def test_read_sequence(self): # given config_path = 'config.txt' seq_path = 'a.txt' expected = 'GATTACA' # when rf = ReadFile() config = rf.get_config(config_path) seq = rf.seq_path(seq_path, config) # then self.assertEqual(seq, expected)
parser.add_argument('-c', type=str, help='Path to the config file', required=True, dest='config_path') parser.add_argument('-o', type=str, help='Path to the output file', required=True, dest='output_path') args = parser.parse_args() rf = ReadFile() config = rf.get_config(args.config_path) nw = NeedlemanWunsh() mat, directmat = nw.calculate_matrix(rf.seq_path(args.seq_a, config), rf.seq_path(args.seq_b, config), config) score, alignments = nw.calculate_result(mat, directmat, rf.seq_path(args.seq_a, config), rf.seq_path(args.seq_b, config), config) # write results to file f = open(args.output_path, 'w') f.write('SCORE=' + str(score) + '\n') f.write('\n') for i in range(len(alignments)): f.write(alignments[i].res_a + '\n') f.write(alignments[i].res_b + '\n') f.write('\n') f.close()