[Bioperl-l] Problems with SearchIO and SearchIO::HTMLResultwriter

[Jason Stajich]

On Mon, 24 Nov 2003, michael watson (IAH-C) wrote:

> Hi
>
> I am having trouble using Bio::SearchIO and Bio::SearchIO::HTMLResultWriter - was there a bug in 1.2.2?  If so is it fixed?
>
> I get:
>
> Can't locate object method "algorithm" via package "Bio::SearchIO::blast" at /data/chicken_genome/bioperl-1.2.2//Bio/SearchIO/Writer/HTMLResultWriter.pm line 183, <GEN1> line 545.
>
> When executing the following:
>
> #!/usr/bin/perl
>
> use Bio::SearchIO;
> use Bio::SearchIO::Writer::HTMLResultWriter;
>
> my $searchio = new Bio::SearchIO (-format => 'blast',
>                                  -file   => $blast_report);
>
> my $writerhtml = new Bio::SearchIO::Writer::HTMLResultWriter();
> my $outhtml = new Bio::SearchIO(-writer => $writerhtml,
>                                    -file   => ">searchio.html");
>
> while(my($result) = $searchio->next_result()) {
>    # get a result from Bio::SearchIO parsing or build it up in memory
>    $outhtml->write_result($searchio);
     The method is called 'write_result' so pass in $result
> }
>
> Thanks
> Mick
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu