[Bioperl-l] AlignIO problems

Stephen Henderson s.henderson@ucl.ac.uk
Tue, 19 Jun 2001 17:48:04 +0100


I am having problems using the AlignIO functions for file-type conversion 
running this program in my Bioperl-0.7 folder

#!/usr/local/bin/perl 
use Bio::AlignIO;


$in = BIO::AlignIO -> new(	-file => "clustalj2.msf",
                         	 	-format => 'msf');

$out = BIO::AlignIO ->new(	-file => ">clustalj2.fas",
                          		-format => 'fasta');


        while (my $aln = $in->next_aln())
        {
                $out-> write_aln($aln);
        }

Results in the following error message:

Can't locate object method "new" via Package "BIO::AlignIO" (perhaps you
forgot to load "BIO::AlignIO"?) at align.pl line 5

Does anybody know what this means? 
-(other packages I have tried seem to work OK 
eg. use BIO::Seq;, use BIO::SeqIO; use BIO::DB::GenBank--are all OK but not
AlignIO in this case)