def test_getKmerREFromPSSM(self): predictedDremeFile = "/projects/bhandare/workspace/PySG/src/resources/dreme.txt" seq = "CTGTCCCTTTTCGGGTTTTTTTTTTCCGAGCGGCCTCGGTGGGTGAAATGAACGACACTCATGCGAGCGACACTAGGGCGCCGTTCGTTCTGTGCACCCA" pssmList = parseDreme.getPSSMListFromDremeFile(predictedDremeFile); kmerREString = compareKmerCommon.getKmerFromPSSM(pssmList, seq) self.assertEqual(kmerREString, '(TCGGGT|TTTTTT)')
def getPredictedKmerList(pssmList, seq): kmerREString = compareKmerCommon.getKmerFromPSSM(pssmList, seq); kmerREString = kmerREString[1:-1] predictedKmerList = kmerREString.split("|") return predictedKmerList;