[Bioperl-l] 1.5.1 todo list

Hilmar Lapp hlapp at gmx.net
Fri Aug 26 03:38:22 EDT 2005

On Aug 24, 2005, at 10:11 AM, Jason Stajich wrote:

> [...]
> What is the status of bioperl code for:
>  Ontology work

The issues with the goflat parser and Ontology.pm loading Graph.pm 
should be fixed. Due to lack of time I haven't been able yet to iron 
out the last wrinkles with the goperl-bridge I wrote, so .obo format is 
not yet supported. I'd really like this to be in 1.6.x though.

>  BioSQL support (from the Core code at least, how much in sync would 
> 1.5.1 be with biosql-perl release?)

I guess you mean bioperl-db? Bioperl-db works with the CVS main trunk 
of bioperl, all tests pass when run against bioperl-live.

>  Bio::FeatureIO stuff + Bio::SeqFeature changes?

The overloads seem to work currently but generally make me feel uneasy 
because they can lead to very subtle and hard to track down bugs and 
should be earmarked for roll back. One could choose to ignore this 
though for 1.5.1 (as opposed to 1.6.x).

>  Bio::DB::GFF work?  the GFF3 schema would be way past 1.5.1, but is 
> that something we'd want to shoot for in 1.6?
>  Other things?

A comprehensive and authoritative set of tests for the SeqFeatureI API 
still needs to be written so that any future f*ups in this area are 
readily and immediately detected. This would then also be the set of 
tests that blesses (or holds up) the 1.6.0 release code. Again, 
although I gave it priority one could choose to ignore it for 1.5.1.


> Please report in.  Times like this sort of make me want a Wiki so we 
> can keep track but I'll at least volunteer to collate the results into 
> a summary email.
> -jason
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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