[Bioperl-l] html stripped from blast report

Brian Osborne brian_osborne at cognia.com
Fri Jul 23 20:27:02 EDT 2004


No, that definitely won't work. I'll remove it from the FAQ and take a

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of ghrose at unm.edu
Sent: Monday, July 19, 2004 4:47 PM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] html stripped from blast report

Dear Bioperl,

I'm trying to use the code in
to strip html out of a blast report that is html format.

******The code


use strict;
use DBI;
use Bio::Perl;
use Bio::SearchIO;
use Bio::SearchIO::blast;
use HTML::Strip;

my $hs = new HTML::Strip;

          # replace the blast parser's _readline method with one that
          # auto-strips HTML:

          sub Bio::SearchIO::blast::_readline {
            my ($self, @args) = @_;
    return $hs->parse($self->SUPER::_readline(@args));

my $in = new Bio::SearchIO(-format => 'blast',
                               -file   => $ARGV[0]);

*******gives me the following error.

georges-Computer:~/Desktop/ben-p020 george$ perl insert_7_4hstrip.pl
p018xnr.html > test3
Can't locate object method "_readline" via package "main" at
insert_7_4hstrip.pl line 17.

I believe I have the HTML::Strip installed correctly.
I'm running this script on macosx10.3.

Can you give me some advise on how to solve this problem?

Thank you,


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