[BioRuby] Bio::Sequence and Bio::Sequence::NA

[Toshiaki Katayama]

Hi Anthony,

Bio::Sequence is a generic container class for a sequence with features which was
introduced relatively recently for interconversion of Bio::GenBank, Bio::EMBL and
Bio::SQL sequence objects (and it also provides common APIs for those seq objects).

Bio::Sequence#na or #auto method extract a sequence from a Bio::Sequence object, so
you should use another variable to store (instead of overriding the object reference).

> biosequence = biosequence.auto

seq = biosequence.auto

so that you can still access to biosequence.features.

% bioruby
bioruby> embl = Bio::EMBL.new(open("http://togows.dbcls.jp/entry/embl/J00231").read)
bioruby> embl.class
  ==> Bio::EMBL
bioruby> embl_bioseq = embl.to_biosequence
bioruby> embl_bioseq.class
  ==> Bio::Sequence
bioruby> embl_seq = embl_bioseq.auto
bioruby> embl_seq.class
  ==> Bio::Sequence::NA

Toshiaki


On 2011/05/16, at 18:07, Anthony Underwood wrote:

> Here's something that has alway puzzled me about BioRuby
> 
> If I start with a Bio::EMBL object and want to extract the features I can do the following
> 
> biosequence = embl_object.to_biosequence
> 
> This returns an instance of a Bio::Sequence class. I can now access the features
> 
> features = biosequence.features
> 
> However if the sequence is nucleotide and I want to translate it I have to do the following
> 
> biosequence.na 
> 
> OR
> 
> biosequence = biosequence.auto
> 
> 
> This returns a Bio::Sequence::NA instance and I can now translate
> 
> protein = biosequence.translate(1,11)
> 
> 
> Why can I not now get at the features
> 
> biosequence.features #=> undefined method `features' for #<Bio::Sequence::NA:0x00000100cae5f8>
> 
> 
> I would have though that after converting to Bio::Sequence::NA or Bio::Sequence:AA the methods available to Bio::Sequence should still be available.
> 
> Can anyone tell me what's going on here. Is there another method I should use?
> 
> 
> Thanks
> 
> Anthony
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