGGG'), index['id2'])
self.assertEqual(DNARead('id3', 'AACCTG'), index['id3'])
index.close()
