[Bioperl-l] Bio::Index::Fastq indexing options

[Evan Staton]

Hi,

Thank you Peter and Chris for your comments. It is encouraging to see
interest in this topic and the potential to move towards a standard.
Unfortunately, I'm not really familiar with OBDA or Biopython's SQLite based
indexing. I will try to make some progress on understanding these formats,
and watch the list to see if there has been any progress on this topic from
the Codefest or elsewhere.

Thanks,

Evan

On Mon, Jul 11, 2011 at 6:43 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Mon, Jul 11, 2011 at 11:19 PM, Chris Fields <cjfields at illinois.edu>
> wrote:
> > On Jul 11, 2011, at 2:47 PM, Peter Cock wrote:
> >>
> >> We've got SQLite based indexing for Biopython's SeqIO module,
> >> and I'd be keen to try and share the same format (table names,
> >> column names etc). I view this as an extension to the existing
> >> flat file and BDB backends for OBDA - what I did for Biopython
> >> with SQLite was very much inspired by that design.
> >>
> >> http://obda.open-bio.org/
> >> http://lists.open-bio.org/pipermail/open-bio-l/2009-August/000561.html
> >
> > I think this is a good plan to follow, at least makes the end-point
> > index less reliant on a specific implementation.
>
> Feel free to ping me if this goes quiet - I had been meaning to
> write up the Biopython SQlite SeqIO index table design, but had
> not got round to it.
>
> >> If any BioPerl folk are at the CodeFest this week before BOSC,
> >> this could be a good project:
> >>
> >> http://www.open-bio.org/wiki/Codefest_2011
> >>
> >> Peter
> >
> > Unfortunately I'm not going this year, but maybe open an IRC
> > channel or something similar so we can participate?  (though the
> > time difference may limit that somewhat).  I am making active
> > plans for attending next year, though.
>
> We can look into that (CC'ing Brad who is organising the
> CodeFest 2011 event).
>
> Looking ahead to next year, ISMB 2012 will be July 15-17, at
> Long Beach, California  (pre-conference SIGs like BOSC
> etc July 13-14). I would hope to attend, but will have to see
> about budgets - I was hoping it would in Europe again ;)
>
> Peter
>
>
>