Ejemplo n.º 1
0
	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;