[Bioperl-l] remote blast update

Jason Stajich jason@chg.mc.duke.edu
Mon, 9 Apr 2001 11:29:11 -0400 (EDT)

fine by me, whoever codes it first wins.  I'm looking forward to
reviewing Harold's stuff.

In the big picture we have to make a distinction between the
number of packages required to run something in bioperl.  Pure perl
solutions are always the best because it puts the least burden on users to
install a lot of extra packages - on top of that CPAN modules are an easy
add on - going to CORBA or required Web services makes it even more work
for a user to get it working on their box.  So we have to consider where
we want to draw those lines.  I still think using the biojava code is a
great way to go with this, but if it is too difficult for people to
install then we have to consider the alternatives.  A native perl XML
parser should be relatively easy with the XML:: modules.

More importantly what should be the interface to Blast modules - we have
quite a few methods if you look at the union of methods of
Bio::Tools::Blast and Bio::Tools::BPlite.  What functionality do people
really need?  I'm happy to keep Tools::Blast around if we move it up to
Bio::Root::RootI spec and simplify some parts of the code (don't think we
are trying to kill it SteveC, we just seem to have a hard time maintaining


On Mon, 9 Apr 2001, Wiepert, Mathieu wrote:

> The Biojava Sax package parses quite a few blast outputs, that would be a
> good template to start with if there is a need to port that code.  The
> parser plugs nicely into XSLT processors now as well.  I know that Harold is
> close to having some CORBA work done, so we might just want use the java
> stuff, rather than port it all?
> Also XML output is an easy hop here so we are definitely looking for
> someone to consider writing an XML blast parser - as a BPlite plugin or
> coder's choice.  Maybe we even go to BlastIO/text, BlastIO/xml,
> BlastIO/asn.1 structure?  Blast is pretty much the staple of
> bioinformatics right now so anything we can do to make handling
> reports easier in bioperl is a big plus.
>  - Mat

Jason Stajich
Center for Human Genetics
Duke University Medical Center