diff --git a/deeprvat/annotations/annotations.py b/deeprvat/annotations/annotations.py index d1c2991a..0f7e98e7 100644 --- a/deeprvat/annotations/annotations.py +++ b/deeprvat/annotations/annotations.py @@ -561,7 +561,6 @@ def deepripe_encode_variant_bedline(bedline, genomefasta, flank_size=75): return encoded_seqs - @click.group() def cli(): pass @@ -1072,7 +1071,6 @@ def aggregate_abscores( all_absplice_scores.to_parquet(ab_splice_agg_score_file) - logging.basicConfig( format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s", level="INFO", @@ -1081,7 +1079,6 @@ def aggregate_abscores( logger = logging.getLogger(__name__) - def deepripe_score_variant_onlyseq_all( model_group, variant_bed, genomefasta, seq_len=200, batch_size=1024, n_jobs=32 ): @@ -1225,6 +1222,7 @@ def merge_abscores( pd.options.mode.chained_assignment = None + @cli.command() @click.argument("annotation_file", type=click.Path(exists=True)) @click.argument("deepripe_file", type=click.Path(exists=True))