def getSketch(self, seq):
"""
Gets the minhash Sketch for a given sequence
:param str seq: A DNA sequence
:return list(int): A list representing the minhash Sketch
"""
window = Window(seq, self.word_size, self.N_BUCKETS)
kmers = window.makeWords(seq)
return self._min_hash.calcSketch(kmers)
def getSketch(self, seq): """ Gets the minhash Sketch for a given sequence :param str seq: A DNA sequence :return list(int): A list representing the minhash Sketch """ window = Window(seq, self.word_size, 2) pairs = [pair for kmer in window.kmers for pair in window.makeKmerPairs(kmer)] return [x[0] for x in self._min_hash.calcSketch(pairs)]
def test_makePairs(self):
"""Test that the pairs are correctly generated"""
k1 = KmerSingle(0, 'AA')
k2 = KmerSingle(1, 'AC')
k3 = KmerSingle(2, 'CT')
p1 = KmerPair(k1, k2)
p2 = KmerPair(k1, k3)
p3 = KmerPair(k2, k3)
expect = [p1, p2, p3]
window = Window("AACT", 2, 2)
words = window.makeKmerPairs("AACT", 3)
self.assertTrue(len(expect), len(words))
def getSketch(self, seq): """ Gets the minhash Sketch for a given sequence :param str seq: A DNA sequence :return list(int): A list representing the minhash Sketch """ window = Window(seq, self.word_size, 2) primary_Sketch = self._min_hash.calcSketch(window.kmers) kmer_pairs = [] for min_hash in primary_Sketch: kmer_pairs.extend(window.makeKmerPairs(min_hash[1])) return [x[0] for x in self._min_hash.calcSketch(kmer_pairs)]
def getSketch(self, seq): """ Gets the minhash Sketch for a given sequence :param str seq: A DNA sequence :return list(int): A list representing the minhash Sketch """ window = Window(seq, self.word_size, 2) return [x[0] for x in self._min_hash.calcSketch(window.kmers)]
class TestWindow(unittest.TestCase):
def setUp(self):
self.window = Window("AAAT", 2, 2)
def test_makeWords(self):
"""Test that kmers are generated correctly"""
kmer_values = ['AA', 'AA', 'AT']
expect = [KmerSingle(i, x) for i, x in enumerate(kmer_values)]
words = self.window.makeWords("AAAT")
def test_makePairs(self):
"""Test that the pairs are correctly generated"""
k1 = KmerSingle(0, 'AA')
k2 = KmerSingle(1, 'AC')
k3 = KmerSingle(2, 'CT')
p1 = KmerPair(k1, k2)
p2 = KmerPair(k1, k3)
p3 = KmerPair(k2, k3)
expect = [p1, p2, p3]
window = Window("AACT", 2, 2)
words = window.makeKmerPairs("AACT", 3)
self.assertTrue(len(expect), len(words))
def setUp(self):
self.window = Window("AAAT", 2, 2)