[Bioperl-l] Blast -- data streams?

Jason Stajich jason.stajich at duke.edu
Thu Nov 3 19:03:29 EST 2005

It does work with streams, nothing in the parsers assumes that it  
needs to be a file.  You pass in -fh to provide a filehandle and - 
file for a file name.

open($fh, "blastp -d nr -i qfile E=1e-5 |") || die $!;
my $in = Bio::SearchIO->new(-fh => $fh, -format=> 'blast');

If you are talking about the the blast wrapper,  
Tools::StandAloneBlast, it creates tempfiles which are either removed  
when the object is destroyed or on the subsequence submit using the  
File::Temp module.

I will reiterate what I've said in the past, Tools::StandAloneBlast  
could DEFINITELY be improved and needs people to adopt it....


On Nov 3, 2005, at 5:09 PM, Renee Halbrook wrote:

> Hi,
> I notice that the Blast web package in bioperl uses a lot of file i/o,
> reading and writing temporary files.
> On a couple of systems I am working with, the problem seems to be  
> that these
> temp files build up, and need to be deleted using a chron job.
> My question is, is there any reason to use file io, rather than  
> working
> directly with data streams?
> Thanks for any feedback,
> Renee
> Renee Halbrook
> Bioinformatics Programmer
> The Carnegie Institution of Washington
> Department of Plant Biology
> 260 Panama Street
> Stanford, CA 94305
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> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

Jason Stajich
Duke University

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