[Bioperl-l] tempfile problem with standalone blast

[Gopal]

Hi Chris,

I followed your suggestion and changed the loop into:

On Fri, Jun 4, 2010 at 12:44 PM, Chris Fields <cjfields at illinois.edu> wrote:

>
> >     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;




  while( my $input = $seqio_obj->next_seq() ) {
$blast_report = $blast_obj->blastall($input);


        while(my $result=$blast_report->next_result){

Now no objects are cached in arrays.  The script worked fine with one genome
already and the other is running.
thanks for cleaning things up. I will remember to avoid this snag.

best,

-gopal












> 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




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