Commits · 5941638564a8d6399de8bdd0a6831f085030d6eb · ensembl-gh-mirror / ensembl

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May 08, 2009
- bug fix for -stats option · 59416385
  Ian Longden authored 15 years ago
  
  59416385
- add Splicing event adaptors · 46c5dc61
  Ian Longden authored 15 years ago
  
  46c5dc61
May 07, 2009
- Computes and stores the transitive closure over all 'is_a' and 'part_of' · 129fe356
  Andreas Kusalananda Kähäri authored 15 years ago
```
relationships in an ensembl_ontology_NN database.  So far only tested
with GO data.
```
  129fe356
- Simplistic OBO v1.2 file parser that also loads the parsed data into an · 2bf4021b
  Andreas Kusalananda Kähäri authored 15 years ago
```
ensembl_ontology_NN database.  Only tested with Gene Ontology (GO) OBO
v1.2 data so far.
```
  2bf4021b
- This SQL file will create an empty ensembl_ontology_NN database. · 7e196506
  Andreas Kusalananda Kähäri authored 15 years ago
```
Currently drops each table before (re-)creating it.
```
  7e196506
- modified to use new_fast method in the constructor for speed purposes · 1d5ee781
  Daniel Rios authored 15 years ago
  
  1d5ee781
- modified implementation of translate method to use codon_table attribute as in Transcript object · 8b3ee83b
  Daniel Rios authored 15 years ago
  
  8b3ee83b
- added method to update a MiscSet object · f04b9481
  Daniel Rios authored 15 years ago
  
  f04b9481
May 06, 2009
- add totals of stable ids not found for each source · 5d57b6f9
  Ian Longden authored 15 years ago
  
  5d57b6f9
- sub transcript_display_xref_sources added · f231086f
  Ian Longden authored 15 years ago
  
  f231086f
- added Fantom source for mouse · ca1c702c
  Ian Longden authored 15 years ago
  
  ca1c702c
- parser for Fantom data · 80e9353a
  Ian Longden authored 15 years ago
  
  80e9353a
- Go status set to XREF now instead of KNWONXREF so that if a gene has a GO... · 6da9ff61
  Ian Longden authored 15 years ago
```
Go status set to XREF now instead of KNWONXREF so that if a gene has a GO reference it does not automatically get set to be a known gene. Added new external source Fantom
```
  6da9ff61
- alternative splicing tables added, dependent_xref table added, go_xref types... · 068e8e49
  Ian Longden authored 15 years ago
```
alternative splicing tables added, dependent_xref table added, go_xref types that were missed somehow have now been added
```
  068e8e49
- go_xref types that were missed somehow have now been added · e18037fa
  Ian Longden authored 15 years ago
  
  e18037fa
- splicing event tables added · 0aa32d0c
  Ian Longden authored 15 years ago
  
  0aa32d0c
- dependent_xref table added · c0de8135
  Ian Longden authored 15 years ago
  
  c0de8135
- more Vega tweaks · 10e42abf
  Steve Trevanion authored 15 years ago
  
  10e42abf
- standard release update of version · b30aba7c
  Ian Longden authored 15 years ago
  
  b30aba7c
- First attempt retrieving splicing event data from the core database · 9b4e851f
  Ian Longden authored 15 years ago
  
  9b4e851f
May 05, 2009
- vega features · eb5399f4
  Steve Trevanion authored 15 years ago
  
  eb5399f4
- Fix spelling mistake. · 29949ebe
  Andreas Kusalananda Kähäri authored 15 years ago
  
  29949ebe
- Add stubs for support for constitutive exons in ExonAdaptor.pm. Actual · 3e55f542
  Andreas Kusalananda Kähäri authored 15 years ago
```
support will be available once a schema patch has been committed and
databases have been patched...
```
  3e55f542
- Add support for constitutive exons in Transcript.pm and Exon.pm. · 0c929aba
  Andreas Kusalananda Kähäri authored 15 years ago
  
  0c929aba
- Patch from Andy Yates for properly matching names of Ensembl Genomes · 1ecf8c72
  Andreas Kusalananda Kähäri authored 15 years ago
```
databases in Registry.
```
  1ecf8c72
Apr 30, 2009
- Corrected CVS web URLs · e910cf2b
  Tim Cutts authored 15 years ago
  
  e910cf2b
Apr 27, 2009
- Rename fetch_ancestor_chart() into _fetch_ancestor_chart() since it is · b01800a7
  Andreas Kusalananda Kähäri authored 15 years ago
```
not really a general purpose method but quite specific to what the web
team will want to do later.
```
  b01800a7
Apr 23, 2009
- Add subclass of StableIdGenerator::EnsemblGeneric to do Anopheles gambiae... · 05356cfe
  Martin Hammond authored 15 years ago
```
Add subclass of StableIdGenerator::EnsemblGeneric to do Anopheles gambiae stable ID incrementation and verification.
```
  05356cfe
- add marmoset analyses · 6b84de27
  Magali Ruffier authored 15 years ago
  
  6b84de27
- new set of sql statements to remove tmp and bak tables used during mapping process · fafcac61
  Daniel Rios authored 15 years ago
  
  fafcac61
- updated documentation with cleanup script · 4aed4fdc
  Daniel Rios authored 15 years ago
  
  4aed4fdc
Apr 22, 2009
- added option -pattern to allow running the script in a group of databases · 2865f70a
  Daniel Rios authored 15 years ago
  
  2865f70a
Apr 21, 2009
- script that will calculate if the assembly table has overlapping regions in same coord_system · a5ea93f0
  Daniel Rios authored 15 years ago
  
  a5ea93f0
Apr 20, 2009
- merge from vega-49-dev · baa53639
  Steve Trevanion authored 15 years ago
  
  baa53639
- merge from 49-dev · 8f5a9b67
  Steve Trevanion authored 15 years ago
  
  8f5a9b67
- Remaining part of db_display_name added for Tgut_symbol. · f09f3df0
  Susan Fairley authored 15 years ago
  
  f09f3df0
- Entry added for Tgut_symbols. These are the gene symbols assigned to... · 76241779
  Susan Fairley authored 15 years ago
```
Entry added for Tgut_symbols. These are the gene symbols assigned to Taeniopygia guttata (zebra finch) genes by Dave Burt.
```
  76241779
Apr 15, 2009
- added FOS ends for zebrafish · d25b3f62
  Kerstin Howe authored 15 years ago
  
  d25b3f62
Apr 14, 2009
- Documentation edited for get_original_seq_region_position · 3e30fdc3
  William McLaren authored 15 years ago
  
  3e30fdc3
Apr 09, 2009
- minor tweaks · edb7ba68
  Daniel Rios authored 15 years ago
  
  edb7ba68