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Bug fix create.py (#56)
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Correct issue where organism and collection date was being added to the comment.cmt file for genbank submissions
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dthoward96 committed May 6, 2024
1 parent 9361e90 commit 43b660e
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))
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