Commits · ec9c73945f5028ea6c07744fe60ec73675805f4f · ensembl-gh-mirror / ensembl

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Oct 06, 2004
- gen tidy · ec9c7394
  Ian Longden authored 20 years ago
  
  ec9c7394
Oct 05, 2004
- Documentation. · 347d6218
  Glenn Proctor authored 20 years ago
  
  347d6218
- Now creates entries in object_xref and identity_xref tables as well as dumping to files. · ed9596ab
  Glenn Proctor authored 20 years ago
  
  ed9596ab
- Added -noflush option and help menu · ab62fc4b
  Abel Ureta-Vidal authored 20 years ago
  
  ab62fc4b
- Bug fix: was preserving newlines in sequence part of RefSeq .rna.fna files. · 540a8afc
  Glenn Proctor authored 20 years ago
  
  540a8afc
Oct 04, 2004
- Initial version of Affy classes to make affy test pass/ · d526a1b6
  Arne Stabenau authored 20 years ago
  
  d526a1b6
- example input file · a5251aff
  Ian Longden authored 20 years ago
  
  a5251aff
- merely inherits from BasicMapper · f85b68fc
  Ian Longden authored 20 years ago
  
  f85b68fc
- first draft release · 1d338160
  Ian Longden authored 20 years ago
  
  1d338160
- Improvements to object_xref/identity_xref table dumping. · ae3617bc
  Glenn Proctor authored 20 years ago
```
Now assigns an analysis ID or creates one if necessary.
```
  ae3617bc
- · ef28b4ab
  Simon White authored 20 years ago
```
added miRNA registry to external_dbs list
```
  ef28b4ab
- NOT ready yet just making sure i have safe copy for now · 3b005faf
  Ian Longden authored 20 years ago
  
  3b005faf
- More implementation: now successfully submits exonerate jobs and dependency job. · f4d79bf4
  Glenn Proctor authored 20 years ago
```
Improved process communication. Implemented parsing.
```
  f4d79bf4
Oct 01, 2004
- written tests for affy features, now write classes to make them pass · 9aacf50b
  Arne Stabenau authored 20 years ago
  
  9aacf50b
- Prototype for exonerate mapping part of new xref system. Still under development. · 710635c9
  Glenn Proctor authored 20 years ago
  
  710635c9
- Temporary utility to dump xref sequences to a FASTA file. Needed for... · 29c744f7
  Glenn Proctor authored 20 years ago
```
Temporary utility to dump xref sequences to a FASTA file. Needed for development/debugging of xref mapping system.
```
  29c744f7
- Temporary utility to dump Ensembl transcript sequences to a FASTA file. Needed... · 90b89adc
  Glenn Proctor authored 20 years ago
```
Temporary utility to dump Ensembl transcript sequences to a FASTA file. Needed for development/debugging of xref mapping system.
```
  90b89adc
Sep 30, 2004
- patch sql added to CVS · c4c481cc
  Arne Stabenau authored 20 years ago
  
  c4c481cc
Sep 29, 2004
- Modified regexp so xref description field no longer has leading spaces. · be76760e
  Glenn Proctor authored 20 years ago
  
  be76760e
Sep 28, 2004
- Added storing of dependent xref label and linkage annotation (mainly for GO... · f6ff3768
  Glenn Proctor authored 20 years ago
```
Added storing of dependent xref label and linkage annotation (mainly for GO dependent xrefs so far).
```
  f6ff3768
- Added parsing of linkage type and label for GO dependent xrefs obtained from SwissProt files. · c40a1f72
  Glenn Proctor authored 20 years ago
  
  c40a1f72
- Added GO to list of sources so that GO refs in SwissProt files can be stored. · 1df93c82
  Glenn Proctor authored 20 years ago
  
  1df93c82
Sep 27, 2004
- Separated out metadata database table creation from population. · 6d760bd4
  Glenn Proctor authored 20 years ago
  
  6d760bd4
- Added taxonomy IDs for new species (tetraodon & bee) · d75bb3ad
  Glenn Proctor authored 20 years ago
  
  d75bb3ad
- Added seq_region_id index to density_feature (speeds up some queries,... · 2422f10f
  Glenn Proctor authored 20 years ago
```
Added seq_region_id index to density_feature (speeds up some queries, particularly those used in the DensityFeatures healthcheck)
```
  2422f10f
Sep 20, 2004
- Added created_date and modified_date columns to stable ID tables. · 6580016e
  Glenn Proctor authored 20 years ago
  
  6580016e
- Updated for release 25 · 2adf703a
  Glenn Proctor authored 20 years ago
  
  2adf703a
Sep 16, 2004
- added some registry info to the tutorial · 43ad974b
  Ian Longden authored 20 years ago
  
  43ad974b
- get_adaptor fixed for dnadb with different species · 79913f4b
  Ian Longden authored 20 years ago
  
  79913f4b
- get_adaptor fixed for dnadb with different species · f3cdc0a8
  Ian Longden authored 20 years ago
  
  f3cdc0a8
- moved query constructors to BaseAdaptor module · 847ebd02
  Daniel Rios authored 20 years ago
  
  847ebd02
Sep 15, 2004
- typo in method name load_registy_with_web_adaptors fixed · 032fb3d4
  Ian Longden authored 20 years ago
  
  032fb3d4
Sep 14, 2004
- stopped shout when set not defined · 47582aae
  Web Admin authored 20 years ago
  
  47582aae
Sep 13, 2004
- make sure add_DNAAdaptor stores the key name for the species and not an alias · df27a496
  Ian Longden authored 20 years ago
  
  df27a496
Sep 10, 2004
- backwards compatibillity fix · 19ab0154
  Ian Longden authored 20 years ago
  
  19ab0154
- added forgotten important detail about using AssemblyMapper vs. using ChainedAssemblyMapper · e1538de3
  Graham McVicker authored 20 years ago
  
  e1538de3
Sep 09, 2004
- much code duplication removed by adding load_adaptors which other load methods... · 181deba4
  Ian Longden authored 20 years ago
```
much code duplication removed by adding load_adaptors which other load methods call. load_adaptors is now also called if an unknown DBAdaptor is passed (which could happen with registry autoloading. Added a test for variation adaptor
```
  181deba4
- get_available_adaptors method added to make DBAdaptors all act the same in the load · 2be4ee3b
  Ian Longden authored 20 years ago
  
  2be4ee3b
Sep 08, 2004
- made some small corrections · 06a19e97
  Graham McVicker authored 20 years ago
  
  06a19e97
Sep 06, 2004
- add_DNAAdaptor now takes the group name and not the actual adaptor · 96990992
  Ian Longden authored 20 years ago
  
  96990992