def test_memory_1(self):
""" mafComparator should be memory clean for seed testing examples
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_1'))
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
for maf1, maf2 in knownValuesSeed:
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.join(tmpDir, 'output.xml'),
'--samples=10', '--logLevel=critical']
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
for i in xrange(0, 4):
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def test_memoryTest_6(self):
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_6'))
i = -1
for maf1, maf2, totalTrue, totalFalse in knownValues:
i += 1
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.abspath(os.path.join(tmpDir, 'output.xml')),
'--samples=1000', '--logLevel=critical',
'--numberOfPairs=%s' % knownValuesNumberOfPairs[i],
]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def test_memory_0(self):
""" mafComparator should be memory clean for bed parsing examples
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_0'))
for maf1, maf2, bed, totalTrue, totalTrueInInterval in knownValuesBed:
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
testBed = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'bed.bed')),
bed, [''])
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.abspath(os.path.join(tmpDir, 'output.xml')),
'--samples=1000', '--logLevel=critical',
]
if bed != '':
cmd += ['--bedFiles', os.path.abspath(os.path.join(tmpDir, 'bed.bed'))]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def test_memory_3(self):
""" mafComparator should be memory clean for known values using --near option
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_3'))
for maf1, maf2, near, totalTrue, totalFalse in knownValuesNear:
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.abspath(os.path.join(tmpDir, 'output.xml')),
'--near=%d' % near,
'--samples=1000', '--logLevel=critical',
]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
global g_header
customOpts = mafval.GenericValidationOptions()
for i in xrange(0, len(g_blocks)):
tmpDir = os.path.abspath(mtt.makeTempDir('memory1'))
testMafPath, g_header = mtt.testFile(
os.path.abspath(os.path.join(tmpDir, 'test.maf')),
g_blocks[i][0], g_headers)
parent = os.path.dirname(os.path.dirname(
os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(
os.path.abspath(os.path.join(parent, 'test', 'mafRowOrderer')))
cmd += ['--maf', testMafPath, '--order', '%s' % g_order]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'ordered.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(
mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
self.assertTrue(
mafval.validateMaf(os.path.join(tmpDir, 'ordered.maf'),
customOpts))
mtt.removeDir(tmpDir)
def test_memoryTest_6(self):
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_6'))
i = -1
for maf1, maf2, totalTrue, totalFalse in knownValues:
i += 1
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.abspath(os.path.join(tmpDir, 'output.xml')),
'--samples=1000', '--logLevel=critical',
'--numberOfPairs=%s' % knownValuesNumberOfPairs[i],
]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
for i in xrange(0, 10):
shuffledBlocks = []
expectedOutput = []
tmpDir = os.path.abspath(mtt.makeTempDir())
order = [1] * len(g_duplicateBlocks) + [0] * len(g_nonDuplicateBlocks)
random.shuffle(order)
random.shuffle(g_duplicateBlocks)
random.shuffle(g_nonDuplicateBlocks)
j, k = 0, 0
for dupBlock in order:
if dupBlock:
shuffledBlocks.append(g_duplicateBlocks[j][0])
expectedOutput.append(g_duplicateBlocks[j][1])
j += 1
else:
shuffledBlocks.append(g_nonDuplicateBlocks[k])
expectedOutput.append(g_nonDuplicateBlocks[k])
k += 1
testMaf = mtt.testFile(os.path.abspath(os.path.join(os.curdir, 'tempTestDir', 'test.maf')),
''.join(shuffledBlocks), g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = [valgrind, '--leak-check=full', '--show-reachable=yes', '--track-origins=yes', '--xml=yes',
'--xml-file=' + os.path.join(tmpDir, 'valgrind.xml')]
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafBlockDuplicateFilter')),
'--maf', os.path.abspath(os.path.join(os.curdir, 'tempTestDir', 'test.maf'))]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'filtered.maf'))]
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeTempDir()
def testMemory2(self):
""" If valgrind is installed on the system, check for memory related errors (2).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
global g_header
for i in xrange(0, len(g_nonOverlappingBlocks)):
tmpDir = os.path.abspath(mtt.makeTempDir('memory2'))
testMafPath, g_header = mtt.testFile(
os.path.abspath(os.path.join(tmpDir, 'test.maf')),
''.join(g_nonOverlappingBlocks[i][0]), g_headers)
parent = os.path.dirname(os.path.dirname(
os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(
os.path.abspath(
os.path.join(parent, 'test', 'mafPositionFinder')))
cmd += [
'--maf', testMafPath, '--seq', g_targetSeq, '--pos',
'%d' % g_nonOverlappingBlocks[i][1]
]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'found.txt'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(
mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
tmpDir = os.path.abspath(mtt.makeTempDir('memeory1'))
customOpts = mafval.GenericValidationOptions()
for a, expected, strand in g_blocks:
testMaf = mtt.testFile(
os.path.abspath(os.path.join(tmpDir, 'test.maf')), ''.join(a),
g_headers)
parent = os.path.dirname(os.path.dirname(
os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [
os.path.abspath(os.path.join(parent, 'test',
'mafStrander')), '--maf',
os.path.abspath(os.path.join(tmpDir, 'test.maf')), '--seq',
'target', '--strand', strand
]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'coerced.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(
mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
self.assertTrue(
mafval.validateMaf(os.path.join(tmpDir, 'coerced.maf'),
customOpts))
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
for i in xrange(0, 10):
shuffledBlocks = []
tmpDir = os.path.abspath(mtt.makeTempDir())
order = [1] * len(g_overlappingBlocks) + [0] * len(g_nonOverlappingBlocks)
random.shuffle(order)
random.shuffle(g_overlappingBlocks)
random.shuffle(g_nonOverlappingBlocks)
j, k = 0, 0
for isOverlapping in order:
if isOverlapping:
shuffledBlocks.append(g_overlappingBlocks[j])
j += 1
else:
shuffledBlocks.append(g_nonOverlappingBlocks[k])
k += 1
testMaf = mtt.testFile(os.path.abspath(os.path.join(os.curdir, 'tempTestDir', 'test.maf')),
''.join(shuffledBlocks), g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = [valgrind, '--leak-check=full', '--show-reachable=yes', '--track-origins=yes', '--xml=yes',
'--xml-file=' + os.path.join(tmpDir, 'valgrind.xml')]
cmd.append(os.path.abspath(os.path.join(parent, 'test', 'mafBlockExtractor')))
cmd += ['--maf', os.path.abspath(os.path.join(os.curdir, 'tempTestDir', 'test.maf')),
'--seq', g_targetSeq, '--start', '%d' % g_targetRange[0],
'--stop', '%d' % g_targetRange[1]]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'extracted.maf'))]
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeTempDir()
def testMemory0(self):
""" If valgrind is installed on the system, check for memory related errors (0).
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_0'))
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
customOpts = mafval.GenericValidationOptions()
for target, mafSeq, solutionDict in g_knownGood:
testMaf = mtt.testFile(
os.path.join(os.path.abspath(tmpDir), 'test.maf'), mafSeq,
g_headers)
cmd = mtt.genericValgrind(tmpDir)
cmd.append(
os.path.abspath(os.path.join(parent, 'test', 'mafCoverage')))
cmd += [
'--maf',
os.path.abspath(os.path.join(tmpDir, 'test.maf')), '--species',
target
]
outpipes = [os.path.join('/dev', 'null')]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(
mafval.validateMaf(os.path.join(tmpDir, 'test.maf'),
customOpts))
self.assertTrue(
mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def dtestMemory2(self):
""" If valgrind is installed on the system, check for memory related errors (2).
"""
valgrind = mtt.which("valgrind")
if valgrind is None:
return
global g_header
for i in xrange(0, len(g_nonOverlappingBlocks)):
tmpDir = os.path.abspath(mtt.makeTempDir())
testMafPath, g_header = mtt.testFile(
os.path.abspath(os.path.join(os.curdir, "tempTestDir", "test.maf")),
"".join(g_nonOverlappingBlocks[i][0]),
g_headers,
)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = [
valgrind,
"--leak-check=full",
"show-reachable=yes",
"--track-origins=yes",
"--xml=yes",
"--xml-file=" + os.path.join(tmpDir, "valgrind.xml"),
]
cmd.append(os.path.abspath(os.path.join(parent, "test", "mafBlockFinder")))
cmd += ["--maf", testMafPath, "--seq", g_targetSeq, "--pos", "%d" % g_nonOverlappingBlocks[i][1]]
outpipes = [os.path.abspath(os.path.join(tmpDir, "found.txt"))]
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, "valgrind.xml")))
mtt.removeTempDir()
def testMemory2(self):
""" If valgrind is installed on the system, check for memory related errors (2).
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
i = -1
for inblocks, seq, start, stop, outblocks in self.testSet:
i += 1
tmpDir = os.path.abspath(mtt.makeTempDir('memory_2'))
random.shuffle(g_nonOverlappingBlocks)
testMaf = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test_%d.maf' % i)),
''.join(map(str, inblocks)), g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(os.path.abspath(os.path.join(parent, 'test', 'mafExtractor')))
cmd += ['--maf', os.path.abspath(os.path.join(tmpDir, 'test_%d.maf' % i)),
'--seq', seq, '--start', '%d' % start,
'--stop', '%d' % stop,
]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'extracted.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def testHardExtraction_0(self):
""" mafExtractor should output trimmed blocks by default.
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
customOpts = mafval.GenericValidationOptions()
i = -1
for inblocks, seq, start, stop, outblocks in self.testSet:
i += 1
tmpDir = os.path.abspath(mtt.makeTempDir('hardextraction_0'))
testMaf = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test_%d.maf' % i)),
''.join(map(str, inblocks)), g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = [os.path.abspath(os.path.join(parent, 'test', 'mafExtractor'))]
cmd += ['--maf', os.path.abspath(os.path.join(tmpDir, 'test_%d.maf' % i)),
'--seq', seq, '--start', '%d' % start,
'--stop', '%d' % stop,
]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'extracted.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mafIsHardExtracted('hardextraction_0_%d' % i, outblocks,
os.path.join(tmpDir, 'extracted.maf')))
self.assertTrue(mafval.validateMaf(os.path.join(tmpDir, 'extracted.maf'), customOpts))
mtt.removeDir(tmpDir)
def testMemory_3(self):
""" mafTransitiveClosure should be memory clean.
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
tmpDir = os.path.abspath(mtt.makeTempDir('memory_3'))
for inMaf, outList in self.knownResults:
testMaf = mtt.testFile(
os.path.abspath(os.path.join(tmpDir, 'test.maf')), inMaf,
g_headers)
parent = os.path.dirname(os.path.dirname(
os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [
os.path.abspath(
os.path.join(parent, 'test', 'mafTransitiveClosure')),
'--maf',
os.path.abspath(os.path.join(tmpDir, 'test.maf')), '--sort'
]
outpipes = [
os.path.abspath(os.path.join(tmpDir, 'transitiveClosure.maf'))
]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def _testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (0).
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
for i in xrange(0, 10):
shuffledBlocks = []
tmpDir = os.path.abspath(mtt.makeTempDir('memory_1'))
order = [1] * len(g_overlappingBlocks) + [0] * len(g_nonOverlappingBlocks)
random.shuffle(order)
random.shuffle(g_overlappingBlocks)
random.shuffle(g_nonOverlappingBlocks)
j, k = 0, 0
for isOverlapping in order:
if isOverlapping:
shuffledBlocks.append(g_overlappingBlocks[j][0])
j += 1
else:
shuffledBlocks.append(g_nonOverlappingBlocks[k][0])
k += 1
testMaf = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test_%d.maf' % i)),
''.join(shuffledBlocks), g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(os.path.abspath(os.path.join(parent, 'test', 'mafPairCoverage')))
cmd += ['--maf', os.path.abspath(os.path.join(tmpDir, 'test_%d.maf' % i)),
'--seq1', 'target.*', '--seq2', g_targetSeq2,
]
outpipes = [os.path.join('/dev', 'null')]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def test_memoryTest_4(self):
""" --wigglePairs options should be memory clean
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_4'))
for maf1, maf2, ref, partner, binlen, valuesDictList in knownValuesWiggles:
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.abspath(os.path.join(tmpDir, 'output.xml')),
'--samples=1000', '--logLevel=critical',
'--wigglePairs=%s:%s' % (ref, partner),
'--wiggleBinLength=%d' % binlen,
]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def test_memory_1(self):
""" mafComparator should be memory clean for seed testing examples
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_1'))
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
for maf1, maf2 in knownValuesSeed:
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.join(tmpDir, 'output.xml'),
'--samples=10', '--logLevel=critical']
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
for i in xrange(0, 4):
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def test_memory_0(self):
""" mafComparator should be memory clean for bed parsing examples
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_0'))
for maf1, maf2, bed, totalTrue, totalTrueInInterval in knownValuesBed:
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
testBed = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'bed.bed')),
bed, [''])
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.abspath(os.path.join(tmpDir, 'output.xml')),
'--samples=1000', '--logLevel=critical',
]
if bed != '':
cmd += ['--bedFiles', os.path.abspath(os.path.join(tmpDir, 'bed.bed'))]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def test_memoryTest_4(self):
""" --wigglePairs options should be memory clean
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_4'))
for maf1, maf2, ref, partner, binlen, valuesDictList in knownValuesWiggles:
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.abspath(os.path.join(tmpDir, 'output.xml')),
'--samples=1000', '--logLevel=critical',
'--wigglePairs=%s:%s' % (ref, partner),
'--wiggleBinLength=%d' % binlen,
]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
mtt.makeTempDirParent()
valgrind = mtt.which("valgrind")
if valgrind is None:
return
shuffledTargets = list(g_targetBlocks)
for i in xrange(0, 20):
tmpDir = os.path.abspath(mtt.makeTempDir("memory1"))
random.shuffle(g_nonTargetBlocks)
random.shuffle(shuffledTargets)
shuffledBlocks = list(shuffledTargets)
lower = 0
for j in xrange(0, len(g_nonTargetBlocks)):
# randomly insert the non target blocks, but keep a record
# of their relative order.
index = random.randint(lower, len(shuffledBlocks))
shuffledBlocks.insert(index, g_nonTargetBlocks[j])
lower = index + 1
testMaf = mtt.testFile(
os.path.abspath(os.path.join(tmpDir, "test.maf")), "".join(shuffledBlocks), g_headers
)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(os.path.abspath(os.path.join(parent, "test", "mafSorter")))
cmd += ["--maf", os.path.abspath(os.path.join(tmpDir, "test.maf")), "--seq", "hg18.chr7"]
outpipes = [os.path.abspath(os.path.join(tmpDir, "sorted.maf"))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, "valgrind.xml")))
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
tmpDir = os.path.abspath(mtt.makeTempDir('memory1'))
customOpts = mafval.GenericValidationOptions()
for reference, inMaf, inFaList, outFa, outMaf in g_knownData:
testMaf = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test.maf')),
''.join(inMaf), g_headers)
testFaNames = testFasta(os.path.abspath(tmpDir), inFaList)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafToFastaStitcher')),
'--maf', os.path.abspath(os.path.join(tmpDir, 'test.maf')),
'--seqs', testFaNames,
'--breakpointPenalty', '6', '--interstitialSequence', '20',
'--outMfa', os.path.abspath(os.path.join(tmpDir, 'out.fa')),
'--outMaf', os.path.abspath(os.path.join(tmpDir, 'out.maf')),]
if reference is not None:
cmd += ['--reference', reference]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def test_memory_3(self):
""" mafComparator should be memory clean for known values using --near option
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('memory_3'))
for maf1, maf2, near, totalTrue, totalFalse in knownValuesNear:
testMaf1 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
maf1, g_headers)
testMaf2 = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
maf2, g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafComparator')),
'--maf1', os.path.abspath(os.path.join(tmpDir, 'maf1.maf')),
'--maf2', os.path.abspath(os.path.join(tmpDir, 'maf2.maf')),
'--out', os.path.abspath(os.path.join(tmpDir, 'output.xml')),
'--near=%d' % near,
'--samples=1000', '--logLevel=critical',
]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def testMemory(self):
""" sharedMaf.h should be memory clean.
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
tmpDir = os.path.abspath(mtt.makeTempDir('allTests'))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(os.path.abspath(os.path.join(os.curdir, 'allTests')))
mtt.runCommandsS([cmd], tmpDir)
self.assertTrue(
mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def test_CuTestMemory(self):
""" If valgrind is installed on the system, check for memory related errors in CuTests.
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
tmpDir = os.path.abspath(mtt.makeTempDir('memory_CuTest'))
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(os.path.abspath(os.path.join(parent, 'test', 'allTests')))
outpipes = [os.path.join('/dev', 'null')]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def testMemory_2(self):
""" the CuTest tests should be memory clean.
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
tmpDir = os.path.abspath(mtt.makeTempDir('memory_2'))
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [
os.path.abspath(
os.path.join(parent, 'test', 'mafTransitiveClosure')), '--test'
]
outpipes = [
os.path.abspath(os.path.join(tmpDir, 'transitiveClosure.maf'))
]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
passed = mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml'))
self.assertTrue(passed)
mtt.removeDir(tmpDir)
def testMemory2(self):
""" If valgrind is installed on the system, check for memory related errors (2).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
global g_header
for i in xrange(0, len(g_knownExcludes)):
tmpDir = os.path.abspath(mtt.makeTempDir('memory2'))
testMafPath, g_header = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test.maf')),
g_knownExcludes[i][0], g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(os.path.abspath(os.path.join(parent, 'test', 'mafFilter')))
cmd += ['--maf', testMafPath, '--excludeSeq', '%s' % g_sequenceList]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'filtered.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
tmpDir = os.path.abspath(mtt.makeTempDir('memory1'))
customOpts = mafval.GenericValidationOptions()
for reference, inMaf, inFaList, outFa, outMaf in g_knownData:
testMaf = mtt.testFile(
os.path.abspath(os.path.join(tmpDir, 'test.maf')),
''.join(inMaf), g_headers)
testFaNames = testFasta(os.path.abspath(tmpDir), inFaList)
parent = os.path.dirname(os.path.dirname(
os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [
os.path.abspath(
os.path.join(parent, 'test', 'mafToFastaStitcher')),
'--maf',
os.path.abspath(os.path.join(tmpDir, 'test.maf')),
'--seqs',
testFaNames,
'--breakpointPenalty',
'6',
'--interstitialSequence',
'20',
'--outMfa',
os.path.abspath(os.path.join(tmpDir, 'out.fa')),
'--outMaf',
os.path.abspath(os.path.join(tmpDir, 'out.maf')),
]
if reference is not None:
cmd += ['--reference', reference]
mtt.recordCommands([cmd], tmpDir)
mtt.runCommandsS([cmd], tmpDir)
self.assertTrue(
mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
shuffledTargets = list(g_targetBlocks)
for i in xrange(0, 20):
tmpDir = os.path.abspath(mtt.makeTempDir('memory1'))
random.shuffle(g_nonTargetBlocks)
random.shuffle(shuffledTargets)
shuffledBlocks = list(shuffledTargets)
lower = 0
for j in xrange(0, len(g_nonTargetBlocks)):
# randomly insert the non target blocks, but keep a record
# of their relative order.
index = random.randint(lower, len(shuffledBlocks))
shuffledBlocks.insert(index, g_nonTargetBlocks[j])
lower = index + 1
testMaf = mtt.testFile(
os.path.abspath(os.path.join(tmpDir, 'test.maf')),
''.join(shuffledBlocks), g_headers)
parent = os.path.dirname(os.path.dirname(
os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(
os.path.abspath(os.path.join(parent, 'test', 'mafSorter')))
cmd += [
'--maf',
os.path.abspath(os.path.join(tmpDir, 'test.maf')), '--seq',
'hg18.chr7'
]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'sorted.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(
mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def testMemory2(self):
""" If valgrind is installed on the system, check for memory related errors (2).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
for i in xrange(0, 10):
tmpDir = os.path.abspath(mtt.makeTempDir('memory2'))
random.shuffle(g_nonDuplicateBlocks)
testMaf = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test.maf')),
''.join(g_nonDuplicateBlocks), g_headers)
expectedOutput = g_nonDuplicateBlocks
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafDuplicateFilter')),
'--maf', os.path.abspath(os.path.join(tmpDir, 'test.maf'))]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'filtered.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
valgrind = mtt.which('valgrind')
if valgrind is None:
return
mtt.makeTempDirParent()
for i in xrange(0, 10):
tmpDir = os.path.abspath(mtt.makeTempDir('memory_1'))
random.shuffle(g_nonOverlappingBlocks)
testMaf = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test_%d.maf' % i)),
''.join(g_nonOverlappingBlocks), g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd.append(os.path.abspath(os.path.join(parent, 'test', 'mafExtractor')))
cmd += ['--maf', os.path.abspath(os.path.join(tmpDir, 'test_%d.maf' % i)),
'--seq', g_targetSeq, '--start', '%d' % g_targetRange[0],
'--stop', '%d' % g_targetRange[1],
'--soft']
outpipes = [os.path.abspath(os.path.join(tmpDir, 'extracted.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
def testMemory1(self):
""" If valgrind is installed on the system, check for memory related errors (1).
"""
mtt.makeTempDirParent()
valgrind = mtt.which('valgrind')
if valgrind is None:
return
for i in xrange(0, 10):
shuffledBlocks = []
expectedOutput = []
tmpDir = os.path.abspath(mtt.makeTempDir('memory1'))
order = [1] * len(g_duplicateBlocks) + [0] * len(g_nonDuplicateBlocks)
random.shuffle(order)
random.shuffle(g_duplicateBlocks)
random.shuffle(g_nonDuplicateBlocks)
j, k = 0, 0
for dupBlock in order:
if dupBlock:
shuffledBlocks.append(g_duplicateBlocks[j][0])
expectedOutput.append(g_duplicateBlocks[j][1])
j += 1
else:
shuffledBlocks.append(g_nonDuplicateBlocks[k])
expectedOutput.append(g_nonDuplicateBlocks[k])
k += 1
testMaf = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test.maf')),
''.join(shuffledBlocks), g_headers)
parent = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
cmd = mtt.genericValgrind(tmpDir)
cmd += [os.path.abspath(os.path.join(parent, 'test', 'mafDuplicateFilter')),
'--maf', os.path.abspath(os.path.join(tmpDir, 'test.maf'))]
outpipes = [os.path.abspath(os.path.join(tmpDir, 'filtered.maf'))]
mtt.recordCommands([cmd], tmpDir, outPipes=outpipes)
mtt.runCommandsS([cmd], tmpDir, outPipes=outpipes)
self.assertTrue(mtt.noMemoryErrors(os.path.join(tmpDir, 'valgrind.xml')))
mtt.removeDir(tmpDir)
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
'''
GIT = mtt.which('git')
def runCommand(cmd):
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
pout, perr = p.communicate()
mtt.handleReturnCode(p.returncode, cmd)
return pout
def getBranch():
branchList = runCommand([GIT, 'branch']).split('\n')
for b in branchList:
if b.startswith('* '):
return b[2:]
