GitLab

Added new option to method fetch_all which is include_lrg. By defualt lrg slices willl NOT be returned if this is not set (default is off) also since at present all lrg regions are non reference this flag must be set too to get the lrg regions.

added new method fetch_by_region_unique which returns the non duplicate regions. This is mainly for getting non duplicated regions like assembly patches or haplotype regions

(replacing splicing_event.type with a reference to attrib_type).

Not properly tested due to lack of data.

fixes for LRGSlices and new methods to find nearest gene to a feature (this will change greatly as this is a very simple case)

  * Use fetch_all_by_Transcript() rather than translation() on the
    transcript to get the canonical translation (and any alternative
    translations).

  * ... then store the translation and any alternative translations.

Solves a problem stopping genebuilders from copying genes from one
database to another.

  * Correct documentation.
  * Use fetch_by_Transcript() to get canonical translation.
  * Modify SQL not to get canonical translation.

  * In the _list_dbIDs() method: Wrap the execute() in an eval() and
    throw() if it fails.

  * In the generic_fetch() method: For multi-species databases, make
    sure we're using the correct SQL table aliases for the seq_region
    and coord_system tables..

associated with the transcript.

get fetch all to ignore LRG_gene this makes it slower but if you are getting all the them then this will be insignificant time difference

Added sanity check to _objs_from_sth to allow fetching DnaAlignFeatures without a slice, so that we can retrieve userdata features for the entire genome

Always de-reference the value got from get_mapping_path().
Found by Magali.

translation ID, and ALWAYS update it to the correct translation ID
later, after storing the translation.

Avoids problems (the canonical_translation_id being duplicated) when
transferring transcripts with translations from another database.

Amonida found this.