def test_greedy_motif_search_4(self):
dna = [
"GACCTACGGTTACAACGCAGCAACCGAAGAATATTGGCAA",
"TCATTATCGATAACGATTCGCCGGAGGCCATTGCCGCACA",
"GGAGTCTGGTGAAGTGTGGGTTATGGGGCAGACTGGGAAA",
"GAATCCGATAACTGACACCTGCTCTGGCACCGCTCTCATC",
"AAGCGCGTAGGCGCGGCTTGGCATCTCGGTGTGTGGCCAA",
"AATTGAAAGGCGCATCTTACTCTTTTCGCTTAAAATCAAA",
"GGTATAGCCAGAAAGCGTAGTTAATTTCGGCTCCTGCCAA",
"TCTGTTGTTGCTAACACCGTTAAAGGCGGCGACGGCAACT",
]
k = 5
t = len(dna)
expected = [
"GCAGC",
"TCATT",
"GGAGT",
"TCATC",
"GCATC",
"GCATC",
"GGTAT",
"GCAAC",
]
result = greedy_motif_search(dna, k, t)
self.assertEqual(expected, result)
def test_greedy_motif_search_heavy(self):
dna = [
'GCGCCCCGCCCGGACAGCCATGCGCTAACCCTGGCTTCGATGGCGCCGGCTCAGTTAGGGCCGGAAGTCCCCAATGTGGCAGACCTTTCGCCCCTGGCGGACGAATGACCCCAGTGGCCGGGACTTCAGGCCCTATCGGAGGGCTCCGGCGCGGTGGTCGGATTTGTCTGTGGAGGTTACACCCCAATCGCAAGGATGCATTATGACCAGCGAGCTGAGCCTGGTCGCCACTGGAAAGGGGAGCAACATC',
'CCGATCGGCATCACTATCGGTCCTGCGGCCGCCCATAGCGCTATATCCGGCTGGTGAAATCAATTGACAACCTTCGACTTTGAGGTGGCCTACGGCGAGGACAAGCCAGGCAAGCCAGCTGCCTCAACGCGCGCCAGTACGGGTCCATCGACCCGCGGCCCACGGGTCAAACGACCCTAGTGTTCGCTACGACGTGGTCGTACCTTCGGCAGCAGATCAGCAATAGCACCCCGACTCGAGGAGGATCCCG',
'ACCGTCGATGTGCCCGGTCGCGCCGCGTCCACCTCGGTCATCGACCCCACGATGAGGACGCCATCGGCCGCGACCAAGCCCCGTGAAACTCTGACGGCGTGCTGGCCGGGCTGCGGCACCTGATCACCTTAGGGCACTTGGGCCACCACAACGGGCCGCCGGTCTCGACAGTGGCCACCACCACACAGGTGACTTCCGGCGGGACGTAAGTCCCTAACGCGTCGTTCCGCACGCGGTTAGCTTTGCTGCC',
'GGGTCAGGTATATTTATCGCACACTTGGGCACATGACACACAAGCGCCAGAATCCCGGACCGAACCGAGCACCGTGGGTGGGCAGCCTCCATACAGCGATGACCTGATCGATCATCGGCCAGGGCGCCGGGCTTCCAACCGTGGCCGTCTCAGTACCCAGCCTCATTGACCCTTCGACGCATCCACTGCGCGTAAGTCGGCTCAACCCTTTCAAACCGCTGGATTACCGACCGCAGAAAGGGGGCAGGAC',
'GTAGGTCAAACCGGGTGTACATACCCGCTCAATCGCCCAGCACTTCGGGCAGATCACCGGGTTTCCCCGGTATCACCAATACTGCCACCAAACACAGCAGGCGGGAAGGGGCGAAAGTCCCTTATCCGACAATAAAACTTCGCTTGTTCGACGCCCGGTTCACCCGATATGCACGGCGCCCAGCCATTCGTGACCGACGTCCCCAGCCCCAAGGCCGAACGACCCTAGGAGCCACGAGCAATTCACAGCG',
'CCGCTGGCGACGCTGTTCGCCGGCAGCGTGCGTGACGACTTCGAGCTGCCCGACTACACCTGGTGACCACCGCCGACGGGCACCTCTCCGCCAGGTAGGCACGGTTTGTCGCCGGCAATGTGACCTTTGGGCGCGGTCTTGAGGACCTTCGGCCCCACCCACGAGGCCGCCGCCGGCCGATCGTATGACGTGCAATGTACGCCATAGGGTGCGTGTTACGGCGATTACCTGAAGGCGGCGGTGGTCCGGA',
'GGCCAACTGCACCGCGCTCTTGATGACATCGGTGGTCACCATGGTGTCCGGCATGATCAACCTCCGCTGTTCGATATCACCCCGATCTTTCTGAACGGCGGTTGGCAGACAACAGGGTCAATGGTCCCCAAGTGGATCACCGACGGGCGCGGACAAATGGCCCGCGCTTCGGGGACTTCTGTCCCTAGCCCTGGCCACGATGGGCTGGTCGGATCAAAGGCATCCGTTTCCATCGATTAGGAGGCATCAA',
'GTACATGTCCAGAGCGAGCCTCAGCTTCTGCGCAGCGACGGAAACTGCCACACTCAAAGCCTACTGGGCGCACGTGTGGCAACGAGTCGATCCACACGAAATGCCGCCGTTGGGCCGCGGACTAGCCGAATTTTCCGGGTGGTGACACAGCCCACATTTGGCATGGGACTTTCGGCCCTGTCCGCGTCCGTGTCGGCCAGACAAGCTTTGGGCATTGGCCACAATCGGGCCACAATCGAAAGCCGAGCAG',
'GGCAGCTGTCGGCAACTGTAAGCCATTTCTGGGACTTTGCTGTGAAAAGCTGGGCGATGGTTGTGGACCTGGACGAGCCACCCGTGCGATAGGTGAGATTCATTCTCGCCCTGACGGGTTGCGTCTGTCATCGGTCGATAAGGACTAACGGCCCTCAGGTGGGGACCAACGCCCCTGGGAGATAGCGGTCCCCGCCAGTAACGTACCGCTGAACCGACGGGATGTATCCGCCCCAGCGAAGGAGACGGCG',
'TCAGCACCATGACCGCCTGGCCACCAATCGCCCGTAACAAGCGGGACGTCCGCGACGACGCGTGCGCTAGCGCCGTGGCGGTGACAACGACCAGATATGGTCCGAGCACGCGGGCGAACCTCGTGTTCTGGCCTCGGCCAGTTGTGTAGAGCTCATCGCTGTCATCGAGCGATATCCGACCACTGATCCAAGTCGGGGGCTCTGGGGACCGAAGTCCCCGGGCTCGGAGCTATCGGACCTCACGATCACC',
]
k = 15
t = len(dna)
expected = [
'GTTAGGGCCGGAAGT', 'CCGATCGGCATCACT', 'ACCGTCGATGTGCCC',
'GGGTCAGGTATATTT', 'GTGACCGACGTCCCC', 'CTGTTCGCCGGCAGC',
'CTGTTCGATATCACC', 'GTACATGTCCAGAGC', 'GCGATAGGTGAGATT',
'CTCATCGCTGTCATC'
]
from motifs.count_matrix import get_count
expected_consensus = 'gttAAAtAgaGatGtG'.upper()
expected_score = 58
result = greedy_motif_search(dna, k, t)
self.assertEqual(expected, result)
cons = consensus(get_count(result))
print(cons)
def test_greedy_motif_search_1(self):
dna = [
"GCCCAA",
"GGCCTG",
"AACCTA",
"TTCCTT",
]
k = 3
t = len(dna)
expected = [
"GCC",
"GCC",
"AAC",
"TTC",
]
result = greedy_motif_search(dna, k, t)
self.assertEqual(expected, result)
def test_greedy_motif_search_0(self):
dna = [
'GGCGTTCAGGCA',
'AAGAATCAGTCA',
'CAAGGAGTTCGC',
'CACGTCAATCAC',
'CAATAATATTCG',
]
k = 3
t = len(dna)
expected = [
'CAG',
'CAG',
'CAA',
'CAA',
'CAA',
]
result = greedy_motif_search(dna, k, t)
self.assertEqual(expected, result)
cons = consensus(get_count(expected))
self.assertEqual(2, score(result, cons))
def greedy_motif_search_with_pseudocounts(dna, k, t):
return greedy_motif_search(dna, k, t, 1)