Bioperl: Blast.pm as BLAST filter?

[Steve Chervitz]

Christian,

Sorry to let you down here, but the Bioperl Blast object doesn't
generate Blast report output. This sort of display functionality
hasn't been a major focus for this module, which is primarily intended
for analysis of the data in the report. There are lots of things you
might want to do with the output, and I thought they were best left
for a different module (to be written).

Steve Chervitz
sac@neomorphic.com


Christian Gruber writes:
 > Hello!
 > 
 > I have a problem concerning BioPerl::Tools::Blast.
 > 
 > I'd like to take a huge BLAST result file, parse it using this class,
 > filter the hits that are interesting, and then print it in the
 > 'natural' BLAST output format.
 > 
 > The first three steps work fine (and really easily!!), but what does
 > not work as easily is the printing of the Blast object. There is a
 > method "to_html" that does kind-of what I mean, but I'd like it in raw
 > text format, like BLAST has produced. Just with a few hits missing.
 > 
 > So: Is there an easy way to print a Bio::Tools::Blast object?
 > 
 > 
 > Thanks in advance
 > 
 > Christian Gruber
 > 
 > 
 > --
 > Christian Gruber      gruber@mips.biochem.mpg.de
 >                       Tel: +49 - 89 / 8578-2663
 > MIPS - Munich Information Center for Protein Sequences
 > http://www.mips.biochem.mpg.de
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