[Bioperl-l] About Bio::DB::GenBank!

[yaofx]

Upgrade to 1.2.2 and it works well.

Thanks a lot!!!

Fengxia


Jonathan Manning wrote:

> I just encountered the same error. It looks like both Bio::DB::GenBank 
> and Bio::DB::GenPept search the protein database. So, Bio::DB::GenBank 
> is not returning anything when you query for an accession.
>
> To verify this, change:
> my $gb = new Bio::DB::GenBank;
> to:
> my $gb = new Bio::DB::GenBank(-format => 'fasta',
>                 -verbose => 1);
>
> For me, this prints:
> url is 
> http://www.ncbi.nih.gov/entrez/eutils/efetch.fcgi?rettype=fasta&db=protein&id=AC068609&tool=bioperl&retmode=text&usehistory=n 
>
>
> Sure enough, visiting this gives me a blank page. However, if I 
> substitute 'db=nucleotide' for 'db=protein' in that url, it works.
>
> This bug seems to exist in 1.2 and 1.2.1, but I think is fixed in 
> 1.2.2. (at least in the CVS head I checked...)
>
> Either upgrade to 1.2.2 or edit Bio/DB/GenBank.pm and change 'protein' 
> to 'nucleotide' in the BEGIN block.
>
> ~Jonathan
>