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- Jan 02, 2019
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Tiago Grego authored
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- Oct 25, 2018
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Wojtek Bazant authored
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- Oct 18, 2018
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Wojtek Bazant authored
It made recognising incorrect entries needlessly slow
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- Oct 15, 2018
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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
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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
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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.
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- Oct 01, 2018
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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.
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- Sep 07, 2018
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Magali Ruffier authored
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- Sep 05, 2018
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Magali Ruffier authored
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Magali Ruffier authored
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Magali Ruffier authored
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Magali Ruffier authored
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- Sep 04, 2018
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Magali Ruffier authored
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Magali Ruffier authored
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- Sep 03, 2018
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Wojtek Bazant authored
+ XrefParser::Database stores a DBConnection, setters delegate to it + New test database, for xrefs + Setup to test XrefParsers + Tests for WormbaseDirectParser
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- Aug 30, 2018
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Magali Ruffier authored
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- Aug 13, 2018
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Magali Ruffier authored
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- Jul 25, 2018
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Magali Ruffier authored
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- Jun 28, 2018
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Magali Ruffier authored
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- Jun 12, 2018
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Magali Ruffier authored
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- Apr 09, 2018
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premanand17 authored
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- Apr 06, 2018
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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.
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- Mar 26, 2018
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Matthew Laird authored
Fix to fix in commit f9dc4756 (ENSCORESW-462). info_text should not have been null'ed by default as the column is NOT NULL.
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- Mar 14, 2018
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premanand17 authored
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- Feb 08, 2018
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Magali Ruffier authored
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Magali Ruffier authored
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- Feb 07, 2018
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Magali Ruffier authored
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- Feb 01, 2018
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Magali Ruffier authored
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- Jan 31, 2018
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Magali Ruffier authored
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Magali Ruffier authored
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- Jan 19, 2018
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Magali Ruffier authored
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Magali Ruffier authored
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Magali Ruffier authored
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- Jan 17, 2018
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Magali Ruffier authored
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- Jan 10, 2018
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Magali Ruffier authored
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Magali Ruffier authored
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- Jan 09, 2018
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Magali Ruffier authored
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Magali Ruffier authored
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- Jan 08, 2018
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Magali Ruffier authored
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Magali Ruffier authored
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