Commits · 2223def0befdc96a8c7424eb98a309a61bee11c3 · ensembl-gh-mirror / ensembl

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Jun 22, 2012
- switching from ok to is & Test::More · 2223def0
  Andy Yates authored 12 years ago
  
  2223def0
- RFAM::EG needs to use the CoreXrefParser · fb266ae2
  Monika Komorowska authored 12 years ago
  
  fb266ae2
- load registry in the main parser · 50996c8c
  Monika Komorowska authored 12 years ago
  
  50996c8c
- Ensembl version of the RFAMParser is not needed · ed1645c7
  Monika Komorowska authored 12 years ago
  
  ed1645c7
- RFAM xrefs need to be parsed using CoreXrefParser for EnsemblGenomes · 931f34a4
  Monika Komorowska authored 12 years ago
  
  931f34a4
- Missed dog and made more species alphabetical · f0f5d623
  Andy Yates authored 12 years ago
  
  f0f5d623
- removed warning in store_alt_alleles when none of the alt_alleles in a set is... · 77f20df7
  Monika Komorowska authored 12 years ago
```
removed warning in store_alt_alleles when none of the alt_alleles in a set is on reference sequence - this is a valid case and doesn't require a warning
```
  77f20df7
- changed miRBase to miRBase::MULTI · 9e5ca802
  Monika Komorowska authored 12 years ago
  
  9e5ca802
- changed miRBase to miRBase::MULTI · b770b554
  Monika Komorowska authored 12 years ago
  
  b770b554
- Allowing backups to go to a directory other than our current working... · 6fe52774
  Andy Yates authored 12 years ago
```
Allowing backups to go to a directory other than our current working directory. Can cause some issues with disk quotas
```
  6fe52774
- changed source definition for RNAMMER and TRNASCAN_SE · 33ae6905
  Monika Komorowska authored 12 years ago
  
  33ae6905
- RFAMParser which loads the registry with EnsemblGenomes databases · eb20db7a
  Monika Komorowska authored 12 years ago
  
  eb20db7a
- generic RFAMParser which RFAMParser_E and RFAMParser_EG inherit from · 4749b9f8
  Monika Komorowska authored 12 years ago
  
  4749b9f8
- RFAMParser which loads the registry with EnsEMBL databases · d8a1585c
  Monika Komorowska authored 12 years ago
  
  d8a1585c
- parser for xrefs from core which are generated by an analysis straight into a core db · 08911acf
  Monika Komorowska authored 12 years ago
  
  08911acf
- removed duplicate store method · b1608d60
  Magali Ruffier authored 12 years ago
```
does not store density feature with value of 0
```
  b1608d60
- updated the $option in repeat coverage case . Repeat coverage script now use... · 72f91cf9
  Thomas Maurel authored 12 years ago
```
updated the $option in repeat coverage case . Repeat coverage script now use "-pattern" to find a database instead of -d.
```
  72f91cf9
- updated the help, the script now use "-pattern" to find a database instead of "-p". · 2f97d9c6
  Thomas Maurel authored 12 years ago
  
  2f97d9c6
- Replaced "$option" from "-d" to "-pattern" for the percent_gc script. · 0df8692c
  Thomas Maurel authored 12 years ago
  
  0df8692c
Jun 21, 2012
- deleted unnecessary module import · e171eaab
  Monika Komorowska authored 12 years ago
  
  e171eaab
- when the band is at the end of the chromosome, make sure the two ends match · 4478c0dc
  Magali Ruffier authored 12 years ago
  
  4478c0dc
- I have added the softshell turtle ( psinensis ) to the projections. · dbc75ca6
  Thomas Maurel authored 12 years ago
  
  dbc75ca6
- Fixing a bug brought up by Nathan where we used version in the select for an xref_id. · fde3eb03
  Andy Yates authored 12 years ago
  
  fde3eb03
- fix module name · 2e97bb88
  Monika Komorowska authored 12 years ago
  
  2e97bb88
- added empty line after _store_or_fetch_xref_pod · 58eda2b0
  Nathan Johnson authored 12 years ago
  
  58eda2b0
- Missing xenopus from the execution order list · a676b36b
  Andy Yates authored 12 years ago
  
  a676b36b
- Switch back to mydir so we don't use a person's own directory · 78bd5c7a
  Andy Yates authored 12 years ago
  
  78bd5c7a
- Cannot have an alias for print and we never did · 5ece2d5f
  Andy Yates authored 12 years ago
  
  5ece2d5f
- Switch to using get_all_GeneMembers() which is the supported API in 68 · b48c591d
  Andy Yates authored 12 years ago
  
  b48c591d
- added RFAM::EG source · 239893e8
  Monika Komorowska authored 12 years ago
  
  239893e8
- RFAM parser for ensembl genomes · df160679
  Monika Komorowska authored 12 years ago
  
  df160679
- Return 1 if we unlinked the file. Otherwise return 0 · bf90fd82
  Andy Yates authored 12 years ago
  
  bf90fd82
- Die if we had no files · acb18be4
  Andy Yates authored 12 years ago
  
  acb18be4
Jun 20, 2012
- fix to make sure that dbname takes priority over pattern · 319742e3
  Dan Staines authored 12 years ago
  
  319742e3
- no clone coordinate system in mouse exists in the new assembly, don't project... · f017c309
  Monika Komorowska authored 12 years ago
```
no clone coordinate system in mouse exists in the new assembly, don't project to clone for mouse either
```
  f017c309
- fixed output message · 2e4b0861
  Monika Komorowska authored 12 years ago
  
  2e4b0861
- corrected file names - fix for Exonerate method override change · 3043d3eb
  Monika Komorowska authored 12 years ago
  
  3043d3eb
- new parser for RFAM xrefs, replaces use of ncRNA_DBParser in ensembl · 35cf179e
  Monika Komorowska authored 12 years ago
  
  35cf179e
- new parser for miRBase xrefs, replaces use of ncRNA_DBParser in ensembl · 3c361f02
  Monika Komorowska authored 12 years ago
  
  3c361f02
- replaced source ncRNA::MULTI with RFAM::MULTI and miRBase::MULTI · d9482c27
  Monika Komorowska authored 12 years ago
  
  d9482c27