Revision history for Perl module Bio::DB::Das::Chado

0.2 Wed Apr 22 14:47:52 2009

• Stand alone module moved out of the GBrowse package

0.21 Thu May 7 20:17:33 EDT 2009

• Fixed Segment features method to support API needed for GBrowse2
• Fixed a bug that caused CDS inferrence to fail for single exon genes that have either a 5' or 3' UTR (but not both) to fail

0.22 Thu May 28 15:53:03 EDT 2009

• Added a rel2abs method to the Segment feature so that uploaded annotations will work correctly.

0.23 Thu Jun 4 11:55:24 EDT 2009

• Fixes to accomidate changes to the Chado GFF3 loader; there is still an outstanding bug associated with searching when the same ID is used in different GFF3 files. While this will be solved soon, a release is needed for a demo.

0.24 Wed Jun 17 03:29:06 EDT 2009

• 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).