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

[Karin Lagesen]

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?

The error I get is:

  File "/usr/local/python//lib/python2.4/site-packages/Bio/Align/AlignInfo.py", line 389, in pos_specific_score_matrix
    raise ValueError("Residue %s not found in alphabet %s"
ValueError: Residue c not found in alphabet Gapped(IUPACAmbiguousDNA(), '-')


Thanks!

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen at medisin.uio.no
http://folk.uio.no/karinlag