[BioPython] alignment alphabet problem - upper/lower case?
Karin Lagesen
karin.lagesen at medisin.uio.no
Thu Dec 13 12:30:43 UTC 2007
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
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