Ejemplo n.º 1
0
	def test_getNumbersForSeqKmerInNegFile(self):
		seq = "GTCTTACAAGAGCCCCGACGCCCCGGCCACTGCGCGCGACTAGCCCTATGTCAGGAAAAAACGCGCACAATGTCCTCCTGCAGGACAGTCGGCTGGCGCTACCGATACGGAT"

		realStart = 0;
		realEnd = 0;

		kmerREString = "(CCCCGA|AAAAAA)"

		numTP, numFP, numFN = compareKmerCommon.getNumbersForSeq(kmerREString, realStart, realEnd, seq);
Ejemplo n.º 2
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	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)
Ejemplo n.º 3
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	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)
Ejemplo n.º 4
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	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)
Ejemplo n.º 5
0
	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)