[BioRuby] Bio::GO::GeneAssociation issue/fix and new unit test file

Ben Woodcroft donttrustben at gmail.com
Sat Apr 17 08:25:12 UTC 2010


Not to be pushy, but is there any movement on this? Ignoring my suggestions
for API changes (which aren't implemented), can the bug fixes be merged?

On 8 April 2010 22:14, Ben Woodcroft <donttrustben at gmail.com> wrote:

> Hi,
> I had some problems parsing gene association files using Bio::Flatfile,
> caused because the parser was attempting to use the split method on a nil.
> The offending line was
> @db_reference      = tmp[5].split(/\|/)  #
> That seemed easy enough to fix, but then I noticed there wasn't any test
> cases to test my changes against, so I made a new file
> test/unit/db/test_go.rb, including a simulation of one that was giving me
> problems. I've collected these changes in a new branch, and you can see the
> difference using the new github compare interface at
> http://github.com/wwood/bioruby/compare/36041377db...gene_association
> Is there any reason that the variables that correspond to arrays in
> GeneAssociation (@db_reference, @with, @db_object_synonym) are singular
> names, and not plural? It would be simple to add a alias_method
> db_references -> db_reference right?
> I also don't agree that the 'GO:' part of the identifier be chopped off by
> default by the goid method - gene association files are not necessarily
> concerned with GO - there are other ontologies out there as well. I
> personally never look at GO identifiers without the 'GO:' bit, so I was
> surprised when I saw that.
> Sound OK?
> Thanks,
> ben

More information about the BioRuby mailing list