From b842a36ed045176e691b5255b0b969d1b624c396 Mon Sep 17 00:00:00 2001 From: jdcla Date: Wed, 4 Sep 2024 14:34:24 -0400 Subject: [PATCH] fix no_backup argument --- transcript_transformer/data.py | 2 +- transcript_transformer/processing.py | 1 - transcript_transformer/ribotie.py | 6 +++++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/transcript_transformer/data.py b/transcript_transformer/data.py index f4f2612..a3851b6 100644 --- a/transcript_transformer/data.py +++ b/transcript_transformer/data.py @@ -56,7 +56,7 @@ def process_seq_data(h5_path, gtf_path, fa_path, backup_path, backup=True): backup_path = os.path.splitext(gtf_path)[0] + ".h5" if os.path.abspath(backup_path) == os.path.abspath(os.path.dirname(h5_path)): print(f"!-> Backup path identical to h5 output path, disabling backup...") - backup=False + backup = False elif not os.path.isfile(h5_path) and os.path.isfile(backup_path): print(f"--> Processed assembly data restored ({backup_path})") shutil.copy(backup_path, h5_path) diff --git a/transcript_transformer/processing.py b/transcript_transformer/processing.py index 20422d9..7faa002 100644 --- a/transcript_transformer/processing.py +++ b/transcript_transformer/processing.py @@ -600,7 +600,6 @@ def csv_to_gtf(h5_path, df, out_prefix, exclude_annotated=False): 3, f'exon_number "{exon}', ) - if feature not in ["transcript", "exon"]: property_list.insert( 3, diff --git a/transcript_transformer/ribotie.py b/transcript_transformer/ribotie.py index 8003ada..fd185cd 100644 --- a/transcript_transformer/ribotie.py +++ b/transcript_transformer/ribotie.py @@ -111,7 +111,11 @@ def main(): assert args.use_ribo, "No ribosome data specified." if not args.results: process_seq_data( - args.h5_path, args.gtf_path, args.fa_path, args.backup_path, ~args.no_backup + args.h5_path, + args.gtf_path, + args.fa_path, + args.backup_path, + not args.no_backup, ) process_ribo_data( args.h5_path,