[Bioperl-l] Using Bio::SearchIO was: StandAloneBlast returning Bio::SearchIO::blast

[Dan Kortschak]

OK I think I'm getting there, however using the lines below (essentially)
I get the follwoing errors back and no HTML:

Can't locate object method "algorithm" via package "Bio::SearchIO::blast" (perhaps you forgot to load "Bio::SearchIO::blast"?) at
/usr/local/share/perl/5.6.1/Bio/SearchIO/Writer/TextResultWriter.pm line 146.
	(in cleanup) Can't use string ("STDOUT") as a symbol ref while "strict refs" in use at
/usr/local/share/perl/5.6.1/Bio/Root/IO.pm line 391.

I have looked through Bio::SearchIO::blast and find no method `algorith'
so I'm not sure where to go from there and secondly (probably more dimly)
I'm trying to output to STOUT since this script is trying to be part of a
web based blast server.

The output section of the script:

my $output=new Bio::SearchIO(-output_format=>'blast',-fh=>STDOUT);

my $report=$blastfactory->blastall(@query);
$output->write_result($report);


thanks for your help
Dan

On Thu, 13 Feb 2003, Ewan Birney wrote:

>
> Got it:
>
>     my $output = Bio::SearchIO->new( -output_format => 'blast', -file =>
> $filename);
>
>     $output->write_result($blast);
>
>
> s/blast/html/ in the output_format, and voila... html

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