def testNonFind(self):
""" mafPositionFinder should not report any lines when blocks do not match.
"""
global g_header
mtt.makeTempDirParent()
for i in xrange(0, len(g_nonOverlappingBlocks)):
tmpDir = os.path.abspath(mtt.makeTempDir('nonFind'))
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 = [
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.fileIsEmpty(os.path.join(tmpDir, 'found.txt')))
mtt.removeDir(tmpDir)
def testNonFind(self):
""" mafPositionFinder should not report any lines when blocks do not match.
"""
global g_header
mtt.makeTempDirParent()
for i in xrange(0, len(g_nonOverlappingBlocks)):
tmpDir = os.path.abspath(mtt.makeTempDir('nonFind'))
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 = [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.fileIsEmpty(os.path.join(tmpDir, 'found.txt')))
mtt.removeDir(tmpDir)
def testNonExtraction(self):
""" mafBlockExtractor should not extract blocks when they do not match.
"""
for i in xrange(0, 10):
tmpDir = os.path.abspath(mtt.makeTempDir())
random.shuffle(g_nonOverlappingBlocks)
testMaf = mtt.testFile(os.path.abspath(os.path.join(os.curdir, 'tempTestDir', 'test.maf')),
''.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', '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.fileIsEmpty(os.path.join(tmpDir, 'extracted.maf')))
mtt.removeTempDir()
def dtestNonFind(self):
""" mafBlockFinder should not report any lines when blocks do not match.
"""
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 = [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.fileIsEmpty(os.path.join(tmpDir, "found.txt")))
mtt.removeTempDir()