default value is core, so running without specifying anything will be as before

Script to examine exons before and after projection. Designed to work with Anacode Support objects, so jiggery pokery with paths needed to get started. Use with arguments similar to the Assembly Mapping pipeline.

Needs more POD.

should be rnorvegicus, not rnovegicus

Bugfix? Previous revision of this script assumed that we could have only one ensembl_id (gene) associated with an OTTG. This is not true as projected genes have the same OTTG attached to them as theier parent gene on the primary assembly.

Attempt to speed up. Previous use of Algorithm::Diff was prohibitively slow, so attempting to use bitmasking on simple cases to go 10x faster on the easy cases.

Fix for production team, for whom changing taxonomy ids (Gorilla) caused it to leave old metadata behind. Failure triggers an attempt to guess taxon id by regexing the end of the dbname off and searching by that instead of taxon id.

Have changed the link for the SO.obo file from http://downloads.sourceforge.net/project/song/Sequence%20Ontology/so_2_5/so.obo2.5 to http://www.sequenceontology.org/resources/obo_files/current_release.obo. This will allow us to get the most up to date version.

 to http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinobo/efo.obo.
We are now getting the EFO.obo file from the head.

SHIP IT! EFO now loads in without complaints from OBOParser. Also now handles duplication relations being inserted.

Added a truth test to see if the $term->{synonyms} reference was there. I'm assuming if it's there then it'll be an array

Switched to Test::More and done_testing(). This should stop tests from failing due to poor test count specification.

Make the verbose doc a bit more verbose. People in workshops could not find this method which points to poor documentation

lrg code works if there are lrg xrefs
there are lrg xrefs when the regular expression to fetch the data from hgnc is correct

Added meta insert as otherwise any schema generated from this file would break when being patched. Also changed the ordering of the fields in protein_feature to avoid poor patch performance