bug in get_proteins_by_id affecting pfam annotator
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Description
First of all thanks for developing DeepBGC and making it available to the community.
I came across a bug in HmmscanPfamRecordAnnotator when generating the proteins_by_id dictionary. The util function get_proteins_by_id is currently looping through all the potential protein ids of a feature (e.g. unique_protein_id, protein_id and locus_tag) and this can cause features with id based on protein_id qualifier to be overwritten by another feature that shares the same protein_id but it was deduplicated using the unique_protein_id. This is causing PFAM_domain features to be incorrectly placed in the genomic sequence because protein_id used in hmmscan output file will match a different feature and pick the incorrect feature location.
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start with the util function get_proteins_by_id and its use in HmmscanPfamRecordAnnotator. Trace how unique_protein_id, protein_id, and locus_tag are handled, then reproduce the incorrect PFAM_domain placement described in the issue. Done means a shared protein_id cannot select the wrong feature location in hmmscan results.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100