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"])