GitLab

Updated ensembl_ontology schema scripts

revert patch 94_95_c

production schema file has been renamed

ENSCORESW-2967: update schema to 96

Use seq_region_start and seq_region_end when updating gene coordinate…

Feature/null ox analysis

C. elegans references use WormBase mapping to INSDC protein ids

Standardise table.sql file

It made recognising incorrect entries needlessly slow

Remove artificial dependency on XML::Simple

return goes back one frame up the stack
next goes back to the closest frame on the stack that supports the
operation (that is close enough in RefSeqGPFFParser alone)
It works unless I subclass create_xrefs, and then my Hive workers die:

Lost control. Check your Runnable for loose 'next' statements that are
not part of a loop       WORKER_ERROR

- New xref: to a WormBase CDS feature
- Modify WormbaseCElegansRefSeqGPFFParser to serve both kinds of files
- extract a utility method from RefSeqGPFFParser
- xref_config.ini stanza for wormbase_cds
- tests for new functionality

- maintain naming convention: WormBase specific stuff says Wormbase at the front
- rewrite WormBaseDirectParser
- WormBaseDirectParser populates protein_ids
- superclass method to make dependent protein_ids as parent
- tap into UniProtParser
  + also skip EMBL scaffold ids (we can't reliably assign them)
- tap into RefSeqGPFFParser
  + extract a method
- tests for new stuff
  + add %args to parametrise test_parser

Benefits for RefSeqGPFFParser:
RefSeq proteins have coordinates as part of their identity, so we
can't reliably sequence match them, we will also pick up all paralogs.
This change fixes this spurious mapping.
Benefits for UniProtParser:
Not the above: UniProt entries are not tied to coordinates so all
paralogs map to the same entry. We can handle versioning and updates
a bit better: if WormBase updates an entry and a protein id changes but
UniProt doesn't reflect this yet, with the change we will still pick up
the UniProt entry although we can't sequence match any more.

create_release_tasks.pl: explicitly dereference arguments to 'keys'

create_release_tasks.pl: distinguish between submitter and assignee