[BioRuby] Error reading GenBank file

Toshiaki Katayama k at bioruby.org
Tue Dec 6 22:37:42 EST 2005

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)
> 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?

Toshiaki Katayama

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