We have a soln for this in bioperl, consider this script in bioperl (using
the live cvs code or 1.0alpha2-rc this weekend)
#!/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);
---
run like this
% perl htmlwriter.pl file.xml > file.html
On Wed, 6 Mar 2002 [EMAIL PROTECTED] wrote:
> Hi, there,
> I saw your mail, while looking desperately for a possibility to convert blast
> output in xml format back to simple text output for simple biologists like me.
> Any help at any point from anybody? That would be great!
>
> Thanks a lot!
>
> Best wishes
>
> Edda
>
>
>
>
>
> *************************************************************************************
> Wiepert, Mathieu [EMAIL PROTECTED]
> Fri, 8 Jun 2001 07:35:26 -0500
>
> Previous message: [Biojava-l] blast xml parser
> Next message: [Biojava-l] LocationTools + Decoratorated Locations = ?
> Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
>
>
>
> My 2 cents...
>
> Thank you for pointing out jaxb, that looks like just what I need at the
> moment :)
>
> In regards to your other comments, I ditto Simon on the use of the SAX
> framework. Saved me tons of time. When the Biojava SAX components were
> first written, I believe there was no XML format for BLAST outputs from any
> program. When I was adding a little functionality, XML just came to NCBI as
> I was doing it, and GCG didn't have it yet. Now that these things exist,
> you may not even need the Biojava SAX parser if you are comfortable with
> XSLT. The uses I saw with parsing BLAST was to get interesting bits from a
> file to build a datamining tool. I saw my possibilities for dealing with
> Blast output as, among other things,
> - a content handler in java with Biojava SAX2 compliant parser and text
> Blast file
> - a content handler in java with SAX2 compliant parser and XML Blast file
> - a stylesheet in java with XALAN XSLT processor
> - standalone XSLT processor like Saxon against text Blast files with Biojava
> SAX parser plugged in
> - standalone XSLT processor like Saxon against XML BLAST files.
>
> This list is not exhaustive, I am sure, and there are different reasons
> people might want to use them. One reason to go with plain SAX rather than
> XSLT, as Simon has pointed out to me before, is if you have very large blast
> files (and I do), using XSLT is not great. It usually tries to instantiate
> your whole document in memory. A sax parser is then just the trick. There
> are ways around this, but I have not explored them.
>
> I can certainly see possibilities to take blast output (in either form, text
> or XML), and constitute Biojava objects with direct binding, using jaxb, if
> that is what it can do. Al the java solutions above could use that quite
> nicely. So, who wants to volunteer to look into this? :)
>
>
> -mat
>
>
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>
--
Jason Stajich
Duke University
[EMAIL PROTECTED]
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