[Bioperl-l] XML Blast parsing?

[Aaron J Mackey]

I've written up some XML::Twig-using scripts to get at data in Blast XML
output ... none of them build up BioPerl Blast hit objects, but you easily
could - Twig has the advantage of not putting the entire document into
memory before you start using it (i.e. it streams nicely).

I don't have the scripts handy at the moment, but I can post them later if
people are interested ...

-Aaron

On Fri, 25 May 2001, Todd Richmond wrote:

> Anybody working on XML Blast parsing? I've written a small hack with
> XML::Simple for parsing single Blast XML files, but it would be nice to
> incorporate this into bioperl in a more seamless way, like say:
>
> my @params = ('database' => $database, 'program' => 'blastx',
>     'format' => 'XML', '_READMETHOD' => 'BlastXML');
> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>
> If I wanted to do this, is it best to try to incorporate it like this? I'm
> thinking it would be relatively easy to duplicate the current Blast parser
> because the majority of the work there seems to be finding the right regular
> expression to correctly parse the report (which the XML format should
> eliminate). Or am I being too naïve?
>
> Todd
>
>

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