[Biojava-l] Blast-xml parser

[Thomas Down]

On Wed, Mar 06, 2002 at 05:07:17PM +0000, Ewan Birney wrote:
> On Wed, 6 Mar 2002, Jason Stajich wrote:
> 
> > #!/usr/bin/perl -w
> > use strict;
> > 
> > use Bio::SearchIO;
> > use Bio::SearchIO::Writer::HTMLResultWriter;
> > 
> > my $in = new Bio::SearchIO(-format => 'blastxml',
> >                            -file   => shift @ARGV);
> > 
> > my $writer = new Bio::SearchIO::Writer::HTMLResultWriter();
> > my $out = new Bio::SearchIO(-writer => $writer);
> > $out->write_result($in->next_result);
> > 
> 
> <sigh>. That's lovely code. I can't believe you Java guys would really
> want to have to make that an object. 

It's got....  dollar-symbols.  eeeeeeeeeee! ;-)

> <grin>
> Can you beat that BioJava?
> </grin>


    http://cvs.biojava.org/cgi-bin/viewcvs/viewcvs.cgi/biojava-live/demos/eventbasedparsing/Blast2HTML.java?rev=1.3&cvsroot=biojava&content-type=text/vnd.viewcvs-markup


I'm not actually going to paste it in here -- it's slightly
too long to do that sensibly.  That said, most of the lines
are just defining the colours to use for different parts of
the document, etc.

Give it a whirl, anyway,

     Thomas.