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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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Premanand Achuthan authored
create_release_tasks.pl: explicitly dereference arguments to 'keys'
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Premanand Achuthan authored
create_release_tasks.pl: distinguish between submitter and assignee
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Premanand Achuthan authored
Merge e! 95 version bumps into master
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- Sep 26, 2018
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Marek Szuba authored
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Marek Szuba authored
Schema patch to update Vertebrates division names in the meta table f…
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Marek Szuba authored
Fixed typo for new Vertebrate division name in metaContainer test
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Thomas Maurel authored
Schema patch to update Vertebrates division names in the meta table from Ensembl to EnsemblVertebrates for consistency. See declaration for details: https://www.ebi.ac.uk/panda/jira/browse/ENSINT-104.
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Thomas Maurel authored
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Marek Szuba authored
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Marek Szuba authored
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- Sep 25, 2018
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Marek Szuba authored
Useful under the circumstance when the person running the script is not in fact the RelCo for the next release, as it has already been the case before. Saves one having to manually reassign all the newly created tickets to the actual RelCo. Conversely, if it is the same person just omit the new argument and the RelCo user name will be used to connect to JIRA. Note that the function validating user names is only applied to RelCo ones. This is intentional, JIRA itself will complain if the submitter is not authorised to create ENSCORESW tickets.
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- Sep 24, 2018
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Marek Szuba authored
Being able to pass a scalar to e.g. keys was an experimental feature that was added in Perl 5.14 and since declared failed, thus causing the script to fail with an "Experimental keys on scalar is now forbidden" error.
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Marek Szuba authored
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Marek Szuba authored
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Marek Szuba authored
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Marek Szuba authored
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- Sep 11, 2018
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Magali Ruffier authored
ENSCORESW-2850: optimised for single species run
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Magali Ruffier authored
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Magali Ruffier authored
ENSCORESW-2837: do not import dependent VGNC
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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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Kieron Taylor authored
ENSCORESW-2853: match Ensembl species names with underscores
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Kieron Taylor authored
Feature/xref config
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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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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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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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Magali Ruffier authored
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