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- Apr 29, 2005
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Will Spooner authored
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Will Spooner authored
Added get_all_homologous_Genes to Bio::EnsEMBL::Gene that returns the Bio::EnsEMBL::Gene and Bio::EnsEMBL::Compara::Homology objects for each corresponding homologous gene in the Compara DB. Changed EnsEMBL::Web::Data::Gene to use this call with the benefit that the Compara DB gets hit obce only per GeneView request
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- Apr 28, 2005
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Glenn Proctor authored
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Glenn Proctor authored
Updated to reflect the fact that gene descriptions are now held in the gene table not in a separate gene_description table.
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- Apr 27, 2005
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Ian Longden authored
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Ian Longden authored
use FULL uniprot files and not species specific .SPC files. Okay this will be alot larger to down load and parse but will contain all the proteins and not just the non-redundant ones. For example. For rat we get 7 more swissprot and 2000 more trembl entrys with the large file. I may need to add a new option on to the parser now to delete the files after loading for those with small disk space but this should be simple enough.
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- Apr 26, 2005
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Jan-hinnerk Vogel authored
query
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Ian Longden authored
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- Apr 25, 2005
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Glenn Proctor authored
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Glenn Proctor authored
Bug fix: some transcript display_xrefs weren't being assigned correctly if the transcript had more than one associated SwissProt ID and each of the SwissProts was associated with a HUGO ID, e.g. haemoglobin beta/delta chains.
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Glenn Proctor authored
Store synonyms as well as primary xref accessions in get_valid_codes (needed since some HUGOs map to secondary SwissProt IDs)
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- Apr 22, 2005
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Glenn Proctor authored
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Glenn Proctor authored
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Glenn Proctor authored
Moved delete_existing to separate metod so it can be called at the start of the process, so generated xref_ids are more sensible.
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- Apr 21, 2005
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Glenn Proctor authored
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Ian Longden authored
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- Apr 20, 2005
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Glenn Proctor authored
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Glenn Proctor authored
Fixed bug causing some gene display_xrefs to be incorrectly assigned.
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Javier Herrero authored
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- Apr 19, 2005
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Ian Longden authored
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Glenn Proctor authored
Removed hardcoded call to slice fetch_by_region to deal with species where 'chromosomes' in microRNA file are actually scaffolds or chunks. Also cache analysis.
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Glenn Proctor authored
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- Apr 18, 2005
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Ian Longden authored
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Arne Stabenau authored
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Arne Stabenau authored
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Arne Stabenau authored
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Arne Stabenau authored
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Arne Stabenau authored
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Arne Stabenau authored
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Arne Stabenau authored
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Arne Stabenau authored
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Arne Stabenau authored
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- Apr 17, 2005
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Ian Longden authored
add synonyms from the dead names column. NOTE still need to get the Mapper routine to dump non primary xref synonyms
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Ian Longden authored
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- Apr 15, 2005
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Glenn Proctor authored
Fixed bug causing query/target identity to not be considered when choosing gene descriptions.
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Ian Longden authored
Do not copy via a specific host (as these now have a max 256 process per user limit). This may be slower than the direct use of a named host (with the nfs directly hanging of it) but will work
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- Apr 14, 2005
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Ian Longden authored
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Glenn Proctor authored
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Ian Longden authored
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- Apr 12, 2005
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Glenn Proctor authored
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