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

Peter Cock p.j.a.cock at googlemail.com
Mon Jul 11 22:43:10 UTC 2011

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 ;)


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