[Bioperl-l] Problems with SearchIO and SearchIO::HTMLResultwr iter

[michael watson (IAH-C)]

Ah, solved by the removal of rather large error in my code.
Sorry.

-----Original Message-----
From: michael watson (IAH-C) [mailto:michael.watson at bbsrc.ac.uk]
Sent: 24 November 2003 14:22
To: 'bioperl-l at bioperl.org'
Subject: [Bioperl-l] Problems with SearchIO and
SearchIO::HTMLResultwriter


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);
}

Thanks
Mick

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