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

[Robert Citek]

On Jan 13, 2008 10:02 PM, Gordon Robertson <agrobertson at telus.net> wrote:
> I'm new to BioRuby, so apologize for asking about something that's
> very basic, and that likely was discussed and resolved in the distant
> past.

This is a perfectly valid question.  IMHO, no need to apologize.

> ...
> I find that the example code given at http://dev.bioruby.org/wiki/en/?
> Tutorial.rd immediately forces the input sequence to lowercase -
>    require 'bio'
>    seq = Bio::Sequence::NA.new("atgcATGcaaaa")
>   "atgcatgcaaaa"
> ...
> Is there such a method, or another (simple) way to have upper and
> lower case characters passed through DNA/RNA methods?

I can repeat the phenomenon using bioruby on Ubuntu:

$ ruby -rbio -e 'puts Bio::Sequence::NA.new("atgcATGcaaaa") '
atgcatgcaaaa

How does one preserve the case of the sequence?

Regards,
- Robert