Commits · 28a00b378cda0295d69d6db3d7381eee18db3d1e · ensembl-gh-mirror / ensembl

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Apr 01, 2005
- Created; base class for parsers that connect to databases. · 28a00b37
  Glenn Proctor authored 20 years ago
  
  28a00b37
- Added source for elegans that uses WormbaseDatabseStableIDParser. · 6544e72d
  Glenn Proctor authored 20 years ago
  
  6544e72d
- Added support for parsing from databases (rather than files). · 4573a115
  Glenn Proctor authored 20 years ago
  
  4573a115
- *** empty log message *** · fcf39ea9
  Glenn Proctor authored 20 years ago
  
  fcf39ea9
- Typo. · 7879f0e8
  Glenn Proctor authored 20 years ago
  
  7879f0e8
Mar 31, 2005
- Removed wormbase info as this will now be obtained only from the wormbase file · ce5aa54a
  Ian Longden authored 20 years ago
  
  ce5aa54a
Mar 30, 2005
- added WormPepParser docs · 94077fdd
  Ian Longden authored 20 years ago
  
  94077fdd
Mar 29, 2005
- use correct source or web will not recognise it · 5c7874c1
  Ian Longden authored 20 years ago
  
  5c7874c1
- reworked to work correctly · d5b9c845
  Ian Longden authored 20 years ago
  
  d5b9c845
- add labels for wormpep · 95f6428a
  Ian Longden authored 20 years ago
  
  95f6428a
- add dependent xref if worm transcript not found and swissprot is given · 6c49467b
  Ian Longden authored 20 years ago
  
  6c49467b
- Cannot parse files with 17 million bases, so removed these huge files · 341f3fe6
  Ian Longden authored 20 years ago
  
  341f3fe6
- tidy up · 9d6ca20c
  Ian Longden authored 20 years ago
  
  9d6ca20c
- case sensetivity issue fixed · 55d4ecc3
  Ian Longden authored 20 years ago
  
  55d4ecc3
Mar 24, 2005
- wormBase stuff added · f27e3298
  Ian Longden authored 20 years ago
  
  f27e3298
- Work still needed on WormPepParser to add if not found and has a swissprot acc. · 112ed948
  Ian Longden authored 20 years ago
  
  112ed948
- wormpep file added. Aswell as other RefSeq entries split into seperate loads · 44dfa0cc
  Ian Longden authored 20 years ago
  
  44dfa0cc
Mar 22, 2005
- sources for the worm · 4c9f730b
  Felix Kokocinski authored 20 years ago
  
  4c9f730b
Mar 21, 2005
- one comma too much... · a9d36a01
  Felix Kokocinski authored 20 years ago
  
  a9d36a01
Mar 18, 2005
- added missing codes, needs cleanup now · f7cad0d1
  Arne Stabenau authored 20 years ago
  
  f7cad0d1
- debugged and tested · ade933cd
  Arne Stabenau authored 20 years ago
  
  ade933cd
- added new sources and removed medline references · a60c15ae
  Ian Longden authored 20 years ago
  
  a60c15ae
- removed medline as this is the same as pubmed · 5f23d5b0
  Ian Longden authored 20 years ago
  
  5f23d5b0
Mar 15, 2005

Removed OMIM for now. As the same acc can have more than one disorder and only... · 39f79a1a

Ian Longden authored 20 years ago

Removed OMIM for now. As the same acc can have more than one disorder and only one can be stored. So disease database still needed for now

39f79a1a

Mar 14, 2005
- hugo gene names now give the descriptions, the display is the disease description · 5c913983
  Ian Longden authored 20 years ago
  
  5c913983
- MIM2 is now OMIM, also uncommented out the rest of the unigene sources · 0ff2ad00
  Ian Longden authored 20 years ago
  
  0ff2ad00
- OMIM source added which contains the disease database in the xref system · 1d858484
  Ian Longden authored 20 years ago
  
  1d858484
- Added Canine affy array as an external db. · 460d94d7
  Craig Melsopp authored 20 years ago
  
  460d94d7
- added UniGene as an external db · 1750774c
  Ian Longden authored 20 years ago
  
  1750774c
Mar 13, 2005
- create submit script for those mappings that produced problems · b98650e0
  Ian Longden authored 20 years ago
  
  b98650e0
- quick test for missing files from mapping · 13a16e95
  Ian Longden authored 20 years ago
  
  13a16e95
Mar 12, 2005
- match only translation for hugo until mart can handle translations and... · 9348d3fd
  Ian Longden authored 20 years ago
```
match only translation for hugo until mart can handle translations and transcripts. Transcript code commented out for now
```
  9348d3fd
- uncommented out unigene for human, the rest will be done if results are okay · 94499cb2
  Ian Longden authored 20 years ago
  
  94499cb2
Mar 11, 2005
- Make label = ID again, not accession. · 173a2304
  Glenn Proctor authored 20 years ago
  
  173a2304
- Check if database already exists before dropping it. · 93043844
  Glenn Proctor authored 20 years ago
  
  93043844
Mar 10, 2005
- update of logic name for vega genscans · d95eddd4
  Steve Trevanion authored 20 years ago
  
  d95eddd4
Mar 08, 2005
- Fixed bug that was causing a small number of HUGO xrefs to have null labels... · 22ae58b7
  Glenn Proctor authored 20 years ago
```
Fixed bug that was causing a small number of HUGO xrefs to have null labels (hence xref displayed was numeric HGNC instead).
```
  22ae58b7
Mar 07, 2005

· a0a0fbc4

Glenn Proctor authored 20 years ago

1. Use double-fork (not Open3) to communicate with LSF processes. More reliable and no quoting strangeness.

2. Add option to automatically upload external_db table

3. Bug fix: transcript/gene display_xrefs were not incorporating RefSeq xrefs since the split into RefSeq_peptide and RefSeq_dna had not been taken into account in the display xref calculation.

a0a0fbc4

Use double-fork (not Open3) to communicate with LSF processes. More reliable... · 658d5dd8
Glenn Proctor authored 20 years ago
```
Use double-fork (not Open3) to communicate with LSF processes. More reliable and no quoting strangeness.
```
658d5dd8

Mar 04, 2005
- added additional Vega attrib types · 5aa7aa76
  Patrick Meidl authored 20 years ago
  
  5aa7aa76