def testGreedyMotifSearch(self):
k = 3
dna = [
'GGCGTTCAGGCA', 'AAGAATCAGTCA', 'CAAGGAGTTCGC', 'CACGTCAATCAC',
'CAATAATATTCG'
]
bestMotifs, _ = greedyMotifSearch(dna, k)
self.assertEquals(bestMotifs, ['CAG', 'CAG', 'CAA', 'CAA', 'CAA'])
def testGreedyMotifSearchWithPseudocount(self):
k = 3
dna = [
'GGCGTTCAGGCA', 'AAGAATCAGTCA', 'CAAGGAGTTCGC', 'CACGTCAATCAC',
'CAATAATATTCG'
]
bestMotifs, _ = greedyMotifSearch(dna, k, True)
self.assertEquals(bestMotifs, ['TTC', 'ATC', 'TTC', 'ATC', 'TTC'])
def testGreedyMotifSearchWithPseudocountFromFile(self):
"""
Greedy Motif Search from file
"""
with open('data/greedyMotifPseudocount.txt') as fp:
vals = [int(x) for x in fp.readline().split()]
k = vals[0]
dna = [seq for seq in fp.readlines()]
bestMotifs, _ = greedyMotifSearch(dna, k, True)
print 'Best Motifs'
for motif in bestMotifs:
print motif
def testGreedyMotifSearchFromFile(self):
"""
Greedy Motif Search from file
"""
with open('data/greedyMotif2.txt') as fp:
vals = [int(x) for x in fp.readline().strip().split(' ')]
k = vals[0]
dna = [seq.strip() for seq in fp.readlines()]
bestMotifs, _ = greedyMotifSearch(dna, k)
print 'Best Motifs'
for motif in bestMotifs:
print motif
def testGreedyMotifSearchWithPseudocountFromFile(self):
"""
Greedy Motif Search from file
"""
with open("data/greedyMotifPseudocount.txt") as fp:
vals = [int(x) for x in fp.readline().split()]
k = vals[0]
dna = [seq for seq in fp.readlines()]
bestMotifs, _ = greedyMotifSearch(dna, k, True)
print "Best Motifs"
for motif in bestMotifs:
print motif
def testGreedyMotifSearchFromFile(self):
"""
Greedy Motif Search from file
"""
with open("data/greedyMotif2.txt") as fp:
vals = [int(x) for x in fp.readline().strip().split(" ")]
k = vals[0]
dna = [seq.strip() for seq in fp.readlines()]
bestMotifs, _ = greedyMotifSearch(dna, k)
print "Best Motifs"
for motif in bestMotifs:
print motif
def testGreedyMotifSearchWithPseudocount(self):
k = 3
dna = ["GGCGTTCAGGCA", "AAGAATCAGTCA", "CAAGGAGTTCGC", "CACGTCAATCAC", "CAATAATATTCG"]
bestMotifs, _ = greedyMotifSearch(dna, k, True)
self.assertEquals(bestMotifs, ["TTC", "ATC", "TTC", "ATC", "TTC"])
def testGreedyMotifSearch(self):
k = 3
dna = ["GGCGTTCAGGCA", "AAGAATCAGTCA", "CAAGGAGTTCGC", "CACGTCAATCAC", "CAATAATATTCG"]
bestMotifs, _ = greedyMotifSearch(dna, k)
self.assertEquals(bestMotifs, ["CAG", "CAG", "CAA", "CAA", "CAA"])
