broadinstitute/oncotator — pull request #254 by LeeTL1220 (2014-12-08 14:41:33+00:00)
Title: Issue 127 uniprot gencode

- Updated preprocessing scripts to create a gencode process.
- Updated TranscriptToUniProtProteinPositionTransformingDatasource to correctly parse new blastp output when creating the uniprot_aa_xform datasource.
- Added unit tests.
- TranscriptToUniProtProteinPositionTransformingDatasource is backwards compatible, but is a bit slower for old datasources.
- Could not make a more graceful implementation (in the time allotted) of the blast'ing. All existing APIs return a text dump of the blastp exe, so the same issue persists.

- I am set to add an upgraded set of UniProt datasources once we issue the new release.