fix no_backup argument

TRISTAN-ORF · Sep 4, 2024 · b842a36 · b842a36
1 parent 0155513
commit b842a36
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git 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
@@ -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
@@ -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,
-Original file line number
+Diff line change
@@ Expand Up @@
 ,
                         f'exon_number "{exon}',
                     )
                 if feature not in ["transcript", "exon"]:
                     property_list.insert(
 ,
@@ Expand Down @@