[BioPython] Biopython hackathon

[Ann Loraine]

Thanks, I meant Bio::DB::GFF -- the schema shown in the paper.

A simple schema that represents features on genomic sequence and
easily supports fast region-based queries is what I'm after. The
indexing scheme in the paper looked good, so I was hoping to find
python code that would hide the details of formulating the SQL. My
main goal is speed -- running the queries and then outputting data in
GFF, bed, or DAS XML, as the need arises.

-Ann

On 3/14/07, Chris Fields <cjfields at uiuc.edu> wrote:
>
> On Mar 14, 2007, at 6:43 PM, Ann Loraine wrote:
>
> > ...
> > (2) Another request is for a Python interface to the Bio::Db::SQL
> > database schema described in:
> >
> > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?
> > cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12368253.
> >
> > The part that seems particularly valuable would be code that to
> > construct the location-based queries.
>
> Did you mean Bio::DB::GFF?  AFAIK Lincoln is moving stuff over to a
> newer system that better facilitates GFF3, namely
> Bio::DB::SeqFeature.  I'm not sure how well Bio::DB::GFF is supported
> currently.
>
> > My apologies if this already exists -- if yes, please let me know
> > where I can find it!!
>
> You can find out about the current state of GBrowse affairs by
> emailing the GBrowse mail list.  Here's the sourceforge link:
>
> http://sourceforge.net/mailarchive/forum.php?forum_id=31947
>
> Scott and Lincoln can indicate where their current focus is re: GFF3
> and sequence feature database development.
>
> chris
>
> > All the best,
> >
> > Ann Loraine
>
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
>


-- 
Ann Loraine, Assistant Professor
Departments of Genetics, Biostatistics,
Computer and Information Sciences
Associate Scientist, Comprehensive Cancer Center
University of Alabama at Birmingham
http://www.transvar.org
205-996-4155