Add interface for MHCflurry 2.0.x #54

christopher-mohr · 2022-04-11T13:53:28Z

This adds a prediction interface for MHCflurry 2.0 (fixes #47).

There are still some things we have to make a decision on. Currently we include specific mhcflurry/nuggets versions as dependencies (pypi/bioconda) which makes it more complicated to use the framework with other versions.

I also realised that the dependencies of MHCflurry 2.0 and the most recent MHCnuggets are not compatible which makes it currently impossible to use these through epytope (there are also tool-specific imports). It should be possible to solve this issue by changing the bioconda recipe accordingly. (see setup.py)

In general, my suggestion would be to

remove the "external tool" dependencies
create separate interafaces for MHCflurry/nuggets in order to allow the use only one of them
put the import of these interfaces optional in try clause

ggabernet

What you propose here sounds good to me and it would allow us to provide older versions when needed

ggabernet · 2022-05-04T14:33:14Z

epytope/EpitopePrediction/ANN.py

+        """
+        # retrieved with `mhcflurry-downloads fetch models_class1_presentation`
+        # `mhcflurry-predict --list-supported-alleles`
+        __alleles = 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would it make sense to read those from a separate file to be able to read the rest of the code in a nicer way here?

add interface for MHCflurry 2

6a485dc

christopher-mohr added the donotmerge label Apr 11, 2022

ggabernet reviewed May 4, 2022

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Add interface for MHCflurry 2.0.x #54

Add interface for MHCflurry 2.0.x #54

christopher-mohr commented Apr 11, 2022 •

edited

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ggabernet May 4, 2022

Add interface for MHCflurry 2.0.x #54

Are you sure you want to change the base?

Add interface for MHCflurry 2.0.x #54

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christopher-mohr commented Apr 11, 2022 • edited Loading

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christopher-mohr commented Apr 11, 2022 •

edited

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