[Biopython] Unable to convert alignment to nexus format

[Morten Kjeldgaard]

Hi,

I am getting an exception when trying to output an alignment in nexus
format:

  ValueError: Need a DNA, RNA or Protein alphabet

The alignment is read by AlignIO.read() in fasta format from an output
file written by Muscle, and so the alphabet specified in the sequences
is IUPACProtein. Apparently, NexusIO checks for ProteinAlphabet and thus
fails. I am using BioPython 1.56.

Here is a 4-line test program generating the exception:

from Bio import AlignIO
alignment = AlignIO.read(open("aln.muscle"), "fasta")
g = open("aln.nexus", "w")
g.write (alignment.format("nexus"))


Any (safe) workarounds here?
Cheers,

Morten


-- 
Morten Kjeldgaard, asc. professor, MSc, PhD
BiRC - Bioinformatics Research Center, Aarhus University
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