Split VaxrankCoreLogic into smaller stateless functions

[iskandr]

The accumulation of cached state on VaxrankCoreLogic made it somewhat hard to refactor so I've split that class up into stateless functions with better documented inputs/outputs.

• Replaced the VaxrankCoreLogic class with a entry-point function called run_vaxrank which returns a VaxrankResults object.
• Moved the helper function which creates variant_to_protein_sequence_dict into a new protein_sequences module. This will probably be deleted in the next PR (since the new Isovar gives back objects that associate each variant with a list of protein sequences). Moved functions which summarize variants or vaccine peptides into methods of VaxrankResults, including the use of GenePathwayCheck.

[coveralls]

Coverage decreased (-0.03%) to 87.99% when pulling 40ebc4e8708c23bc3cf64c5811611d40051388d8 on deconstruct-VaxrankCoreLogic into f129952f21ec57ab687c1eca28e6f589f39a5aae on master.