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

Dr. Harry Wild h.wild@elegene.de
Tue, 12 Mar 2002 13:36:58 +0100


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