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

[Mehta, Perdeep]

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