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 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)