[Bioperl-l] blast2table using SearchIO

[Jason Stajich]

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
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