Commits · 3bc4c26c1cf97be1d058118526cc13fea5bdf908 · ensembl-gh-mirror / ensembl

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Oct 11, 2004
- documentation and tidy up · 3bc4c26c
  Ian Longden authored 20 years ago
  
  3bc4c26c
Oct 08, 2004
- bugfix and adding of overlap_size method · 32dff732
  Arne Stabenau authored 20 years ago
  
  32dff732
- added test for suspected problem and for overlap size function · bc9c4ae5
  Arne Stabenau authored 20 years ago
  
  bc9c4ae5
- additional index for evidence table · 63dec523
  Steve Trevanion authored 20 years ago
  
  63dec523
Oct 07, 2004
- run_matching now needs xref to get the xref fasta files · f0153fec
  Ian Longden authored 20 years ago
  
  f0153fec
- xref sequence dumps are now configurable. See get_set_lists method · 2bf1df17
  Ian Longden authored 20 years ago
  
  2bf1df17
- Added (largely untested) dependent xref dumping. · 6ca670c0
  Glenn Proctor authored 20 years ago
  
  6ca670c0
- Dump a few more xrefs. · a2d9fe77
  Glenn Proctor authored 20 years ago
  
  a2d9fe77
- More informative output · 83a0c150
  Glenn Proctor authored 20 years ago
  
  83a0c150
- changes from branch-vega-23-dev · 3ec37fc5
  Patrick Meidl authored 20 years ago
  
  3ec37fc5
- Added dumping of files suitable for loading into target core database: · f6782625
  Glenn Proctor authored 20 years ago
```
 - xref.txt - contains xrefs that were mapped to e! objects during the mapping run
 - external_db.txt - contains the unique list of xref sources from the xrefs above in a format suitable for loading into the existing external_db table

Doesn't do dependent xrefs yet.
```
  f6782625
Oct 06, 2004
- call to new vega subroutine added · f16bed60
  Steve Trevanion authored 20 years ago
  
  f16bed60
- *** empty log message *** · 175a1024
  Steve Trevanion authored 20 years ago
  
  175a1024
- removes all traces of supercontigs · 36705e45
  Steve Trevanion authored 20 years ago
  
  36705e45
- Simple example of how to write a method class · b07132cf
  Glenn Proctor authored 20 years ago
  
  b07132cf
- Base class with most of exonerate functionality and overridable methods · 31c60b77
  Glenn Proctor authored 20 years ago
  
  31c60b77
- removed hard coded xref database stuff amd added use . for directory if none specified · 325dca7e
  Ian Longden authored 20 years ago
  
  325dca7e
- Moved most exonerate-specific stuff into XrefMapper::Methods::ExonerateBasic · 60450512
  Glenn Proctor authored 20 years ago
```
Disabled automatic loading of object_xrefs etc, now written to file.
```
  60450512
- small fixes for new input format · 853c2dd9
  Ian Longden authored 20 years ago
  
  853c2dd9
- changed to key value pairs · 73b9be6a
  Ian Longden authored 20 years ago
  
  73b9be6a
- input file is now key value pairs · a3a8e772
  Ian Longden authored 20 years ago
  
  a3a8e772
- made db.pm do the database type stuff · 20d0e4fd
  Ian Longden authored 20 years ago
  
  20d0e4fd
- 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