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 biocondarecipe 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
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 thebiocondarecipe accordingly. (see setup.py)In general, my suggestion would be to
tryclause