[Bioperl-l] project ideas

[Jason Stajich]

Thanks very much for volunteering Richard.

Basically - look at t/SeqIO.t adding more tests in the way they are
written:
ok( $seq->primary_id, '123445');

is the basic way to improve these tests.

For most sequence formats we at least test that the parser doesn't fall
over.  But we don't necessarily test each field in the created Bio::Seq or
Bio::Seq::RichSeq object.  What would be great is to take one of the
example embl or genbank files (or provide another entry file which has
more annotations in it if you like) and test that all of the data in the
file is available and correct in the created sequence object.

Additionally we should test for some of the newer genbank/embl entries
which are supposed to contain some more features - There is supposed to be
more info from Third-Party-Annotators included in records, etc.

I think a lot of the changes are discussed here, but I've not had time to
really go through it all:
http://www.ncbi.nlm.nih.gov/projects/collab/

It is quite possible that none of the changes will pose a problem for our
parsers but want to make sure of that.

At least this is what I'd like to see done - you or others may have more
thoughts on what needs to be improved with the tests.

For now, just submit the changes as an attached diff file (gotten like
this:
% cvs diff t/SeqIO.t > SeqIO_tests.diff
)
to bugzilla under a 'feature request' heading and a developer will commit
them - we can get you a r/w account once you feel comfortable with the
toolkit and the dev process.

Thanks for helping out,
-jason
On Wed, 12 Feb 2003, Richard Adams wrote:

> I'd like to start contributing to bioperl so if it's a good place to
> start I'll volunteer
> for designing new Bio::SeqIO test cases, if it's still going.
> Let me know what sort of tests you'd need.
>
> Richard Adams
> Universitry of Edinburgh
> UK
>
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> Bioperl-l mailing list
> Bioperl-l at bioperl.org
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu