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()