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()