Jeroen F.J. Laros authored 9 years ago and Vermaat committed 9 years ago

Existing `transcript_to_protein` is factored out into a separate
`mutalyzer.ncbi` module.

Add Ter as a valid AA in the HGVS grammar

Previously, the `PSubst` rule did not register `MutationType`, so it
was a bit awkward how to check for a `p.` substitution. We can now:

    >>> grammar.parse('NP_00011.1:p.Asp23Tyr').RawVar.MutationType
    'subst'

Refactor unit tests using py.test

Especially lxml takes very long to install. By specifying the `-O0`
compiler flag this is reduced by more than half.

The actual unit tests are slightly slower with the non-optimized
C modules, but we have a netto win.

Travis CI updates

Release 2.0.13

Fix query bug in update transcript-protein links

Test database migrations

Push to release branch requires passing status checks

Release 2.0.12

Fix transcript protein link query

Bi-directional cachinig of transcript-protein links

Previously transcript-protein links were assumed to always be
indexed by transcript, and cached entries were allowed to have
a `null` protein (meaning caching the knowledget that there is
no link for this transcript).

Now we can cache links in both directions. Both transcript and
protein are allowed to be `null` (but not at the same time),
and the protein column has a new unique constraint.

Fix off-by-one in slicing chromosome by gene name

The original code would always add one extra downstream base to
the slice (for genes on the forward and reverse strand).

Correcting this implies that cached slices will not be used by
new queries requesting the exact same gene and number of upstream
and downstream bases, effectively invalidating them.

However, most existing cache entries affected by this bug will be
on GRCh37/hg19, whereas current slices by gene name will yield
GRCh38/hg38 slices.

The only cache issue I see is trying to use existing cache
entries created by slicing by gene name, by re-slicing by
explicit coordinates instead of gene name. To get the old cache
entry one would have to add an extra downstream base.