def main():
parser = argparse.ArgumentParser(description="Map score values")
cmd = DefaultCommandHelper(parser)
cmd.add_db_args()
cmd.add_transform_args()
parser.add_argument(
"--skip-empty-scores",
dest="skip_empty_scores",
action="store_true",
default=False,
help="Skip transformation for empty scores",
)
args, logger = cmd.parse_args("scores-transform")
db = cmd.open_db()
try:
transforms = cmd.get_transforms()
predictors = transforms.keys()
logger.info("Transforming scores ...")
progress = RatedProgress(logger, name="SNVs")
rows_count = updated_count = 0
for row in db.query_scores(predictors=predictors):
rows_count += 1
scores = row["scores"]
upd_scores = {}
for predictor in transforms:
score = scores[predictor]
if args.skip_empty_scores and score is None:
continue
prev_score = score
for name, func in transforms[predictor]:
try:
score = func(score)
except:
raise Exception("Error transforming the {} score {} with {}".format(predictor, score, name))
if prev_score != score:
upd_scores[predictor] = score
if len(upd_scores) > 0:
db.update_scores(row["id"], upd_scores)
updated_count += 1
progress.update()
progress.log_totals()
logger.info("Commit ...")
db.commit()
logger.info(
"Finished. Total rows = {}, updated rows = {}, elapsed time = {}".format(
rows_count, updated_count, progress.elapsed_time
)
)
except:
return cmd.handle_error()
finally:
db.close()
return 0
