Commits · 547d5b7be4965051e41308146b9fa1032fd4a231 · ensembl-gh-mirror / ensembl

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Aug 01, 2012
- updated instructions · 547d5b7b
  Monika Komorowska authored 12 years ago
  
  547d5b7b
- don't parse ArrayExpress xrefs · fd7a2842
  Monika Komorowska authored 12 years ago
  
  fd7a2842
- remove user and pass method call from methid new · ed8df18a
  Monika Komorowska authored 12 years ago
  
  ed8df18a
- delete user and pass method calls · 36e6715c
  Monika Komorowska authored 12 years ago
  
  36e6715c
- added config file for analyses to run after otherfeatures handover · b8a7c680
  Magali Ruffier authored 12 years ago
  
  b8a7c680
- look up stable_ids in core and create direct xrefs · 7e845316
  Monika Komorowska authored 12 years ago
  
  7e845316
- set_display_xrefs deleted, no need to override this method as gene and... · 89053cc6
  Monika Komorowska authored 12 years ago
```
set_display_xrefs deleted, no need to override this method as gene and transcript display xrefs are set separately in DisplayXrefs.pm
```
  89053cc6
- no longer loading ArrayExpress xrefs, this is done in parsing using data directly from the core db · 1bfa4b68
  Monika Komorowska authored 12 years ago
  
  1bfa4b68
- removed user and pass methods, no longer required in DirectXrefs.pm · 2d711c28
  Monika Komorowska authored 12 years ago
  
  2d711c28
- changes for new ArrayExpress xref source · 4eda6b63
  Monika Komorowska authored 12 years ago
  
  4eda6b63
- script to run a single query across several databases · 02173540
  Magali Ruffier authored 12 years ago
```
can be run across several hosts at a time
```
  02173540
- fix to set_display_xrefs · d641354d
  Monika Komorowska authored 12 years ago
  
  d641354d
Jul 31, 2012
- [ENSCORESW-220]. Being removed in favor of our new generate_default_aliases.pl... · 723fe498
  Andy Yates authored 12 years ago
```
[ENSCORESW-220]. Being removed in favor of our new generate_default_aliases.pl code for the production DB.
```
  723fe498
- Adding new script for autogenerating aliases · ac81f789
  Andy Yates authored 12 years ago
  
  ac81f789
- added output message that xrefs will be created during the mapping stage · aa689741
  Monika Komorowska authored 12 years ago
  
  aa689741
- Shebang change and small formatting. · c14bd627
  Andreas Kusalananda Kähäri authored 12 years ago
  
  c14bd627
- delete records from display_xref_priority and gene_desc_priority when status... · 254abeb8
  Monika Komorowska authored 12 years ago
```
delete records from display_xref_priority and gene_desc_priority when status is reset to parsing_finished or mapping_finished
```
  254abeb8
- gene count is run for all species, not just karyotype ones · a5b9335c
  Magali Ruffier authored 12 years ago
```
added option run_all to run even if there has been no change to the species
```
  a5b9335c
- added an option to run all stats even if there has not been any change · 9eb599e1
  Magali Ruffier authored 12 years ago
  
  9eb599e1
- added tables display_xref_priority and gene_desc_priority - they are used in... · 12a2fda4
  Monika Komorowska authored 12 years ago
```
added tables display_xref_priority and gene_desc_priority - they are used in DisplayXrefs.pm http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-219
```
  12a2fda4
- changes to set_display_xrefs and set_gene_descriptions... · cab6889e
  Monika Komorowska authored 12 years ago
```
changes to set_display_xrefs and set_gene_descriptions http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-219
```
  cab6889e
Jul 30, 2012
- added GeneCount · 2ff62262
  Magali Ruffier authored 12 years ago
  
  2ff62262
- get_production_DBAdaptor inherited from Base.pm · e695ccc5
  Magali Ruffier authored 12 years ago
  
  e695ccc5
- added gene count to summary · 2c53e67f
  Magali Ruffier authored 12 years ago
  
  2c53e67f
- added get_production_DBAdaptor here as it is used in many other modules · 7ab7cb57
  Magali Ruffier authored 12 years ago
  
  7ab7cb57
- new gene count method, divided in coding/pseudogene/noncoding groups · 15ff57b5
  Magali Ruffier authored 12 years ago
  
  15ff57b5
- fixed sql statement · c9a0ca5e
  Monika Komorowska authored 12 years ago
  
  c9a0ca5e
- added method create_xrefs · 30fdc09a
  Monika Komorowska authored 12 years ago
  
  30fdc09a
- added method get_meta_value · 951fdb96
  Monika Komorowska authored 12 years ago
  
  951fdb96
- call ArrayExpressParser to create direct xrefs- this has to be done during... · 0321a6f0
  Monika Komorowska authored 12 years ago
```
call ArrayExpressParser to create direct xrefs- this has to be done during mapping as we need current gene stable_ids to generate ArrayExpress xrefs
```
  0321a6f0
- added methods user and pass · e1edd3df
  Monika Komorowska authored 12 years ago
  
  e1edd3df
- Switched checksum table to MyISAM. Load speed has dramatically improved · 26cb6033
  Andy Yates authored 12 years ago
  
  26cb6033
- missed the TABLE directive · edf654d5
  Andy Yates authored 12 years ago
  
  edf654d5
- Missed source ID · 3153bfed
  Andy Yates authored 12 years ago
  
  3153bfed
- missed a , · 69426e0e
  Andy Yates authored 12 years ago
  
  69426e0e
- cannot name a primary key · c769362e
  Andy Yates authored 12 years ago
  
  c769362e
- Extra ) · dd253b42
  Andy Yates authored 12 years ago
  
  dd253b42
- Missed writing to the output filehandle · 5f3f7829
  Andy Yates authored 12 years ago
  
  5f3f7829
Jul 27, 2012
- Correcting PubMed xref problem where xref table entries contained gene IDs not... · c654df96
  Derek Wilson authored 12 years ago
```
Correcting PubMed xref problem where xref table entries contained gene IDs not PMIDs by changing parameters in add_xref call.
```
  c654df96
- [ENSCORESW-214 ]. Supporting the norestore pahse · ab16b009
  Andy Yates authored 12 years ago
  
  ab16b009