Commits · 0323765dc066962d8a247b727761aae514f2bac6 · ensembl-gh-mirror / ensembl · GitLab

This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated Jul 01, 2022.

04 Nov, 2009 1 commit
- get the refseq data from the normal ccds database rather than the tracker ccds database · 0323765d
  Ian Longden authored Nov 04, 2009
  
  0323765d
30 Oct, 2009 2 commits
- changed rcp to scp · 4ca48827
  Nathan Johnson authored Oct 30, 2009
  
  4ca48827
- Uses DBI to attain persistant session READ lock · 310a3a8e
  Nathan Johnson authored Oct 30, 2009
```
removed -probe_mapping options as this is obsolete
Still needs tweaking for ens-genomics2 as we're not picking up the hostname alias
```
  310a3a8e
29 Oct, 2009 3 commits
- Be more straight-forward. · ca188a21
  Andreas Kusalananda Kähäri authored Oct 29, 2009
  
  ca188a21
- Deprecated the following three methods: · e2a0c596
  Andreas Kusalananda Kähäri authored Oct 29, 2009
```
  - get_all_AffyFeatures()
  - get_all_OligoFeatures()
  - get_all_OligoFeatures_by_type()

Functionality is instead provided by the Ensembl Functional Genomics
API.
```
  e2a0c596
- Added mysql dirs for ens-staging1&2 · 1a94b667
  Nathan Johnson authored Oct 29, 2009
  
  1a94b667
28 Oct, 2009 8 commits
- Remove excessive tabs. · 9df42048
  Andreas Kusalananda Kähäri authored Oct 28, 2009
  
  9df42048
- Sort a list and outdent one of the items. · 93023fe7
  Andreas Kusalananda Kähäri authored Oct 28, 2009
  
  93023fe7
- Use CORE::length() rather than just length() to disambiguate. · 316e66b5
  Andreas Kusalananda Kähäri authored Oct 28, 2009
  
  316e66b5
- added ncbigene · aac80749
  Bronwen Aken authored Oct 28, 2009
  
  aac80749
- *** empty log message *** · e15f6d4c
  William McLaren authored Oct 28, 2009
  
  e15f6d4c
- Removed references to Oligo and Affy as now in efg · d1a7d97d
  Nathan Johnson authored Oct 28, 2009
  
  d1a7d97d
- removed old Affy classes modules as these are now in efg · a3d4c21a
  Nathan Johnson authored Oct 28, 2009
  
  a3d4c21a
- The list of command line switches was inconsistent. · 2a6eee42
  Andreas Kusalananda Kähäri authored Oct 28, 2009
  
  2a6eee42
27 Oct, 2009 9 commits
- Removed Oligo Classes and Adaptors · ce87f468
  Nathan Johnson authored Oct 27, 2009
  
  ce87f468
- Removed old probe mapping scripts · 9072f20c
  Nathan Johnson authored Oct 27, 2009
  
  9072f20c
- Changed StructuralVariationFeature to StructuralVariation · 830757f3
  William McLaren authored Oct 27, 2009
  
  830757f3
- removed data patches · 69be0ab2
  Nathan Johnson authored Oct 27, 2009
  
  69be0ab2
- Added patch_56_57c, which adds ALT_GENE to the external_db.type enumeration. · 105a0526
  Michael Schuster authored Oct 27, 2009
  
  105a0526
- updated with affy tidy patch details · b9dc5742
  Nathan Johnson authored Oct 27, 2009
  
  b9dc5742
- added affy tidy patch · cec0e1af
  Nathan Johnson authored Oct 27, 2009
  
  cec0e1af
- Subroutine store() formatted for readability. · 304738db
  Andreas Kusalananda Kähäri authored Oct 27, 2009
  
  304738db
- removed AffyAlign from core entries as this is now in efg · 6896b18e
  Nathan Johnson authored Oct 27, 2009
  
  6896b18e
23 Oct, 2009 1 commit
- Added check for stop codons so transcripts with stops in the translation are ignored · a9d4f478
  Julio Fernandez Banet authored Oct 23, 2009
  
  a9d4f478
21 Oct, 2009 1 commit
- Added danio->stickleback GO term projection. · c9ee626c
  Glenn Proctor authored Oct 21, 2009
  
  c9ee626c
20 Oct, 2009 10 commits
- Avoiding global variables when sorting the translation lengths, · 92eb77c5
  Amonida Zadissa authored Oct 20, 2009
```
instead saving the transcripts and their lengths separately and then
sorting their lengths.
```
  92eb77c5
- More air in the usage info. · ac3ecb59
  Andreas Kusalananda Kähäri authored Oct 20, 2009
  
  ac3ecb59
- Properly qute strings and variables. Fix documentation. · 13f7b192
  Andreas Kusalananda Kähäri authored Oct 20, 2009
  
  13f7b192
- Added a simple to use wrapper script for "run.pl". · 61e8df1a
  Andreas Kusalananda Kähäri authored Oct 20, 2009
  
  61e8df1a
- Modified for difference between real KSH and pd-KSH. · ca62e7ed
  Andreas Kusalananda Kähäri authored Oct 20, 2009
  
  ca62e7ed
- Add a simple to use wrapper script for "manage_id_mapping_tables.pl". · f2574a32
  Andreas Kusalananda Kähäri authored Oct 20, 2009
  
  f2574a32
- Formatting. · 018250d3
  Andreas Kusalananda Kähäri authored Oct 20, 2009
  
  018250d3
- Add additional info to the documentation. · 03d5544c
  Andreas Kusalananda Kähäri authored Oct 20, 2009
  
  03d5544c
- Added "ALT_GENE" value to attribute "type" in external_db table (jb16) · ad75c56f
  Amy Tang authored Oct 20, 2009
  
  ad75c56f
- This patchfile is confused as to what version it applies to. Now corrected. · 0bd0e743
  Andreas Kusalananda Kähäri authored Oct 20, 2009
  
  0bd0e743
19 Oct, 2009 2 commits
- Added get_all_StructuralVariationFeatures method · 5cebf8d4
  William McLaren authored Oct 19, 2009
  
  5cebf8d4
- gorilla_protein added. · aa95c303
  Amy Tang authored Oct 19, 2009
  
  aa95c303
16 Oct, 2009 3 commits
- Added gorilla_cdna · 450efdd5
  Amy Tang authored Oct 16, 2009
  
  450efdd5
- Added in new type field "ALT_GENE" to match the latest external_dbs.txt · a6f6a2b1
  Amy Tang authored Oct 16, 2009
```
file (version 1.203)
```
  a6f6a2b1
- Added 8 Aspergillus species; also added a RNAMMER and TRNASCAN Sources · 997a67f4
  Arnaud Kerhornou authored Oct 16, 2009
  
  997a67f4