[Bioperl-l] AlignIO problems

[Heikki Lehvaslaiho]

Stephen,

There is a small (duplicated) typo in your script. 
'BIO::AlignIO' should be 'Bio::AlignIO'. Note the case in Bio.
Fix it and your script will fly.

	-Heikki

Stephen Henderson wrote:
> 
> 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)
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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