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  1. Jan 02, 2019
  2. Oct 25, 2018
  3. Oct 18, 2018
  4. Oct 15, 2018
    • Wojtek Bazant's avatar
      Fix bug: use return instead of next · 4ab71f7e
      Wojtek Bazant authored
      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
      4ab71f7e
    • Wojtek Bazant's avatar
      C. elegans specific parsing of RefSeq_dna file · 7d6346f7
      Wojtek Bazant authored
      - 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
      7d6346f7
    • Wojtek Bazant's avatar
      C. elegans references use WormBase mapping to INSDC protein ids · d66449b6
      Wojtek Bazant authored
      - 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.
      d66449b6
  5. Oct 01, 2018
    • Marek Szuba's avatar
      Remove artificial dependency on XML::Simple · ddb71bb1
      Marek Szuba authored
      The only part of the xref-mapping pipeline that depended on the
      long-deprecated module XML::Simple was TAIROntologyParser - which did
      not actually *use* that module for anything. Get rid of the useless
      import, thus making it unnecessary for XML::Simple to be mentioned in
      the cpanfile.
      ddb71bb1
  6. Sep 07, 2018
  7. Sep 05, 2018
  8. Sep 04, 2018
  9. Sep 03, 2018
  10. Aug 30, 2018
  11. Aug 13, 2018
  12. Jul 25, 2018
  13. Jun 28, 2018
  14. Jun 12, 2018
  15. Apr 09, 2018
  16. Apr 06, 2018
    • Matthew Laird's avatar
      ENSCORESW-2553 · 5dfe4299
      Matthew Laird authored
      - Update RefSeqCoordinateParser such that it fetches the RefSeq accession either from the stable_id or the display_xref in the otherfeatures database.
      5dfe4299
  17. Mar 26, 2018
  18. Mar 14, 2018
  19. Feb 08, 2018
  20. Feb 07, 2018
  21. Feb 01, 2018
  22. Jan 31, 2018
  23. Jan 19, 2018
  24. Jan 17, 2018
  25. Jan 10, 2018
  26. Jan 09, 2018
  27. Jan 08, 2018