[Bioperl-l] Newbie: Problems with Bio::SeqIO and TrEMBL

[Heikki Lehvaslaiho]

Harry,

The error message does make sense, but it trires to tell you that the format
is wrong. TrEMBL files are protein files translated from EMBL and they are
in SWISS-PROT format. Try:

my $in  = Bio::SeqIO->new('-file' => "E:\\hum.dat",
                          '-format' => 'swiss');



Yours,
	-Heikki


"Dr. Harry Wild" wrote:
> 
> Hello all,
> 
> I'm trying to read in a TrEMBL file using Bio::SeqIO,
> but it doesn't work. Perl tells me:
> 
> Can't call method "isa" on an undefined value at
> E:/Perl/site/lib/Bio/Annotation.pm line 401, <GEN0> line 22.
> 
> Reading in EMBL files works fine, why doesn't it work with TrEMBL?
> I thought the formats of EMBL and TrEMBL should be the same.
> 
> I use the following code:
> my $in  = Bio::SeqIO->new('-file' => "E:\\hum.dat",
>                          '-format' => 'EMBL');
> my $out = Bio::SeqIO->new('-file' => ">E:\\hum.fasta",
>                          '-format' => 'fasta');
> while ( my $seq = $in->next_seq() ) {$out->write_seq($seq); }
> 
> Thanks for help,
> Harry Wild
> 
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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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