[Question] How can I use precomputed genes via GFF format with DeepBGC?
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Description
I have already run Pyrodigal on ~50k genomes and would like to run DeepBGC on these genomes without rerunning Pyrodigal in the backend. Is there similar usage to antiSMASH where precompute gene models can be provided via GFF? If so, what command can I run? If not, would this be in scope to add in a future update?
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First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing DeepBGC's command-line input handling and how it invokes Pyrodigal. Determine whether precomputed gene models in GFF can be supplied for the 50k genomes; done means documenting a working command or defining the required future support if it is not currently possible.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100