def test_frequent_kmers_hamming_reverse(self):
dna = 'ACGTTGCATGTCGCATGATGCATGAGAGCT'
k = 4
d = 1
expected = {'ATGT', 'ACAT'}, 9
actual = motifs.frequent_kmers(dna, k, d, True)
self.assertEqual(expected, actual)
def test_frequent_kmers_hamming(self):
dna = 'ACGTTGCATGTCGCATGATGCATGAGAGCT'
k = 4
d = 1
expected = {'GATG', 'ATGC', 'ATGT'}, 5
actual = motifs.frequent_kmers(dna, k, d, False)
self.assertEqual(expected, actual)
def find_ori(file, txt=''):
if file:
dna = ''.join(f.strip() for f in open(file).readlines())
# utils.plot_skew(dna)
min_skew = motifs.get_min_skew_position(dna)[0]
print(min_skew)
L = 500
dna_box = dna[min_skew - L:min_skew + L]
else:
dna_box = txt
k = 9
d = 1
most_freq_kmer = motifs.frequent_kmers(dna_box, k, d, True)
print('Found ORI', most_freq_kmer)
def test_frequent_kmers2(self):
dna = 'AAGCAAAGGTGGG'
k = 2
expected = {'AA', 'GG'}, 3
actual = motifs.frequent_kmers(dna, k)
self.assertEqual(expected, actual)
def test_frequent_kmers(self):
dna = 'ACGTTGCATGTCGCATGATGCATGAGAGCT'
k = 4
expected = {'CATG', 'GCAT'}, 3
actual = motifs.frequent_kmers(dna, k)
self.assertEqual(expected, actual)