[Bioperl-l] How put tmp file in the tmp directory when using Bio::Tools::Run::StandAloneBlastPlus?

Chris Fields cjfields at illinois.edu
Sun Jun 6 19:37:32 EDT 2010


You really need to read all relevant documentation prior to firing off emails to the list.  This is answered in the StandAloneBlastPlus installed documentation ('perldoc Bio::Tools::Run::StandAloneBlastPlus'):

 Cleaning up temp files
       Temporary analysis files produced under a single factory instances can
       be unlinked by running


       Tempfiles are generally not removed unless this method is explicitly
       called. "cleanup()" only unlinks "registered" files and databases. All
       temporary files are automatically registered; in particular,
       "anonymous" databases (such as

          -db_data => 'myseqs.fas',
          -create => 1

       without a "-db_name" specification) are registered for cleanup. Any
       file or database can be registered with an internal method:



On Jun 6, 2010, at 5:52 PM, Peng Yu wrote:

> The following perl program generate tmp files at the current
> directory, which is annoying. Is there a way to put the tmp files in a
> tmp directory say /tmp?
> #!/usr/bin/env perl
> use strict;
> use warnings;
> use Bio::Tools::Run::StandAloneBlastPlus;
> use Bio::Perl;
> my $factory = Bio::Tools::Run::StandAloneBlastPlus->new();
> my $seq1 = Bio::Perl::read_sequence('first.fa');
> my $seq2 = Bio::Perl::read_sequence('second.fa');
> print $seq1->seq, "\n";
> print $seq2->seq, "\n";
> my $blast_result=$factory->bl2seq(-method=>'blastn',
>  -query=> $seq1,
>  -subject=> $seq2
> );
> -- 
> Regards,
> Peng
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

More information about the Bioperl-l mailing list