[Bioperl-l] Saving BLAST reports

Jason Stajich jason at cgt.duhs.duke.edu
Wed Jun 25 13:05:05 EDT 2003

Sure - that's the point and quite often people run the analysis separately
from the parsing.

i.e. I might do
% blastp -i sequences.fas -d swissprot E=0.01 -o myseqs.BLASTP

The I have a script
% cat parsescript.pl
#!/usr/bin/perl -w
use strict;
use Bio::SearchIO;

my $parser = new Bio::SearchIO(-file => 'myseqs.BLASTP',
                               -format => 'blast');
# parser is a SearchIO object
while( my $result = $parser->next_result ) {

Now if you still want to run your standaloneblast and have it also save
that file as well as give you the report, then just provide a
'-o' parameter to StandAloneBlast - it will write the output to that file
(but NOT append mind you) and instantiate a SearchIO object using that
file as well.  It should *NOT* be cleaned up when the StandAloneBlast
object is cleaned up, whereas temporary files (created when you don't
provide a -o option) are.


On Wed, 25 Jun 2003, Michael R Olson wrote:

> Is there any (not hideously difficult) way to retrieve information about
> a BLAST report after the process dies?  That said, let me rephrase the
> question.  My program, right now, runs a blast search using
> StandAloneBlast.pm.  It gets the results as a SearchIO object, and deals
> with them however is appropriate, no problem.  However, what I would
> like to be able to do, is the next time I run the program, be able to
> read in information from a file to recreate the SearchIO object, rather
> than run the BLAST search again.  Is this possible?
> Thanks
> Mike
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> Bioperl-l at portal.open-bio.org
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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