[Bioperl-l] how to delete temporary files when running standaloneblast

[Jason Stajich]

this was fixed after the release - add
$self->_io_cleanup();

In the _setinput method
sub _setinput {
    my ($self, $executable, $input1, $input2) = @_;
    my ($seq, $temp, $infilename1, $infilename2,$fh ) ;
#  If $input1 is not a reference it better be the name of a file with
#  the sequence/ alignment data...
>>>>>    $self->_io_cleanup();

  SWITCH:  {

...


Or checkout the latest branch version of the module with
% cvs -d:pserver:cvs@cvs.open-bio.org:/home/repository/bioperl export -r
branch-1-0-0 bioperl-live/Bio/Tools/Run/StandAloneBlast.pm

and pop that into your src tree.
Can also navigate to that version through the website cvs.open-bio.org if
you like.

-j

On Thu, 18 Apr 2002, Marc Logghe wrote:

> Hi all,
> Using one factory object I run through a multiple fasta file, blasting every
> sequence using the same factory object.
> Since the factory object is still in scope (till the script ends) all
> temporary blast output files (one per query sequence) are kept. They are
> deleted as soon as the factory objects is out of scope. (At least that is
> what I expect, because it is still running). How can I force to delete the
> temporary file as soon as the blast output has been parsed ?
> TIA
> Marc
>
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>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu