Commits · 1df2e976f0ba35711eaf224b93bf89622a7aae79 · ensembl-gh-mirror / ensembl

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Mar 29, 2012
- Canis_familiaris refseq url has gone trinomial to canis_lupus_familiaris · 1df2e976
  Kieron Taylor authored 12 years ago
  
  1df2e976
- deleted extra quote · 85952d2e
  Monika Komorowska authored 12 years ago
  
  85952d2e
- name column changed to common_name in species table · 4e1c6cc9
  Monika Komorowska authored 12 years ago
  
  4e1c6cc9
- Reclassified pseudogenes into 'pseudogene' category instead of 'short non-coding' · 7edb69ed
  Kieron Taylor authored 12 years ago
  
  7edb69ed
Mar 28, 2012
- attribute_type table does not exist. attrib_type does · cfc5e443
  Andy Yates authored 12 years ago
  
  cfc5e443
- Added a --dropbak/-dB option for dropping the backup table before the script exits. · d4b48798
  Andreas Kusalananda Kähäri authored 12 years ago
  
  d4b48798
Mar 27, 2012
- updated ccds and lrg documentation · deff9c21
  Monika Komorowska authored 13 years ago
  
  deff9c21
- update direct xref documentation · bddc00f4
  Monika Komorowska authored 13 years ago
  
  bddc00f4
- changes for xrefs with evidence > 2 · 93e29f8b
  Monika Komorowska authored 13 years ago
  
  93e29f8b
- select transcripts only to get rid of duplicate sql query results · 613ee0e2
  Monika Komorowska authored 13 years ago
  
  613ee0e2
- escape underscores so they are not treated as a wildcard character · 94f7ff7c
  Monika Komorowska authored 13 years ago
  
  94f7ff7c
- change to exonerate lsf job submission · b539dc02
  Monika Komorowska authored 13 years ago
  
  b539dc02
- fixed a bug which applied incorrect accessions to clone based vega gene display xrefs · c7905a58
  Monika Komorowska authored 13 years ago
  
  c7905a58
- updates for release 67 · 1c76c838
  Monika Komorowska authored 13 years ago
  
  1c76c838
- deleted deprecated method · 96ee12ef
  Monika Komorowska authored 13 years ago
  
  96ee12ef
- Missed imports · 68719e57
  Andy Yates authored 13 years ago
  
  68719e57
- Removed elegans-specfic definition of get_set_lists · 53933a43
  Kevin Howe authored 13 years ago
  
  53933a43
- Make help more readable. · 98372bd7
  Andreas Kusalananda Kähäri authored 13 years ago
  
  98372bd7
Mar 24, 2012

Switch to using $subsequence_slice than $self for the start and end values. If... · bb304116

Andy Yates authored 13 years ago

Switch to using $subsequence_slice than $self for the start and end values. If we don't then we will try to retrieve all repeat features for an entire chromosome.

bb304116

Mar 23, 2012
- Explaining that the fetch_by_X_id methods will return a slice on the forward strand · 040a03e9
  Andy Yates authored 13 years ago
  
  040a03e9
- Simplification of the AUTOLOAD since there were blocks of code which could... · 00eedb68
  Andy Yates authored 13 years ago
```
Simplification of the AUTOLOAD since there were blocks of code which could never be called. Removed these unused blocks.
```
  00eedb68
Mar 22, 2012
- removed new_build_gene_descriptions - method deprecated · b1b1df9e
  Monika Komorowska authored 13 years ago
  
  b1b1df9e
- added gene_description_sources sub · a96e6742
  Monika Komorowska authored 13 years ago
  
  a96e6742
- updated sql statement label · b74f204f
  Monika Komorowska authored 13 years ago
  
  b74f204f
- Testing different sources · f0c7f992
  Bronwen Aken authored 13 years ago
  
  f0c7f992
- fixed problem where alternative translations could not be retrieved by dbID · 7e7ae643
  Dan Staines authored 13 years ago
  
  7e7ae643
- added ignore sql for EntrezGene xrefs with display labels like '%LOC%' · 52cf94e5
  Monika Komorowska authored 13 years ago
  
  52cf94e5
- added ignore sql for EntrezGene xrefs with accessions like '%LOC%' · 9d1eb029
  Monika Komorowska authored 13 years ago
  
  9d1eb029
- species.pm for pig · fc77a81a
  Monika Komorowska authored 13 years ago
  
  fc77a81a
- Only get a checksum analysis IF we had checksum mappings · e7953f2e
  Andy Yates authored 13 years ago
  
  e7953f2e
- logic names are always lower cased · ee5a8108
  Andy Yates authored 13 years ago
  
  ee5a8108
Mar 21, 2012
- Do not join to seq_region unless we have to i.e. when we've got a multispecies DB · dced304c
  Andy Yates authored 13 years ago
  
  dced304c
Mar 20, 2012
- Escape _ in the input parameters as otherwise we spend a lot of time doing... · ed88ee23
  Andy Yates authored 13 years ago
```
Escape _ in the input parameters as otherwise we spend a lot of time doing very expensive LIKE operations
```
  ed88ee23
- Use 'biotypes_include' (same as 'biotypes') and 'biotypes_exclude' · 92e9f90d
  Andreas Kusalananda Kähäri authored 13 years ago
```
(rather than 'not_biotypes'), for cleaner looking configuration.
```
  92e9f90d
- Split the parsing of a location string away from the use case · 04bdd5c1
  Andy Yates authored 13 years ago
  
  04bdd5c1
- Support strands · 5c0b426b
  Andy Yates authored 13 years ago
  
  5c0b426b
- Now used IP addresses internally rather than trying to figure out the · 29b02806
  Andreas Kusalananda Kähäri authored 13 years ago
```
canonical human-readable names of the hosts.

Reformat.
```
  29b02806
- Fixing to use SUPER::seq() on the subsequence slice and then using the block fetched repeats · e3299418
  Andy Yates authored 13 years ago
  
  e3299418
- Use $genes not @genes when accessing the values · c1ab1c34
  Andy Yates authored 13 years ago
  
  c1ab1c34
Mar 19, 2012
- Tidied up detritus left by removing duplicate masking step. · 48f3ceff
  Kieron Taylor authored 13 years ago
  
  48f3ceff