[Biopython] convert to interleaved nexus
natassa
natassa_g_2000 at yahoo.com
Tue Mar 26 01:25:43 UTC 2013
Hi,
I am trying to convert a phylip alignment to interleaved nexus and I cannot. Something like:
def Convert_alnformat(alnfile, out, informat, outformat):
alignment=AlignIO.read(alnfile, informat, alphabet=Gapped(IUPAC.unambiguous_dna))
SeqIO.write(alignment,out, outformat)
will give me a sequential nexus, while I can;'t seem to get hold of the write_nexus_data method of the Bio:Nexus:Nexus:Nexus class.
As this is called internally by AlignIO or SeqIO , I am unsure of how to even call it within my function. I tried:
from Bio.Nexus import Nexus
then in the function
Nexus.Nexus.write_nexus_data( alignment,interleave=True)
and I get
TypeError: unbound method write_nexus_data() must be called with Nexus instance as first argument (got MultipleSeqAlignment instance instead)
I understand that the alignment object is not a nexus instance, but I don't see what i should do.
Can you please help?
thanks,
Natassa
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