[Bioperl-l] Bio::Tools::Run::StandAloneBlast

[Jason Stajich]

$blast_result ISA Bio::SearchIO object not a filename.
If you do
print ref($blast_result)

You'll see that StandAloneBlast is returning you a SearchIO object.

-jason

On Thu, 13 Nov 2003, Mehta, Perdeep wrote:

> Thank you. It has worked, but what this statement is for
>
> my $in = new Bio::SearchIO(-format => 'blast',
>                             -file   => $blast_result);
>
> and why the following didn't work;
> write_blast(">roa1.blast",$blast_result);
>
> Thanks to all for responding.
> perdeep
>
> -----Original Message-----
> From: Wes Barris [mailto:wes.barris at csiro.au]
> Sent: Wednesday, November 12, 2003 11:27 PM
> To: Mehta, Perdeep
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Bio::Tools::Run::StandAloneBlast
>
>
> Mehta, Perdeep wrote:
>
> > You are right. I mixed up the things I'm not sure of. I had tried write_blast() also and that also threw errors. Then I thought to try the method with $in ... and drop the write_blast() call altogether. I thought $in... gives more control. However, it didn't as well. Here is the right error message that I got with the code included earlier. I'm sorry for the confusion.
>
> Change these lines:
>
> my $blast_result = $factory->blastall($seq_object);
> # Parse Blast results
> my $in = new Bio::SearchIO(-format => 'blast',
>                             -file   => $blast_result);
> while( my $result = $in->next_result ) {
>
> to this:
>
> my $blast_result = $factory->blastall($seq_object);
> # Parse Blast results
> while( my $result = $blast_result->next_result ) {
>
>
> >>test2.pl
> >
> > ------------- EXCEPTION  -------------
> > MSG: Could not open Bio::SearchIO::blast=HASH(0x140b4c910) for reading: No such file or directory
> > STACK Bio::Root::IO::_initialize_io /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm:260
> > STACK Bio::Root::IO::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/Root/IO.pm:206
> > STACK Bio::SearchIO::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/SearchIO.pm:123
> > STACK Bio::SearchIO::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/SearchIO.pm:155
> > STACK toplevel test2.pl:21
> > --------------------------------------
> >
> > Also isn't that $blast_result contains the result from blastall search.
> >
> > Thanks,
> > perdeep
> >
> > 	-----Original Message-----
> > 	From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
> > 	Sent: Wed 11/12/2003 6:18 PM
> > 	To: Mehta, Perdeep
> > 	Cc: bioperl-l at bioperl.org
> > 	Subject: Re: [Bioperl-l] Bio::Tools::Run::StandAloneBlast
> >
> >
> >
> > 	Are you SURE you're running the same script which giving that error - you
> > 	must be missing the write_blast() call in your code.
> >
> > 	The problem seems to be whereever you are calling write_blast, you are
> > 	passing in $in (A Bio::SearchIO::blast object) NOT $result (A
> > 	Bio::Search::Result::ResultI object).
> >
> >
> > 	-jason
> >
> > 	On Wed, 12 Nov 2003, Mehta, Perdeep wrote:
> >
> > 	> Hi,
> > 	>
> > 	> I'm struggling to find the reason why my following test code to parse Blast output is not functioning. Just beginning to learn Bioperl and couldn't figure out what's missing.
> > 	>
> > 	> #!/usr/bin/perl -w
> > 	> #
> > 	> use strict;
> > 	>
> > 	> use Bio::Perl;
> > 	> use Bio::Tools::Run::StandAloneBlast;
> > 	> use Bio::SearchIO;
> > 	>
> > 	>   # this script will only work with an internet connection
> > 	>   # on the computer it is run on
> > 	>
> > 	>   # Get the protein sequence
> > 	>    my $seq_object = get_sequence('swissprot',"ROA1_HUMAN");
> > 	>
> > 	>   # Set database to search against
> > 	>    my $DB = "/refseqdb/complete/rs_rel2";
> > 	>
> > 	>   # Create factory for stand alone Blast and search
> > 	>    my @params = ('program'  => 'blastp','database' => $DB);
> > 	>    my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
> > 	>    my $blast_result = $factory->blastall($seq_object);
> > 	>
> > 	>   # Parse Blast results
> > 	>    my $in = new Bio::SearchIO(-format => 'blast',
> > 	>                               -file   => $blast_result);
> > 	>    while( my $result = $in->next_result ) {
> > 	>       while( my $hit = $result->next_hit ) {
> > 	>         while( my $hsp = $hit->next_hsp ) {
> > 	>           if( $hsp->length('total') > 100 ) {
> > 	>             if ( $hsp->percent_identity >= 75 ) {
> > 	>                 print "Hit= ",        $hit->name,
> > 	>                       ",Length=",     $hsp->length('total'),
> > 	>                       ",Percent_id=", $hsp->percent_identity, "\n";
> > 	>            }
> > 	>           }
> > 	>         }
> > 	>       }
> > 	>    }
> > 	>
> > 	> exit;
> > 	>
> > 	> Blastall runs fine though. Error appears to be Blast result parsing related. Here is the error message that I get;
> > 	> >test.pl
> > 	> Can't locate object method "algorithm" via package "Bio::SearchIO::blast" (perhaps you for
> > 	> got to load "Bio::SearchIO::blast"?) at /usr/local/lib/perl5/site_perl/5.6.1/Bio/SearchIO/
> > 	> Writer/TextResultWriter.pm line 146, <STREAM> line 197.
> > 	>
> > 	> Thank you in advance for any help.
> > 	> perdeep
> > 	>
> > 	> Perdeep K. Mehta, PhD
> > 	> Hartwell Center for Bioinformatics & Biotechnology
> > 	> St. Jude Children's Research Hospital
> > 	> Memphis, TN 38105-2794
> > 	> Tel: 901-495 3774
> > 	> http://www.hartwellcenter.org
> > 	>
> > 	>
> > 	>
> > 	> _______________________________________________
> > 	> Bioperl-l mailing list
> > 	> Bioperl-l at portal.open-bio.org
> > 	> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > 	>
> >
> > 	--
> > 	Jason Stajich
> > 	Duke University
> > 	jason at cgt.mc.duke.edu
> >
> >
> >
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
>

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