Commits · dbbd0e94ea9b82bf23e512d5ec499c4cb64fa921 · ensembl-gh-mirror / ensembl

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Jul 05, 2006
- *** empty log message *** · dbbd0e94
  Glenn Proctor authored 18 years ago
  
  dbbd0e94
- Now use API rather than direct SQL. Creates a transcript attribute for each... · 10c1f71c
  Glenn Proctor authored 18 years ago
```
Now use API rather than direct SQL. Creates a transcript attribute for each frameshift intron, the value of the attribute being the number of the intron in the transcript, starting from 1.
```
  10c1f71c
- Doc fix. · 771abd71
  Glenn Proctor authored 18 years ago
  
  771abd71
Jul 04, 2006
- stable Id mapping ported to perl · 687ad4c2
  Patrick Meidl authored 18 years ago
  
  687ad4c2
- object cache for stable Id mapping · 536254dd
  Patrick Meidl authored 18 years ago
  
  536254dd
- some script utilities (configuration parsing, logging and various other stuff) · ed2f3ec0
  Patrick Meidl authored 18 years ago
  
  ed2f3ec0
- Now takes into account the possibility of no DNA (or protein) reference · bd4334cc
  Kevin Howe authored 18 years ago
```
sequences
```
  bd4334cc
- added Stickleback · 3fad7820
  Simon White authored 18 years ago
  
  3fad7820
- Added elephant, armadillo, rabbit, tenrec, cat · 48491029
  Kevin Howe authored 18 years ago
  
  48491029
Jul 03, 2006
- Now just change linkage_type to IEA, don't add it to existing one. · c1dbe6ef
  Glenn Proctor authored 18 years ago
  
  c1dbe6ef
Jun 30, 2006
- Replaced space with tab in frameshift attribute · a40a8c43
  Kevin Howe authored 18 years ago
  
  a40a8c43
Jun 29, 2006
- Add information for Aedes xref · 5da1f284
  Karyn Megy authored 18 years ago
  
  5da1f284
- mainly typos · 1c86bb45
  Felix Kokocinski authored 18 years ago
  
  1c86bb45
- modules/t/ditag.t · 33e2e5d3
  Felix Kokocinski authored 18 years ago
  
  33e2e5d3
- ditag analysis entry, again · bad5394f
  Felix Kokocinski authored 18 years ago
  
  bad5394f
- ditag analysis entry · c56d617f
  Felix Kokocinski authored 18 years ago
  
  c56d617f
- improved fetch_by_slice method · 5485a8fd
  Felix Kokocinski authored 18 years ago
  
  5485a8fd
Jun 28, 2006
- Removed ditag as it doesn't have seq_region_* · c2ef12ea
  Glenn Proctor authored 18 years ago
  
  c2ef12ea
- Correct patch version. · 45d9c3e3
  Glenn Proctor authored 18 years ago
  
  45d9c3e3
- Schema version patch. · 4919b40d
  Glenn Proctor authored 18 years ago
  
  4919b40d
- Add schema version patch. · 52488935
  Glenn Proctor authored 18 years ago
  
  52488935
- Change oligo_feature.analysis_id to be int(10) unsigned. Should have been part of patch_39_40_a.sql · f630f688
  Glenn Proctor authored 18 years ago
  
  f630f688
- Add meta table entry for patch_39_40_h.sql (already applied). · 2610bd36
  Glenn Proctor authored 18 years ago
  
  2610bd36
- Added trailing $ to file matching regexp so (e.g.) emacs backup files... · 5e9412e9
  Glenn Proctor authored 18 years ago
```
Added trailing $ to file matching regexp so (e.g.) emacs backup files (patch_39_40_a.sql~) are not considered to be valid patches.
```
  5e9412e9
- include ditag tables · 26d4fbfa
  Felix Kokocinski authored 18 years ago
  
  26d4fbfa
- Patch to add ditag and ditag_feature tables. · e4934c3d
  Glenn Proctor authored 18 years ago
  
  e4934c3d
- Added ditag & ditag_feature tables, plus relevant patch line. · 215e961d
  Glenn Proctor authored 18 years ago
  
  215e961d
- added DitagFeature Adaptor · 6cc4d939
  Felix Kokocinski authored 18 years ago
  
  6cc4d939
- added ditag tables · dd714c5f
  Felix Kokocinski authored 18 years ago
  
  dd714c5f
- added notes about writing patches · b3d75c93
  Patrick Meidl authored 18 years ago
  
  b3d75c93
- test functions for the ditag modules · 394a5a13
  Felix Kokocinski authored 18 years ago
  
  394a5a13
- db adaptors for ditag and aligned ditag-feature modules · 99843ad8
  Felix Kokocinski authored 18 years ago
  
  99843ad8
- modules to handle ditags and aligned ditag-features in ensembl · 1c762e92
  Felix Kokocinski authored 18 years ago
  
  1c762e92
Jun 27, 2006
- Added RNA pseudogene counts; contribute to GeneNo_RNA_pseu attribute. · 4c54e14c
  Glenn Proctor authored 18 years ago
  
  4c54e14c
- added a few more lines to explain how to use the schema_patch.pl script with variation databases · 8ec5f251
  Daniel Rios authored 18 years ago
  
  8ec5f251
- added option to use it with ensembl-variation databases · 6a7b0dee
  Daniel Rios authored 18 years ago
  
  6a7b0dee
- *** empty log message *** · 9653915a
  Glenn Proctor authored 18 years ago
  
  9653915a
- Changed to store intron number in *gene*. · c3f89435
  Glenn Proctor authored 18 years ago
  
  c3f89435
- Stop it complaining about uninitialised value. · 4cf661d2
  Glenn Proctor authored 18 years ago
  
  4cf661d2
- Store intron number as attribute value instead of intron length. · 4a519c20
  Glenn Proctor authored 18 years ago
```
Also delete existing frameshift attributes by default.
```
  4a519c20