Add subsequence method ProteinSequence

[iskandr]

Currently there are two very similar classes in Isovar and Vaxrank: isovar.ProteinSequence and vaxrank.MutantProteinFragment. While I'm currently refactoring Vaxrank to work with the new Isovar API, it would actually simplify that code to simply use isovar.ProteinSequence instead (and get rid of MutantProteinFragment.

This requires moving some additional functionality into Isovar: (1) distinguishing mutated from non-mutated sequences and (2) slicing through a sequence to get a subsequences.

Major changes:

• Gave ProteinSequence a more straight-forward __init__ method and moved the logic for building a ProteinSequence from a list of Translation objects into the class method from_translations.
• Added contains_mutation property to TranslationKey (which is inherited by Translation and ProteinSequence).

Minor changes:

• Renamed Translation.variant_aa_interval_start to Translation.mutation_start_idx
• Renamed Translation.variant_aa_interval_end to Translation.mutation_start_idx
• Renamed ProteinSequence.mutation_start to ProteinSequence.mutation_start_idx
• Renamed ProteinSequence.mutation_end to ProteinSequence.mutation_end_idx
• Added contains_deletion property to ProteinSequence, to help distinguish deleted amino acids from other kinds of mutations
• Added common.normalize_base0_range_indices to convert negative and None indices into a non-negative start/end pair, and also check that they're contiguous (stride == 1).

Along with the additional functionality on ProteinSequence, this PR also fixes many failing tests due to more stringent contig name checking recently added to Varcode.

[coveralls]

Coverage increased (+0.2%) to 92.96% when pulling 4ae511624e6a64cf2ba4164f51fbedc261afafd2 on add-slice-method-to-protein-sequence into 6456397fca2e1e2ef0b604202f4bba4de8c7a92a on master.