def read_batchscore_config(config_file):
with open(config_file) as f:
config_yaml = f.read()
config = yaml.load(config_yaml)
# List of dataset names
datasets = config['datasets']
# List of scoring runs with the run id, scorer, and params.
# Initialize the scorers
scorers = []
scs = config['scorers']
ids = set()
for sc in scs:
batchscore_id = sc['id']
if batchscore_id in ids:
raise ValueError("Duplicate scorer id: %s" % batchscore_id)
ids.add(batchscore_id)
scorer_name = sc['scorer']
if 'params' in sc:
params = sc['params']
else:
params = {}
scorer = get_scorer(scorer_name, **params)
scorer.set_output_id(batchscore_id)
scorers.append(scorer)
return datasets, scorers
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])
