[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.
-jason
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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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
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