def main(args):
logging.basicConfig(level=logging.getLevelName(args.logging))
logging.info('User args: %s' % pformat(args))
config = load_config_from_json_file(
args.config,
['gap', 'same', 'diff', 'max_number_of_paths', 'max_sequence_length'])
logging.info('Config is: \n%s' % pformat(config))
seq1 = load_fasta_file(args.input1)
seq2 = load_fasta_file(args.input2)
if config['max_sequence_length'] != 0 and max(
len(seq1), len(seq2)) > config['max_sequence_length']:
raise ValueError('Sequence exceeded max_sequence_length ')
score_matrix, nodes_mapping = solve(seq1, seq2, config['gap'],
config['diff'], config['same'])
logging.debug('Score matrix: \n%s' % pformat(score_matrix))
logging.debug('Nodes mapping: (target_node): [(parent_node),...]\n%s' %
pformat(nodes_mapping))
logging.info('Alignments score: %s' % score_matrix[len(seq1), len(seq2)])
paths = PathResolver(nodes_mapping).resolve_paths(
len(seq1), len(seq2), config['max_number_of_paths'])
allignments = [get_allignments(path, seq1, seq2) for path in paths]
for (allignment_1, allignment_2), i in zip(allignments,
range(len(allignments))):
logging.info('[A%04d] %s' % (i, allignment_1))
logging.info('[A%04d] %s' % (i, allignment_2))
if args.output:
save_output(
args.output, {
'seq1': seq1,
'seq2': seq2,
'config': config,
'allignments': allignments,
'score_matrix': score_matrix.tolist()
})
logging.info('Saved output to %s' % args.output)
def test_path_resolving_from_bottom_right(self):
nodes_mapping = PathResolvingTest.get_nodes_mapping()
path_resolver = PathResolver(nodes_mapping)
paths = path_resolver.resolve_paths(4, 5)
self.assertEqual(len(paths), 2)
def test_path_resolving_from_bottom_right_with_restrictions(self):
max_number_of_paths = 1
nodes_mapping = PathResolvingTest.get_nodes_mapping()
path_resolver = PathResolver(nodes_mapping)
paths = path_resolver.resolve_paths(4, 5, max_number_of_paths)
self.assertEqual(len(paths), max_number_of_paths)
def test_path_resolving_from_top_left(self):
nodes_mapping = PathResolvingTest.get_nodes_mapping()
path_resolver = PathResolver(nodes_mapping)
paths = path_resolver.resolve_paths(0, 0)
self.assertEqual(len(paths), 1)