[Bioperl-l] Parseing tRNA sequences out of genbank file
awitney at sghms.ac.uk
Tue Feb 1 11:26:21 EST 2005
I have just discovered the problem, it was in the header, my original header
looked like this:
LOCUS unknown id 4290252 bp dna linear UNK
And everything is treated as protein. But changing to this
LOCUS unknown 4290252 bp dna linear UNK
So I guess you can't have any spaces in Locus names?
> Very weird - one would probably need to see the genbank file to figure
> out what is going on.
> A quick fix would be to force the sequence to dna first:
> It would be interesting to figure out why the alphabet is being guessed
> as not DNA though.
> Jason Stajich
> jason.stajich at duke.edu
> On Feb 1, 2005, at 7:38 AM, Adam Witney wrote:
>> I am parsing a genbank file and it contains an entry like so...
>> tRNA complement(1326335..1326419)
>> /product="transfer RNA-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
>> STACK Bio::SeqFeature::Generic::seq
>> 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
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