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

Chris Fields cjfields at illinois.edu
Mon Jul 11 22:19:21 UTC 2011

On Jul 11, 2011, at 2:47 PM, Peter Cock wrote:

> On Mon, Jul 11, 2011 at 7:48 PM, Chris Fields <cjfields at illinois.edu> wrote:
>> Forgot to mention, for more info on this, see:
>> http://www.bioperl.org/wiki/HOWTO:SQLite_for_BioPerl_indexing
>> This is also filed in Redmine as a bug I believe.
>> chris
> 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.

> 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.


More information about the Bioperl-l mailing list