New test case for applying the current release's patches. This downloads the last release of the core schema, finds all patches relevant to this release and patches the DB accordingly. The code requires access to CVSWEB and so supports proxies but can also skip the tests if the schema cannot be found. Failure of this test is not an issue for external users & so should not be punished as such

First draft of revised projections. Exclusions in place for inappropriate mammalian traits on birds and reptiles. Also platypus.

Awaiting GOA full blacklist of undesirable projections.

translated sequence, not transcript sequence.

phase change was removed because it meant that an exon whose sequence
and position had not changed would become a candidate for similarity
mapping.  This caused lots of criss-crossing stable ID history entries
between genes/transcripts/translations in some gene families.

Better version. We now avoid gzipping which should give us a good speed boost and bring us closer to the original speed

Switching the logic around here. It makes sense if we are trying to read from a file which hasn't closed yet then maybe we're not going to get all the data into the file.

sequence.  This means that the translation stable ID version might be
incremented independently of the transcript stable ID version if there
was a phase change in an exon.

Changing markup from Markdown to Textile as it supports table formatting which Markdown can only do via hardcoded HTML tables