[Bioperl-l] Bio::Tools::Blast.pm & unacceptable memory usage

[Jason Stajich]

Charles -
Don't use Bio::Tools::Blast it is deprecated.

use Bio::SearchIO or Bio::Tools::BPlite.

-jason

On 13 Aug 2002, Charles Hauser wrote:

> Hi,
>
> I am new to using bioperl and would like to parse large numbers of blast
> reports.  I read at:
> http://doc.bioperl.org/bioperl-live/Bio::Tools::Blast
>
> Parsing large numbers of Blast reports (a few thousand or so) with
> Bio::Tools::Blast.pm may lead to unacceptable memory usage situations.
> This is somewhat dependent of the size and complexity of the reports.
> ...snip...
> When using the parse_blast.pl or parse_multi.pl scripts in
> examples/blast/ of the bioperl distribution), don't supply
> a -signif command-line parameter.
>
>
> I tried to run parse_multi.pl with -signif 1e-25 and the job died.  Is
> there a fix for this problem?
>
> regards,
>
> Charles
>
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu