[BioRuby] Error reading GenBank file
Toshiaki Katayama
ktym at hgc.jp
Wed Dec 7 06:27:34 EST 2005
On 2005/12/07, at 19:03, Pjotr Prins wrote:
> On Wed, Dec 07, 2005 at 06:55:16PM +0900, Toshiaki Katayama wrote:
>> 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
>
> Why not return a nil? Or raise an exception at initialization if
> illegal tags are not allowed.
>
> Pj.
I just commited a patch to make the following code will work
without errors even if the input file contains an empty entry
(e.g. file attached in Urban's post).
Toshiaki
Bio::FlatFile.auto(ARGF) do |ff|
ff.each_entry do |gb|
# genbank/genbank.rb
p gb.entry_id
p gb.length
p gb.strand
p gb.natype
p gb.circular
p gb.division
p gb.date
p gb.basecount
# genbank/common.rb
p gb.definition
p gb.versions
p gb.accessions
p gb.acc_version
p gb.accession
p gb.version
p gb.gi
p gb.nid
p gb.keywords
p gb.segment
p gb.source
p gb.common_name
p gb.organism
p gb.taxonomy
p gb.references
p gb.comment
p gb.features
p gb.origin
p gb.naseq
end
end
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