[Bioperl-l] Blast XML Output

[Chervitz, Steve]

Craig,

Yes, I am in fact overhauling Bio::Tools::Blast, and yes it would be nice to
have a parser capable of handling XML-formatted reports. Don't tie it into
the existing Bio::Tools::Blast module, since this is going away (only to
re-surface as a new, improved, more maintainable set of modules ;-). 

Steve

Craig Atkinson [mailto:caa@uvic.ca] wrote:

> I understand nobody is actively maintaining the Blast.pm package...
> (Although --
> http://bio.perl.org/pipermail/bioperl-l/2001-June/005874.html --
> indicates SteveC is still working on an overhaul?)
> 
> Since I am looking at (for work) Blast-XML output parsing ability..
> I figured --what the hey -- see how it might fit into the 
> existing Bioperl
> Blast
> module.
> 
> My thoughts are on creating a Bio::Tools::Blast::XML module that is
> called from Bio::Tools::Blast automatically if XML is recognized or a
> parameter indicates that  the format of the BLAST report is XML.
> Use the XML::Parser module to parse the xml, and return an object
> identical to that of the regular html/txt file parser.
> 
> Although if there are soon to be changes to Blast, perhaps it would be
> better to make it callable directly.
> 
> I've read a few inquiries on the archived mailing list about the
> availability
> of this feature, and I believe it may clear up a few of those 
> bug reports as
> well, as it will reduce the ambiguity of parsing a text file.
> 
> Comments, Suggestions?
> 
> ---------------
> Craig Atkinson
> caa@uvic.ca
> 
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