[Bioperl-l] Parsing html blast output?

[Edith Schlagenhauf]

Hi,

I usually let blastcl3 produce the raw text blast output
for parsing and after that use the Bioperl htmlizer.
I don't know if this is more elegant ;-) but I guess
it is less error-prone.

Edith

On Tue, 12 Aug 2003, Wes Barris wrote:

> Hi,
>
> I know it is possible to use the SearchIO functions to parse either
> text blast output or xml blast output.  However, I would like to know
> if it is possible to parse html blast output?  For example, if I wanted
> to parse the output of this command:
>
> blastcl3 -d nr -p blastn -T -i fasta.txt -o blast.html
>
> When I try parsing the above "blast.html" file using example number 4
> from this file:
>
> 	http://bioperl.org/HOWTOs/html/Graphics-HOWTO.html
>
> I get errors.
>
> What I ended up doing is writing a perl "de-htmlizer" that I use to
> convert an html blast output file into a text-only blast output file.
> Then I run the result through a bioperl blast parsing script.  Is
> there a more elegant way to do this?
>
> --
> Wes Barris
> E-Mail: Wes.Barris at csiro.au
>
>
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>


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Dr Edith Schlagenhauf
Bioinformatics
Institute of Plant Biology
University of Zurich
Zollikerstrasse 107
CH-8008 Zurich
SWITZERLAND

e-mail: ediths AT botinst DOT unizh DOT ch
Tel.:	+41 1 634 82 78
Fax :	+41 1 634 82 04

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