[Bioperl-l] blast2table using SearchIO

Steve Chervitz sac@bioperl.org
Fri, 22 Nov 2002 22:52:58 -0800 (PST)


This particular fix is checked in on the bioperl-live main trunk. I renamed the
method to result_count() to be consistent with our Bio::Search terminology. I
can add in report_count() for backward compatibility.

Yes, convergence is in progress. 

Steve

--- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> It's not going to work until steve and I converge our objects.
> We made different assumptions about the Bio::Search objects' API.  Many
> posting about this on the mailing list.  Steve may have fixed things with
> what is in CVS but I'm not sure.  Something on the checklist before 1.2
> release.
> 
> -jason
> 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> On Fri, 22 Nov 2002, Fernan Aguero wrote:
> 
> > Hi! I am trying some examples from the man/pod docs.
> >
> > The data: a blast report, containing multiple queries
> > against the same database.
> >
> > The goal: get this data in tabular form (tab-delimited).
> >
> > OK, so I know I can parse myself the file and print
> > individual columns myself (I am still used to BPlite and
> > friends), but I saw there were some *TableWriter modules
> > associated with SearchIO, so I tried ...
> >
> > My script (mostly derived from man/pod docs):
> >
> > --- Start script ---
> >
> > use Bio::SearchIO;
> > use Bio::SearchIO::Writer::HitTableWriter;
> >
> > $in			= Bio::SearchIO->new( -format	=>	'blast' );
> > $writer = Bio::SearchIO::Writer::HitTableWriter->new();
> > $out		= Bio::SearchIO->new( -writer	=>	$writer );
> >
> > while ( $result = $in->next_result() ) {
> > 	$out->write_result( $result, ($in->report_count - 1 ? 0 :	1) );
> > 	}
> >
> > --- End script ---
> >
> >
> > And I get this error:
> > Using default column map.
> > Can't locate object method "report_count" via package
> "Bio::SearchIO::blast" (perhaps you forgot to load "Bio::SearchIO::blast"?)
> at /home/fernan/develop/blast2table.pl line 11, <STDIN> line 59.
> > cat: stdout: Broken pipe
> >
> > I only seem to find 'report_count' in psiblast.pm, the other
> > ocurrences are just in pods.
> >
> > Any ideas of what is going on? Maybe I am missing something?
> > Documentation error? Bug?
> >
> > TIA, Fernan
> >
> > --
> > F e r n a n   A g u e r o
> > http://genoma.unsam.edu.ar/~fernan
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
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=====
Steve Chervitz
sac@bioperl.org

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