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

[Adam Witney]

Hi Jason,

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

Fixes it....

So I guess you can't have any spaces in Locus names?

Cheers

Adam


> 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:
> $seq->alphabet('dna');
> 
> It would be interesting to figure out why the alphabet is being guessed
> as not DNA though.
> 
> -jason
> 
> 
> --
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
> 
> On Feb 1, 2005, at 7:38 AM, Adam Witney wrote:
> 
>> 
>> Hi,
>> 
>> I am parsing a genbank file and it contains an entry like so...
>> 
>>      tRNA            complement(1326335..1326419)
>>                      /product="transfer RNA-Leu"
>>                      /gene="tRNA-Leu"
>>                      /anticodon="(pos:1326383..1326385,aa:Leu)"
>>                      /note="tRNA Leu anticodon CAA, Cove score 51.10"
>> 
>> 
>> However this code
>> 
>> ...
>>       if($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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> 


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