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

[Anthony Underwood]

Dear Toshiaki

Thank you for your reply.

I have just tested your code below and all worked OK. I have
found unexpectedly that embl_bioseq.translate works even though
embl_bioseq.methods does not list translate as an available method.
What extra methods does a Bio::Sequence::NA object instantiated using the
auto method give?

Thanks again for your advice, Anthony

On 17 May 2011 02:33, Toshiaki Katayama <ktym at hgc.jp> wrote:

> 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
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
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> > BioRuby at lists.open-bio.org
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>
>