[Bioperl-l] Parseing tRNA sequences out of genbank file

[Adam Witney]

Hi,

I am parsing a genbank file and it contains an entry like so...

     tRNA            complement(1326335..1326419)
                     /product="transfer RNA-Leu"
                     /gene="tRNA-Leu"
                     /anticodon="(pos:1326383..1326385,aa:Leu)"
                     /note="tRNA Leu anticodon CAA, Cove score 51.10"


However this code

...
      if($feat->primary_tag eq 'tRNA')
         {         
          my $seq_obj = $feat->seq;
          my $gene_length = length($seq_obj->seq);
 
... 

I get this error

------------- EXCEPTION  -------------
MSG: Sequence is a protein. Cannot revcom
STACK Bio::PrimarySeqI::revcom
/usr/local/lib/perl5/site_perl/5.8.4/Bio/PrimarySeqI.pm:378
STACK Bio::SeqFeature::Generic::seq
/usr/local/lib/perl5/site_perl/5.8.4/Bio/SeqFeature/Generic.pm:613
STACK toplevel ../../1.0b1/sql/scripts/gene_upload.pl:379

--------------------------------------

I am trying to get the DNA sequence corresponding to the tRNA, why does it
think it is a protein sequence? It works fine for tRNA's which aren't on the
reverse strand

Thanks for any help

Adam


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