[BioRuby] Error reading GenBank file

Urban Hafner urban at bettong.net
Tue Dec 6 07:21:48 EST 2005


Hej,
I'm trying to read a GenBank file like this:

ff = Bio::FlatFile.auto(filename)
ff.each_entry |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)
        from
/home/users/hafner/lib/site_ruby/1.8/bio/db/genbank/common.rb:239:in
`origin'
        from
/home/users/hafner/lib/site_ruby/1.8/bio/db/genbank/genbank.rb:72:in
`naseq'
        from ../additional_mouse_smars.rb:76
        from
/home/users/hafner/lib/site_ruby/1.8/bio/io/flatfile.rb:196:in
`each_entry'
        from ../additional_mouse_smars.rb:75
        from ../additional_mouse_smars.rb:72

As an example file take AJ271885:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=11342587

Urban



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