[Bioperl-l] tempfile problem with standalone blast

[Chris Fields]

On Jun 4, 2010, at 10:45 AM, Gopal wrote:

> Hi Chris,
> 
> this is the code. Sorry I did not realize I should post the code:
> 
> 
> ...
>     while( my $input = $seqio_obj->next_seq() ) {
> #    
>      $blast_report = $blast_obj->blastall($input);
>      
>      push(@reports,$blast_report);
>      
>      }
> ...

Yep, you're caching your SearchIO instances here.  No need; if you want to cache you should cache the Result object instead.  Something like 

push(@reports, $blast_report->next_result);

Probably best to rethink this strategy unless you have absolutely no other way to deal with your data, if you have lots of BLAST reports you will suck up memory very quickly.

> -- 
> Gopal Gopinathrao, PhD
> Bioinformaticist / Biologist
> CFSAN, US FDA
> www.patrn.net/patrn
> gopal.gopinathrao at fda.hhs.gov
> P: 301-210-7881


chris