[BioRuby] GFF3

[Pjotr Prins]

On Wed, Aug 18, 2010 at 05:21:24PM +0900, Tomoaki NISHIYAMA wrote:
> Hi,
>
> Here is how the trans-splicing gene rps12 looks like in the genomic  
> context.
> http://www.ncbi.nlm.nih.gov/nuccore/7525012?report=graph&v=60000:170000

Cool, huh :)

> The gene number within a genome doesn't grow so much.  So, the
> memory becomes problematic only if you are dealing with multiple
> genomes or more fine features.

Yup. That is where we are heading. 100K people project, for example.

> Saving memory is another kind of optimization.  It's good if we can
> achieve to do with less memory.  I just don't care much as far as
> the problem fit in the memory I can use and run in a reasonable
> time.

Sure, but I think it is short sighted to load everything in RAM when
we think in more general BioRuby terms.

> Oh, I meant relational database. It is for flexibility.
> Its just easier for me to use a RDBMS than to think of a new way
> to do without it.  So, its just expression of my way.

Sure, feel free to use an RDBMS. Just don't expect everyone to.

> If you are always to query from the gene name, then gene name to
> seekpos index will be sufficient.  But, then I would rather consider
> to store the parsed data object in PStore than to parse the GFF file
> again.

PStore is cool too.

Pj.