[Bioperl-l] writing blastxml

Chris Fields cjfields at uiuc.edu
Sun Dec 10 13:45:26 EST 2006


On Dec 8, 2006, at 2:47 PM, Bob Freeman wrote:

> Can't seem to find a good post on this to answer my question:
>
> Does anyone know a good way to (re)write BLAST reports in XML format?
> I've got about 30,000 reports I need to rewrite for a (good!) piece
> of java software that will only import xml formatted BLAST reports.
> Right now, all mine are plain text.
>
> I don't think bioperl can do this yet, correct? If not, any
> suggestions, besides reblasting all 30,000? I'd like to save a few
> trees and lumps of coal.
>
> TIA,
> Bob

The only BioPerl writers for BLAST reports are in BSML and HTML, not  
BLAST XML.  I don't think there there have been any requests for it,  
and no one has really stepped forward to submit one.

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list