split apart dependencies of vaccine peptide selection

* added unit tests for individual ranking components
* vaccine peptide sorting by four criteria (mutant epitope score, negative wildtype epitope score, number mutated residues, distance of mutation start the edge of vaccine peptide)
* print and write FASTA of vaccine peptides with a little mutation metadata
* print epitopes associated with each mutation
It's just the FASTA <http://en.wikipedia.org/wiki/FASTA_format> format,
which seems pretty standard as a way to distinguish metadata from
sequences.

On Sun, Nov 16, 2014 at 2:13 PM, Tavi Nathanson <notifications@github.com>
wrote:

> In immuno/mutation_report.py:
>
> > +            epitope_scorer = simple_ic50_epitope_scorer
> > +
> > +        vaccine_peptide_records = select_vaccine_peptides(
> > +            source_sequences,
> > +            epitope_scorer=epitope_scorer,
> > +            vaccine_peptide_length=peptide_length,
> > +            padding=padding
> > +        )
> > +
> > +        if args.vaccine_peptide_count:
> > +            n = args.vaccine_peptide_count
> > +            vaccine_peptide_records = vaccine_peptide_records[:n]
> > +
> > +        string_lines = []
> > +        for i, record in enumerate(vaccine_peptide_records):
> > +            line = ">%d Gene=%s, Transcript=%s, Mut=%s (%d:%d), Score=%0.6f" % (
>
> Random: why is ">" on each line? Just for readability?
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/hammerlab/immuno/pull/164/files#r20412214>.
>