def test_chunk_sizes(self): text = "AAACCCAAA" chunk_size = 'm' pattern = "CC" self.assertTrue(( fftmatch.fft_match_index_n_log_m(text, pattern, chunk_size) == \ np.array(boyermoore.boyer_moore_match_index(text,pattern))).all())
def test_long_stream(self, func): np.random.seed(67+2) text = ''.join(np.random.choice(list('AGCT'), size=100000)) pattern = ''.join(np.random.choice(list('AGTC'), size=3)) self.assertTrue((func(text=text, pattern=pattern) == \ np.array(boyermoore.boyer_moore_match_index(text=text, \ pattern=pattern))).all(), msg=format_error_message(func))
def test_long_stream(self, func): np.random.seed(67 + 2) text = ''.join(np.random.choice(list('AGCT'), size=100000)) pattern = ''.join(np.random.choice(list('AGTC'), size=3)) self.assertTrue((func(text=text, pattern=pattern) == \ np.array(boyermoore.boyer_moore_match_index(text=text, \ pattern=pattern))).all(), msg=format_error_message(func))
def test_long_stream(self, func): #if func == fftmatch.fft_match_index_n_sq_log_n_naive: # return #You shall not pass np.random.seed(67+2) texts = np.random.choice(list('AGCT'), size=(10000,31)).tolist() texts = [''.join(_list) for _list in texts] pattern = ''.join(np.random.choice(list('AGTC'), size=3)) expected_output = [boyermoore.boyer_moore_match_index(text=text,\ pattern=pattern) for text in texts] expected_output = np.array(expected_output) out = func(texts=texts, pattern=pattern) self.assertTrue(ndarrays_equal(out, expected_output), msg=format_error_message(func))
def test_long_stream(self, func): #if func == fftmatch.fft_match_index_n_sq_log_n_naive: # return #You shall not pass np.random.seed(67 + 2) texts = np.random.choice(list('AGCT'), size=(10000, 31)).tolist() texts = [''.join(_list) for _list in texts] pattern = ''.join(np.random.choice(list('AGTC'), size=3)) expected_output = [boyermoore.boyer_moore_match_index(text=text,\ pattern=pattern) for text in texts] expected_output = np.array(expected_output) out = func(texts=texts, pattern=pattern) self.assertTrue(ndarrays_equal(out, expected_output), msg=format_error_message(func))
title = title + str(count[title]) genomes[title] = genome sorted_genomes = collections.OrderedDict(sorted(genomes.items(), key=lambda t: t[0])) genome_strings = sorted_genomes.values() genome_titles = sorted_genomes.keys() # Parse args if args.algorithm == 'nlogn': for gn in genomes: matches = fft.fft_match_index_n_log_n(genomes[gn], args.pattern) print gn, ': Found matches at indices', matches.tolist() elif args.algorithm == 'nlogm': if len(genomes) > 1: matches = fft.fft_match_index_n_sq_log_m(genomes.values(),\ args.pattern[0], args.b) print 'found matches at', matches.tolist() else: for gn in genomes: matches = fft.fft_match_index_n_log_m(genomes[gn], args.pattern[0],args.b) print gn, ': Found matches at indices', matches.tolist() elif args.algorithm == 'boyermoore': for gn in genomes: matches = bm.boyer_moore_match_index(genomes[gn], args.pattern) print gn, ': Found matches at indices', matches.tolist() elif args.algorithm == 'opencv': matches = cvmatch.cv_match_index_chunk(genomes.values(), args.pattern[0], args.b) print genomes[genomes.keys()[0]] print genomes.keys(), ': Found matches at indices', matches.tolist()
sorted_genomes = collections.OrderedDict( sorted(genomes.items(), key=lambda t: t[0])) genome_strings = sorted_genomes.values() genome_titles = sorted_genomes.keys() # Parse args if args.algorithm == 'nlogn': for gn in genomes: matches = fft.fft_match_index_n_log_n(genomes[gn], args.pattern) print gn, ': Found matches at indices', matches.tolist() elif args.algorithm == 'nlogm': if len(genomes) > 1: matches = fft.fft_match_index_n_sq_log_m(genomes.values(),\ args.pattern[0], args.b) print 'found matches at', matches.tolist() else: for gn in genomes: matches = fft.fft_match_index_n_log_m(genomes[gn], args.pattern[0], args.b) print gn, ': Found matches at indices', matches.tolist() elif args.algorithm == 'boyermoore': for gn in genomes: matches = bm.boyer_moore_match_index(genomes[gn], args.pattern) print gn, ': Found matches at indices', matches.tolist() elif args.algorithm == 'opencv': matches = cvmatch.cv_match_index_chunk(genomes.values(), args.pattern[0], args.b) print genomes[genomes.keys()[0]] print genomes.keys(), ': Found matches at indices', matches.tolist()