[Bioperl-l] SearchIO and WU-BLAST ....

[Steve Chervitz]

In the meantime, try creating the SearchIO object with '-format' => 'psiblast'.
This uses a different parser which should support WU-BLAST. 

Steve

--- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> 
> The code was best tested on NCBI blast output - can you send a blast
> report which causes this behavior and I'll see what patch is needed.
> Your version of wu-blast is helpful too.
> 
> -j
> On Tue, 26 Mar 2002 morgarws@mh.us.sbphrd.com wrote:
> 
> >
> > I'm having a problem with the SearchIO module and parsing WashU Blast
> output
> > .. The SearchIO parser is skipping groups of HSPs that have been combined,
> > i.e. the only HSPs that are found are those where the P(N) is P(1). Is this
> a
> > known problem with SearchIO or have I missed something (likely)? Here is
> some
> > code that doesn't work for hits that have more than 1 HSP combined:
> >
> > use Bio::SearchIO;
> >
> > my $searchio = Bio::SearchIO->new('-format' => 'blast',
> > 				  '-file' => 'gbfunc-test.fasta.out');
> > while (my $result = $searchio->next_result()) {
> >
> > # Get info about the entire report
> >     print "DB: " .  $result->database_name . "\n";
> >
> > # get info about each hit
> >     my ($hit, $hsp);
> >     while ($hit = $result->next_hit) {
> > 	my $hit_name = $hit->name ;
> > 	my $hit_description = $hit->description;
> > 	my $hit_rawscore = $hit->raw_score;
> > 	my $hit_length = $hit->length;
> > 	my $hit_significance = $hit->significance;
> > 	print "Hit: [$hit_name] [$hit_description]\n      [$hit_rawscore]
> > [$hit_length] [$hit_significance]\n";
> >
> > # get info about the hsp(s) of the hit
> > 	while ($hsp = $hit->next_hsp()) {
> > 	    my $hsp_part;
> > 	    my $hsp_percent_id = $hsp->percent_identity();
> > 	    my $hsp_length = $hsp->length();
> > 	    print "  HSP: [$hsp_percent_id] [$hsp_length]\n";
> > 	}
> >     }
> > }
> >
> > Regards,
> >
> > Bill Morgart
> > morgarws@Molbio.sbphrd.com
> >
> >
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
> _______________________________________________
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> Bioperl-l@bioperl.org
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=====
Steve Chervitz
sac@bioperl.org

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