[Bioperl-l] blast2table using SearchIO

[Leonardo Marino-Ramirez]

Fernan,

I just found out about this feature and you and others may like it ...

If you are running BLAST locally, try including the -m 9 flag when you run
your blast searches.

Example:

blastall -i <your_sequence> -d <your_db> -p <your_blast_program> -m 9

Leonardo


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
>
>