Outsource supported alleles

KohlbacherLab / epytope

Python-based framework for computational immunomics

http://fred-2.github.io/

BSD 3-Clause "New" or "Revised" License

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Outsource supported alleles #63

Closed jonasscheid closed 2 years ago

jonasscheid commented 2 years ago

Adressing #61

Supported alleles of a predictor are currently stored within each predictor class. A more appealing way would be to outsource this information to a file. I'm proposing a predictor_version.txt file for storing the supported alleles in epytope/Data/supportedAlleles/external | pssm | ann.

I only did it for netmhcpan 4.1 as an example Please let me know what you think. Once we agreed on the implementation, I will change it for the other predictors as well

b-schubert commented 2 years ago

I would suggest storing the HLA allele string as a frozen set or other python object and then optional importing the set when initializing the explicit prediction object to avoid IO

jonasscheid commented 2 years ago

Adjusted according to feedback by @b-schubert. Supported alleles are now stored in a python file containing the frozenset of supported alleles for each predictor. Files are stored under epytope/Data/supportedAlleles/pssm|ann|external