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create.py duplicate strain name bug #50

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Apr 4, 2024
Merged

create.py duplicate strain name bug #50

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2 changes: 1 addition & 1 deletion create.py
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Original file line number Diff line number Diff line change
Expand Up @@ -399,7 +399,7 @@ def create_genbank_files(organism, config_dict, metadata, fasta_file, submission
# Retrieve the source df"
source_df = metadata.filter(regex="^gb-seq_id$|^src-|^ncbi-spuid$|^ncbi-bioproject$|^organism$|^collection_date$").copy()
source_df.columns = source_df.columns.str.replace("src-","").str.strip()
source_df = source_df.rename(columns = {"gb-seq_id":"Sequence_ID", "collection_date":"Collection_date", "ncbi-spuid":"strain"})
source_df = source_df.rename(columns = {"gb-seq_id":"Sequence_ID", "collection_date":"Collection_date"})
# Add BioProject if available
if "ncbi-bioproject" in source_df:
source_df = source_df.rename(columns={"ncbi-bioproject": "BioProject"})
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