Added argument for specifying NetMHCIIpan/NetMHCIIpanEL version

[ldhtnp]

I added the argument --netmhc_pan_version to pvacseq, pvacbind, pvacfuse, pvacsplice, and pvacvector. The argument supports four versions: 4.0, 4.1, 4.2, and 4.3. I also added an argument that can be used to list the valid versions valid_netmhcpan_versions. Alongside the additions I had to make to get the arguments implemented, I had to modify the code used to remove the sample name and grab the method name in output_parser.py because the method name can now include a version number. Before this modification, the version number would be trimmed and dropped off of the method name resulting in issues downstream.

This is for issue #457

[susannasiebert]

This looks pretty good overall. I made a few comments for suggested changes.

[susannasiebert]

Also, you'll want to add tests for your new command in the test_pvacseq|bind|vector|splice.py files. Check out how the valid_alleles and valid_algorithms are tested in there and implement similar checks. That should probably get your coverage up as well and make the coveralls check pass.

[susannasiebert]

I think we are missing the standalone valid_netmhciipan_versions command from the pVACfuse tree. You will also want to add documentation for the new commands in each of the docs/pvacseq|fuse|splice|bind|vector/additional_commands.rst files.

[susannasiebert]

The Features documentation pages for the various tools (e.g., https://pvactools.readthedocs.io/en/latest/pvacseq/features.html) has a table that list the version of each tool that is supported. We should add the additional NetMHCIIpan/NetMHCIIpanEL versions, note the default, as well as the one version that is IEDB API-only.

[susannasiebert]

+1