[Bioperl-l] results problem with StandAloneBlast

Sendu Bala sb at mrc-dunn.cam.ac.uk
Mon Jun 5 10:13:03 EDT 2006


Jason Stajich wrote:
> It depends on how you have run StandAloneBlast -- if the stream you are 
> dealing with is not a file, but a datastream as in the STDOUT from 
> BLAST, then the seek won't work (as it wouldn't work for a zcat on 
> gzipped file).  I think the default StandAloneBlast behavior is to 
> operate on a STDOUT stream so seeking won't work no matter what.

As far as I can see, when you say blastall() on a StandAloneBlast, it 
eventually does:

if ($self->_READMETHOD =~ /^(Blast|SearchIO)/i )  {
     $blast_obj = Bio::SearchIO->new(-file=>$outfile,
			            -format => 'blast' );
}

So seeking should work? Tools like StandAloneBlast creating temp files 
for their results prior to parsing is actually one of things I don't 
like about the bioperl tool system.


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