[Bioperl-l] parsing tblastn using BPlite

Chervitz, Steve Steve_Chervitz@affymetrix.com
Fri, 26 Oct 2001 17:52:32 -0700


Jason Eric Stajich writes [mailto:jason@cgt.mc.duke.edu]
> ... snip ...
> Additionally, I have started work on a simpler search result parsing
> system (Bio::SearchIO) which may be more intiutive and will 
> do event based
> parsing.
> It can currently only handle ncbi XML reports, but would like to
> integrate text blast reports, hmmer, and possibly FASTA (if 
> there are some
> volunteers out there to help) perhaps to be included in the 
> 1.0 release.

I've actually been working on the same thing. My new revamped version of
Bio::Tools::Blast (Bio::Tools::BlastIO - not yet checked in) uses a
SeqIO-like mechanism with text-based blast reports. The new parsing strategy
is also event based.

The reason why I have not checked it in is that I'd like to generalize the
framework to make it easy to incorporate other types of searches, such as
Fasta. So I've been playing around with Aaron's Bio::Search modules. I've
converted Bio::Search::Processor into what presumably you've done with
Bio::SearchIO. My Bio::Tools::BlastIO is now Bio::Search::Processor::Blast.

Check out this post for some of the issues that I'm pondering:

A nice feature of the Bio::Search system is that there's a natural framework
for segregating the different aspects common to all search-type algorithms
(Processor, Result, Hit, and though it's not there yet, Run).

Perhaps we should both check in what we have so we can coordinate our
efforts better. (I could also use another pair of eye/hands; my progress of
late has been rather choppy as I find myself spending most of my free time
chasing after an energetic 9-month old. 8)