griffithlab / griffithlab/pVACtools
local DB for net-chop-method and netmhc-stab
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- Dominant language
- Python
- Stars
- 188
- Forks
- 81
- Avg merge
- 9d 17h
- Merged PRs (30d)
- 6
Description
Hello, as far as I understood, the two methods, query the server:
--net-chop-method {cterm,20s}
NetChop prediction method to use ("cterm" for C term
3.0, "20s" for 20S 3.0).
--netmhc-stab Run NetMHCStabPan after all filtering and add
stability predictions to predicted epitopes
Is there a local database option akin to --iedb-install-directory for mhc-i predictions?
Would it be possible to have those locally for netmch-stab and net-chop as I have a large dataset and dont want to be blacklisted?
Thank you!
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
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Research direction
Start by tracing the handling of --net-chop-method and --netmhc-stab, then compare it with the existing --iedb-install-directory option. Determine how local NetChop and NetMHCStabPan data or execution would be configured, and define tests showing that large datasets can use the local option without querying the remote servers.
Written by the indexing model from the issue text.
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