def test_getNumbersForSeqKmerInNegFile(self): seq = "GTCTTACAAGAGCCCCGACGCCCCGGCCACTGCGCGCGACTAGCCCTATGTCAGGAAAAAACGCGCACAATGTCCTCCTGCAGGACAGTCGGCTGGCGCTACCGATACGGAT" realStart = 0; realEnd = 0; kmerREString = "(CCCCGA|AAAAAA)" numTP, numFP, numFN = compareKmerCommon.getNumbersForSeq(kmerREString, realStart, realEnd, seq);
def test_getNumbersForSeqTwoKmersInSeq(self): seq = "CTGTCCCTTTTCGGGTTTTTTTTTTCCGAGCGGCCTCGGTGGGTGAAATGAACGACACTCATGCGAGCGACACTAGGGCGCCGTTCGTTCTGTGCACCCA" kmerREString = "(TCGGGT|TTTTTT)" realKmer = "TCGGGTTTTTTTTTTCCGA" realStart = 10; realEnd = realStart + len(realKmer) numTP, numFP, numFN = compareKmerCommon.getNumbersForSeq(kmerREString, realStart, realEnd, seq); self.assertEqual(numTP, 12) self.assertEqual(numFP, 0) self.assertEqual(numFN, 7)
def test_getNumbersForSeqOneKmerInOneKmerOut(self): seq = "ATCCCTAACTCCGGCAAAAAAAAAACCGGAAACTACATCGCTCTCCACCGGTGCAGACGTCGCCTCGCGCCCCGAAACCGGTGCTGGCAGGGTACGTAAT" kmerREString = "(CCCCGA|AAAAAA)" realKmer = "CCGGCAAAAAAAAAACCGG" realStart = 10 realEnd = realStart + len(realKmer) numTP, numFP, numFN = compareKmerCommon.getNumbersForSeq(kmerREString, realStart, realEnd, seq); self.assertEqual(numTP, 6) self.assertEqual(numFP, 6) self.assertEqual(numFN, 13)
def test_getNumbersForSeqTwoKmers(self): seq = "GGAACCGCXXXXXXGGGGGCGACYYYYYYGGGCATTGAGCTC" realStart = 4; realEnd = 44 kmerREString = "(XXXXXX|YYYYYY)" numTP, numFP, numFN = compareKmerCommon.getNumbersForSeq(kmerREString, realStart, realEnd, seq); self.assertEqual(numTP, 12) self.assertEqual(numFP, 0) self.assertEqual(numFN, 28)
def test_getNumbersForSeqKmerNotFound(self): seq = "XXXXXXGCCCCCXXXXXXGGGGGCGACYYYYYYGGGCATTGAGCTC" realStart = 4; realEnd = 44 kmerREString = "(ABCDEF|XYZFFF)" numTP, numFP, numFN = compareKmerCommon.getNumbersForSeq(kmerREString, realStart, realEnd, seq); self.assertEqual(numTP, 0) self.assertEqual(numFP, 12) self.assertEqual(numFN, 40)