def main():
args = parse_args()
# Get scorer
scorer = get_scorer(args.scorer_name, **args.scorer_params)
# Get alignment and supplementary inputs
alignment = Alignment(args.align_file, **args.align_params)
# Score
scores = scorer.score(alignment)
# Output
header = list_scorer_params(scorer)
scores_cols = [scores]
write_scores(alignment, scores_cols, [args.scorer_name], header=header, f=sys.stdout)
if args.draw:
draw_scores(alignment, scores_cols, [args.scorer_name])
def main():
parser = argparse.ArgumentParser(
description="Batch score the conservation of multiple alignments, using multiple scorers.")
parser.add_argument('config_file',
help="YAML config file specifying the dataset and scorers. See `exapmles/example.yaml` for an example.")
args = parser.parse_args()
dataset_names, scorers = read_batchscore_config(args.config_file)
# Sanity check the output dirs
for ds_name in dataset_names:
ds_dir = os.path.join(OUTPUT_DIR, "batchscore-%s" % ds_name)
if not os.path.exists(ds_dir):
os.mkdir(ds_dir)
for scorer in scorers:
sc_dir = os.path.join(ds_dir, scorer.output_id)
if os.path.exists(sc_dir):
resp = raw_input("%s exists. Overwrite? y/[n]: " % sc_dir)
if resp != 'y':
sys.exit(0)
try:
for filename in os.listdir(sc_dir):
os.remove(os.path.join(sc_dir, filename))
os.rmdir(sc_dir)
except OSError:
raise OSError("Could not overwrite directory %s" % sc_dir)
# Perform the scoring
for ds_name in dataset_names:
ds_dir = os.path.join(OUTPUT_DIR, "batchscore-%s" % ds_name)
for scorer in scorers:
sc_dir = os.path.join(ds_dir, scorer.output_id)
os.mkdir(sc_dir)
params_file = os.path.join(ds_dir, "%s.params" % scorer.output_id)
with open(params_file, 'w') as f:
f.write(list_scorer_params(scorer))
scorer.set_output_dir(sc_dir)
run_experiments(ds_name, scorers)
