[BioRuby] Error reading GenBank file

[Toshiaki Katayama]

On 2005/12/06, at 21:21, Urban Hafner wrote:
> Hej,
> I'm trying to read a GenBank file like this:
>
> ff = Bio::FlatFile.auto(filename)
> ff.each_entry |gb|

  ff.each_entry do |gb|

>   p gb.naseq
> end
>
> What I get is not the sequence object but this error:
>
> /home/users/hafner/lib/site_ruby/1.8/bio/db.rb:223:in `tag_cut':
> undefined method `[]=' for nil:NilClass (NoMethodError)
(snip)
> As an example file take AJ271885:
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=11342587

I could not reproduce this error with this entry.

I suspect that your input file is not in GenBank format but, for example,
saved in HTML or something?

Regards,
Toshiaki Katayama