Skip to content

Commit

Permalink
Bug fix create.py
Browse files Browse the repository at this point in the history
Correct issue where organism and collection date was being added to the comment.cmt file for genbank submissions
  • Loading branch information
dthoward96 authored May 6, 2024
1 parent 9361e90 commit e90c043
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion create.py
Original file line number Diff line number Diff line change
Expand Up @@ -407,7 +407,7 @@ def create_genbank_files(organism, config_dict, metadata, submission_name, submi
# Retrieve Structured Comment df
comment_df = metadata.filter(regex="^cmt-")
if not comment_df.empty:
comment_df = metadata.filter(regex="^gb-seq_id$|^cmt-|^organism$|^collection_date$").copy()
comment_df = metadata.filter(regex="^gb-seq_id$|^cmt-").copy()
comment_df.columns = comment_df.columns.str.replace("cmt-", "").str.strip()
comment_df = comment_df.rename(columns = {"gb-seq_id": "SeqID"})
columns_no_prefix_suffix = list(filter(lambda x: (x not in ["SeqID", "StructuredCommentPrefix", "StructuredCommentSuffix"])==True, comment_df.columns))
Expand Down

0 comments on commit e90c043

Please sign in to comment.