[BioRuby] Bio::Sequence forces a DNA sequence to lowercase?

[Toshiaki Katayama]

On 2008/02/02, at 0:48, Robert Citek wrote:

> On Jan 30, 2008 10:10 AM, Jan Aerts <jan.aerts at bbsrc.ac.uk> wrote:
>> So the 'right' way to do it is to create a Bio::Sequence object as you
>> did above and then attach a Bio::Feature object to it describing the
>> start codon.
>
> On Feb 1, 2008 9:39 AM, Adam Kraut <adamnkraut at gmail.com> wrote:
>> I am also new to Bioruby so there may be a more fitting solution that's
>> already been discussed.
>
> Thanks, Jan and Adam.  Jan's solution is probably the right way.
> Unfortunately, I'm new enough to ruby that I'm not sure how to make
> that work for me.  Adam's solution may not be the "right" way, but it
> works good enough for me for now.


In the current implementation of the Bio::Sequence class,
some methods like 'translate', 'complement', 'molecular_weight', 'names' ...
depends on the case of the sequence. If we re-implement all these methods
to normalize the sequence (internally) before they do the job,
we may conserve the original cases.

Regards,
Toshiaki Katayama