[BioPython] alignment alphabet problem - upper/lower case?

[Peter]

Karin Lagesen wrote:
> I have an alignment that I read in with :
>
> alignment = Clustalw.parse_file(infile, alphabet=IUPAC.IUPACAmbiguousDNA())
>
> This works fine with upper case alignments.
>
> However, I am now working with alignments that are in lower case. I
> would still like to use the same alphabet, but I don't know how to get
> it to accept lower case?

You can't use the *same* alphabet, because IUPAC.IUPACAmbiguousDNA()
is explicitly defined with upper case letters.  You need to use a
different alphabet - either a generic DNA alphabet where the letters
are not specified, or create a lower case equivalent of
IUPAC.IUPACAmbiguousDNA().

Peter