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prihoda avatar prihoda commented on August 18, 2024 1

Great, would you be up to implementing that behavior in your PR? @LuisFF

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prihoda avatar prihoda commented on August 18, 2024

Hi @LuisFF, thanks for reporting this. I'll need to think for a bit since it's been a while since I wrote the code :)

I would be careful around changing the logic of get_proteins_by_id, it's used in multiple places and not sure if it's safe to be able to only access the feature using its first protein ID, as proposed in your PR. Currently, it allows mapping from any of the potential protein IDs.

If I understand it correctly, this could also be solved by removing the protein_id qualifier when entering the unique_protein_id, correct? Here:

deepbgc/deepbgc/util.py

Lines 503 to 505 in c836f08

if protein_id != new_protein_id:
logging.warning('Setting new unique_protein_id %s for CDS %s', new_protein_id, protein_id)
feature.qualifiers['unique_protein_id'] = [new_protein_id]

from deepbgc.

LuisFF avatar LuisFF commented on August 18, 2024

Hi @prihoda, thanks for looking into this.

Yes, removing the protein_id qualifier from subsequent CDS features with that same qualifier value is another way of solving this issue. That avoids any side effects I may overlooked in #79.

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LuisFF avatar LuisFF commented on August 18, 2024

Hi @prihoda , I pushed the suggested changes.

Please let me know if there's anything else needed.

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