[Bioperl-l] Re: Running BLAST locally

[Jason Stajich]

On Wed, 23 Jan 2002, Simon Chan wrote:

> Hi All,
>
> *** Jason, thanks.  Your sugggestion worked!
>
> So here's the code I've got:
>
> my $factory = Bio::Tools::Run::StandAloneBlast->new ( database => 'refseq', program => 'blastn');
>
> my $seq_in = Bio::SeqIO->new ( -file => 'inputfilename', -format => 'fasta');
>
> my $seq = $seq_in->next_seq();
>
> my $blast_report = $factory->blastall($seq);

This ISA Bio::Tools::BPlite object.

Then see the BPlite documentation as to how to access the data stored in
this object.

>
> So now, I want to parse it.  I'm using BPlite.pm.  From the docs, this is how we use BPlite:
>
> my $report = Bio::Tools::BPlite->new (-fh => \*STDIN);
>
> So $blast_report contains the BLAST output in object form.  How would you pass $blast_report into BPlite?  I've tried outputting
> $blast_report into a file using SeqIO and then inputting it into BPlite -file => "filename" (I know, that's a pretty odd way
> of doing it ;-) and I've also tried using a filehandle to read in value like so:
>
> open (INPUT, "<filename");
> my $report = Bio::Tools::BPlite->new (-fh => \*INPUT);
>
> So how would the non-rookie bio-perl users pass $blast_report into BPlite? :-)  The Pasteur tutorial is very good at showing rookies how to use modules, however, it doesn't spend too much time explaining  them.
>
> Once again, many thanks, All.
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu