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Bio-DB-Das-Chado-0.24
River stage zero No dependents
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Changes for version 0.24 - 2009-06-17

  • made the srcfeature method always return something; it no longer depends on the call to the constructor to set it.
  • Made using organism information more robust; now checks abbreviation and "genus species", and if it fails at everything, throws an error.
  • Added an option to the Chado constructor called -reference_class that allows the user to specify what feature type_id to use as the srcfeature. For example, if you have motifs mapped to a polypeptide and that polypeptide mapped to a region, you can speicify either "region" or "polypeptide" for the reference_class. Note that this does not automatically turn on recursive mapping, so by default, the motifs wouldn't be visible on the region. I honestly don't know for sure if recursive mapping still works--I haven't tested it in a long time.
  • Fixed a bug that sometimes prevented GBrowse from finding the subfeatures of features (like mRNAs of genes couldn't be found).

Modules

Bio::DB::Das::Chado
DAS-style access to a chado database
Bio::DB::Das::Chado::Segment
DAS-style access to a chado database
Bio::DB::Das::Chado::Segment::Feature

Provides

Bio::DB::Das::ChadoIterator
in lib/Bio/DB/Das/Chado.pm

Other files