def testorder(self):
""" mafRowOrderer should order blocks according to user input
"""
global g_header
mtt.makeTempDirParent()
customOpts = mafval.GenericValidationOptions()
for i in xrange(0, len(g_blocks)):
tmpDir = os.path.abspath(mtt.makeTempDir('order'))
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 = []
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)
ordered = mafIsOrdered(os.path.join(tmpDir, 'ordered.maf'),
g_blocks[i][1], g_header)
self.assertTrue(
mafval.validateMaf(os.path.join(tmpDir, 'ordered.maf'),
customOpts))
self.assertTrue(ordered)
if ordered:
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 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 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 testCoercion(self):
""" mafStrander should coerce blocks into strandedness based on user input
"""
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('coercion'))
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 = [
os.path.abspath(os.path.join(parent, 'test',
'mafStrander')), '--maf',
os.path.abspath(os.path.join(tmpDir, 'test.maf')), '--seq',
'target.chr0', '--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(
mafIsCoerced(os.path.join(tmpDir, 'coerced.maf'), expected))
self.assertTrue(
mafval.validateMaf(os.path.join(tmpDir, 'coerced.maf'),
customOpts))
mtt.removeDir(tmpDir)
def testCoverage_0(self):
""" mafCoverage should output numbers that accurately reflect the coverage between sequences.
"""
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('testCoverage_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 = [
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(tmpDir, 'output.txt')]
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(
coverageIsCorrect(os.path.join(tmpDir, 'output.txt'),
solutionDict))
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 testNonExtraction1(self):
""" mafExtractor should not extract blocks when they do not match.
"""
customOpts = mafval.GenericValidationOptions()
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('nonExtraction_1'))
block = '''a degree=4
s simChimp.chrA 15393341 348 + 53121445 ATATTGAGGAGCAGGATGGGTATAGAGGCCCTGACCCATTAATGTGTAAGCACTAGGCAGCTGGGAGATACCCCAGAGGGCGGGGTCACTGAATTCACTGGCCCACCACTGTAAATACATTCTAACCAGTGGGTTTAGGGCTCTGTGCATTAGAACCACTCTGAAGAAGTGTAACACACCACCTAGTGAGCTGCCGGGCCGCCAGCAACTTCTTTTTCCCACATGACCCATGCAAGCCCGTGATTTCTCCCTGGTACATGATATTTGGGATTCCAGGGACCTAATGGAGCATGCTATTCCTGTGTTAGTTATCACTTCGAAGGGGGTGCAAGAGTGTAAGTAATGGGT
s simGorilla.chrA 15595743 348 + 53120926 ATATTGAGGAGCAGGATGGGTATAGAAGCCCTGACCCATTAATGTGTAAGCACTAGGCAGCTGGGAGATACTCCAGAGGGAGGGGTCACTGAATTCACTGGCCCACCACTGTAAATACATTCTAACCAGTGGGTTTAGGGCTCGGTGCATTAGAACCACCCTGAAGAAGTGTAACGCACCACCTAGTGAGCTGCCGGGCCGCCAGCAACTTCTTTTTCCCACATGACCCATGCATGCCCGTGATTTCTCCCTGGTACATGGTTTTTGGGATTCCAGGGACCTAATGGAGCATACTATTCCTGTGTTAGTTATCACTTCGAAGGGGGTGCGAGAGTGTAAGTAATGGGT
s simHuman.chrA 36713600 348 - 53106993 ATATTGAGGAGCAGGATGGGTATAGAAGCCCTGACCTATTAATGTGTAAGCACTAGGCAGCTGGGCGATACCCCAGAGGGAGGGGTCACTGAATTCACTGGCCCACCACTGTAAATACATTCTAACCAGTGGGTTTAGGGCTCTGTGCATTAGAACCACCCTGAAGAAGAGTAACGCACCACCTAGTGAGCTGCCGGGCCGCCAGCAAGTTCTTTTTCCCACATGACCCATGCAAGCCCGTGATTTCTCCCTGGTACATGATATTTGGGATTCCAGGGACCTAATGGAGCATGCTATTCCTGTGTTAGTTATCACTTCGAAGGGGGTGCAAGAGTGTAAGTAATGGGT
s simOrang.chrE 126390 348 + 37692687 ATTTTGAGGAGCAGGATGGGTATAGAAGCCCTGACCCATTAATGTGTGAGCTCTAGGCAGCTTGGAGATACTGCAGAGGGAGGGGTCACTGAATTCACTGGCCCACCACTGTAAATACATACTAACCGGTGGGTTTAGGGCTCTGTGCATTAGAACCACCCTGAGGAAGTGTAACGCACCACCTAGTGAGCTGCCGGGCCACCAGCAACTTCTTTTTCCCACATGACCCATGCAAGCCCGTGATTTCTCCCTGGTACATGATCTTTGGGATTCCAGGGACCTAATGGCGGATGCTATTCCTGTGTTAGTTATCACTTCGAAGGGGGCGCAAGAGTGTAAGTAATGGGT
s target.chr0 36713600 348 - 53106993 ATATTGAGGAGCAGGATGGGTATAGAAGCCCTGACCTATTAATGTGTAAGCACTAGGCAGCTGGGCGATACCCCAGAGGGAGGGGTCACTGAATTCACTGGCCCACCACTGTAAATACATTCTAACCAGTGGGTTTAGGGCTCTGTGCATTAGAACCACCCTGAAGAAGAGTAACGCACCACCTAGTGAGCTGCCGGGCCGCCAGCAAGTTCTTTTTCCCACATGACCCATGCAAGCCCGTGATTTCTCCCTGGTACATGATATTTGGGATTCCAGGGACCTAATGGAGCATGCTATTCCTGTGTTAGTTATCACTTCGAAGGGGGTGCAAGAGTGTAAGTAATGGGT
'''
testMaf = mtt.testFile(os.path.abspath(os.path.join(tmpDir, 'test.maf')),
block, 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.maf')),
'--seq', 'simHuman.chrA', '--start', '%d' % 29953315,
'--stop', '%d' % 29953315,
'--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.mafIsEmpty(os.path.join(tmpDir, 'extracted.maf'), g_headers))
self.assertTrue(mafval.validateMaf(os.path.join(tmpDir, 'extracted.maf'), customOpts))
mtt.removeDir(tmpDir)
def testExtraction(self):
""" mafExtractor should output blocks that meet the criteria for extraction. That is they contain the target sequence and have at least one base in the target range.
"""
mtt.makeTempDirParent()
customOpts = mafval.GenericValidationOptions()
for i in xrange(0, 10):
shuffledBlocks = []
tmpDir = os.path.abspath(mtt.makeTempDir('extraction'))
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(tmpDir, 'test_%d.maf' % i)),
''.join(shuffledBlocks), 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', 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(mafIsExtracted(os.path.join(tmpDir, 'extracted.maf')))
self.assertTrue(mafval.validateMaf(os.path.join(tmpDir, 'extracted.maf'), customOpts))
mtt.removeDir(tmpDir)
def testAllTests(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('memory0'))
customOpts = mafval.GenericValidationOptions()
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 testFastaStitch(self):
""" mafToFastaStitcher should produce known output for a given known input
"""
mtt.makeTempDirParent()
tmpDir = os.path.abspath(mtt.makeTempDir('fasta'))
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 = []
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(
fastaIsCorrect(os.path.abspath(os.path.join(tmpDir, 'out.fa')),
outFa))
self.assertTrue(
mafIsCorrect(os.path.abspath(os.path.join(tmpDir, 'out.maf')),
outMaf))
self.assertTrue(
mafval.validateMaf(os.path.join(tmpDir, 'out.maf'),
customOpts))
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 testNonExtraction0(self):
""" mafExtractor should not extract blocks when they do not match.
"""
customOpts = mafval.GenericValidationOptions()
mtt.makeTempDirParent()
for i in xrange(0, 10):
tmpDir = os.path.abspath(mtt.makeTempDir('nonExtraction_0'))
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 = [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.mafIsEmpty(os.path.join(tmpDir, 'extracted.maf'), g_headers))
self.assertTrue(mafval.validateMaf(os.path.join(tmpDir, 'extracted.maf'), customOpts))
mtt.removeDir(tmpDir)