[Bioperl-l] Blast XML Output

[Craig Atkinson]

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