More Python issues

This time completely unrelated to Phycas. I've been using Biopython to concatenate several nexus files that share some taxa into one nexus file. This is something I have been doing on my Mac, but I have been attempting this again on my new (to me) PC. After installing Python and Biopython, I tried to run the script with the appropriate modifications for the nexus files I am attempting to combine. I immediately ran into some issues.


getattr(self,'_'+line.command)(line.options)
AttributeError: 'Nexus' object has no attribute '_mitochondrial'']'

Considering my script (below) has no mention of mitochondrial, nor does Nexus.py in the Biopython package, this must be something about the nexus files themselves. When I look in the nexus file, it is divided into a taxa block and a character block. If I combine the two into a single data block and remove all of the information in the taxa block (other than the number of taxa, which I leave in the dimensions of the data block), everything works smoothly!

I don't know if this is related to the Mac/PC switch or whether it was just something about the newer version of Biopython, but I am glad it works.



from Bio.Nexus import Nexus

handles = [open('COI.nex', 'r'), open('cytb.nex','r'), open('RAG1.nex','r')]
  
nexi =  [(handle.name, Nexus.Nexus(handle)) for handle in handles]

combined = Nexus.combine(nexi)
combined.write_nexus_data(filename='COMBINED.nex')