Commits · cfe26ad219e6a815d15596c18c75833a1e96061a · ensembl-gh-mirror / ensembl

This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated Jan 30, 2023.

05 Dec, 2014 4 commits
- update master schema to release 79 · cfe26ad2
  Magali Ruffier authored Dec 05, 2014
  
  cfe26ad2
- wrong taxonomy id for tasmanian devil · 3ad784b1
  Magali Ruffier authored Dec 05, 2014
  
  3ad784b1
- Ontology test database patched. · 51dd37ae
  Alessandro Vullo authored Dec 05, 2014
  
  51dd37ae
- Though it wasn't case sensitive. · 33aaf50a
  Alessandro Vullo authored Dec 05, 2014
  
  33aaf50a
04 Dec, 2014 2 commits
- Type added to the synonym table. · 352182a9
  Alessandro Vullo authored Dec 04, 2014
  
  352182a9
- Patches for 79: schema version and synonym type. · c136c0b9
  Alessandro Vullo authored Dec 04, 2014
  
  c136c0b9
03 Dec, 2014 7 commits
- added xref config for tasmanian devil with up-to-date list of sources · a4c5a080
  Magali Ruffier authored Dec 03, 2014
  
  a4c5a080
- ENSCORESW-1119 : refseq_import source added for vervet monkey and flycatcher · 6df52229
  Magali Ruffier authored Dec 03, 2014
  
  6df52229
- Merge pull request #45 from rishidev/master · e9e810c7
  Alessandro Vullo authored Dec 03, 2014
```
Vervet-AGM added to xrefs config
```
  e9e810c7
- Vervet-AGM added to xrefs config · 3b24e51d
  rishidev authored Dec 03, 2014
  
  3b24e51d
- Skip the correct amount of tests. · baf55198
  Alessandro Vullo authored Dec 03, 2014
  
  baf55198
- Zip based array slurping and corresponding tests. · ac70524a
  Alessandro Vullo authored Dec 03, 2014
  
  ac70524a
- bzip2 based array slurping and corresponding tests. · 1c20e6a2
  Alessandro Vullo authored Dec 03, 2014
  
  1c20e6a2
02 Dec, 2014 7 commits
- Some zip related tests. · 9ea373a2
  Alessandro Vullo authored Dec 02, 2014
  
  9ea373a2
- Implements reading a zip file content into memory. · 62e6ea58
  Alessandro Vullo authored Dec 02, 2014
  
  62e6ea58
- Some bzip2 related tests. · 7423b3ca
  Alessandro Vullo authored Dec 02, 2014
  
  7423b3ca
- Implements loading of bzip2 file content into memory. · bbb0258c
  Alessandro Vullo authored Dec 02, 2014
  
  bbb0258c
- Work with zip files. · bb5fb867
  Alessandro Vullo authored Dec 02, 2014
  
  bb5fb867
- Work with bz2 files. · aea17f43
  Alessandro Vullo authored Dec 02, 2014
  
  aea17f43
- Necessary header to proceed with the implementation of Bzip/Zip routines. · 7592f8cb
  Alessandro Vullo authored Dec 02, 2014
  
  7592f8cb
01 Dec, 2014 1 commit
- ENSCORESW-1137: regexp now deals with GN that have or have not evidence level... · 6efa6842
  Magali Ruffier authored Dec 01, 2014
```
ENSCORESW-1137: regexp now deals with GN that have or have not evidence level tags, and stores only the gene name
```
  6efa6842
28 Nov, 2014 13 commits
- strange typo went in there, corrected · 7646007a
  Magali Ruffier authored Nov 28, 2014
  
  7646007a
- utility script to convert tables between MyISAM and InnoDB · 65d0ebb9
  Magali Ruffier authored Nov 28, 2014
```
useful if wanting to scp an InnoDB database for example
```
  65d0ebb9
- ENSCORESW-1134: HGNC download file does not contain the version CCDS ids,... · d0a3ce9b
  Magali Ruffier authored Nov 28, 2014
```
ENSCORESW-1134: HGNC download file does not contain the version CCDS ids, fetch dbprimary_acc to match
```
  d0a3ce9b
- warn if no file could be found at the location · 437c9c53
  Magali Ruffier authored Nov 28, 2014
  
  437c9c53
- ENSCORESW-1132 : updated file location, files are now numbered · 0a61c9e7
  Magali Ruffier authored Nov 28, 2014
  
  0a61c9e7
- added RefSeq_import source for all Ensembl species · 13e25390
  Magali Ruffier authored Nov 28, 2014
  
  13e25390
- ENSCORESW-1119 : allow to skip import if no otherfeatures database, or no refseq_import data found · b3764922
  Magali Ruffier authored Nov 27, 2014
  
  b3764922
- ENSCORESW-1116 : first attempt at storing some form of scoring in the overlap mappings · 26152269
  Magali Ruffier authored Nov 27, 2014
  
  26152269
- adding some more methods for object_xref and identity_xref addition · d8476454
  Magali Ruffier authored Nov 27, 2014
```
required for RefSeqCoordinateParser
```
  d8476454
- ENSCORESW-366: CGNC parser updated to working link · 056751a8
  Magali Ruffier authored Nov 27, 2014
```
some sanity checks to make sure the file contains the data we expect
```
  056751a8
- first pass CGNCParser for chicken names · 39f0a770
  Magali Ruffier authored Oct 02, 2014
```
recovered from cvs commits in 2012, not tested
```
  39f0a770
- Merge pull request #43 from fergalmartin/master · 1c141542
  Magali Ruffier authored Nov 28, 2014
```
Change to xref_config.ini for flycatcher
```
  1c141542
- Change to xref_config.ini for flycatcher · ec4e98bd
  Fergal Martin authored Nov 28, 2014
  
  ec4e98bd
27 Nov, 2014 2 commits

Merge pull request #42 from arnaudxk/master · 42847297

Magali Ruffier authored Nov 27, 2014

Removed method 'set_source_id_to_external_name' to revert back to the default behaviour which is to report the display db name in the source field of the gene description.

42847297

Update eukaryota.pm · 872bf221

Arnaud Kerhornou authored Nov 27, 2014

Removed method 'set_source_id_to_external_name' to revert back to the default behaviour which is to report the display db name in the source field of the gene description.

872bf221

26 Nov, 2014 4 commits
- Merge pull request #41 from arnaudxk/master · 6068c540
  Alessandro Vullo authored Nov 26, 2014
```
Added ncRNA_EG::EG source to species, Triticum aestivum
```
  6068c540
- Added ncRNA_EG::EG source to species, Triticum aestivum · 046d0eb1
  Arnaud Kerhornou authored Nov 26, 2014
  
  046d0eb1
- Merge pull request #40 from danstaines/master · 1d92442c
  Magali Ruffier authored Nov 26, 2014
```
changed attributes to use correct casing as per GFF spec
```
  1d92442c
- changed attributes to use correct casing as per http://gmod.org/wiki/GFF3.... · 97cb2e76
  Dan Staines authored Nov 25, 2014
```
changed attributes to use correct casing as per http://gmod.org/wiki/GFF3. Extended testcase to include transcript to test Parent attribute
```
  97cb2e76