def testSyntegenyBlockConstruction(self): pos = list(syntegenyBlockConstruction(3, 'AAACTCATC', 'TTTCAAATC')) self.assertEqual(4, len(pos)) self.assertTrue((0, 0) in pos) self.assertTrue((0, 4) in pos) self.assertTrue((4, 2) in pos) self.assertTrue((6, 6) in pos)
def testSyntegenyBlockConstructionFromFile(self): with open('data/syntegy/syntegenyBlocks.txt') as fp: kmerLength = int(fp.readline().strip()) seq1 = fp.readline().strip() seq2 = fp.readline().strip() kmerPos = list(syntegenyBlockConstruction(kmerLength, seq1, seq2)) for pos in kmerPos: print pos