[BioRuby] Error reading GenBank file

Toshiaki Katayama ktym at hgc.jp
Wed Dec 7 04:55:16 EST 2005

On 2005/12/07, at 18:13, Toshiaki Katayama wrote:
> So, it is a problem with Bio::FlatFile module.

Sorry, it was a problem with Bio::GenBank module.

To say more precisely, your file contained 2 entries in logic.
One is a genbank:AJ271885 and the other is empty entry.

>> And that's what I get:
>> Bio::Sequence::NA

This is a result from the first entry,

>> NoMethodError: undefined method `[]=' for nil:NilClass

and this is a error caused by the second entry.

What is the best interface for the empty or incomplete entry?
raise an exception? or just returns empty string?

  irb> gb = Bio::GenBank.new('')
  irb> p gb.naseq
  NoMethodError: undefined method `[]=' for nil:NilClass


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