Splitting a concatenated nexus file with biopython

split_concat_nexus.py

from Bio.Nexus import Nexus

aln = Nexus.Nexus()
aln.read('my-properly-formatted-nexus-file.nex')

# assuming your partitions are defined in a charset block like:
#
# begin sets;
# charset bag2 = 1-186;
# charset bag3 = 187-483; 
# charset bche = 484-990;
# end;

# get count of charsets:
len(aln.charsets.keys())

# take a gander at the charsets:
aln.charsets()

# split the concatenated file into charsets files (prepending whatever text you place after filename='')
aln.write_nexus_data_partitions(filename='my', charpartition=aln.charsets)

# this will output in the os.getcwd():
# 
# test_bag2
# test_bag3
# test_bche

Hi Brant
I keep getting this error:

Traceback (most recent call last):
File "", line 1, in
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 640, in read
self._parse_nexus_block(title, contents)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 683, in _parse_nexus_block
raise NexusError('Unknown command: %s ' % line.command)
Bio.Nexus.Nexus.NexusError: Unknown command: format

Seems to be something with my nexus format? Or possibly its not finding the correct file? When I include the full directory before the filename, there is no error, but then "len(aln.charsets.keys())" returns length 0 even though I have 30 charsets in the file. Can you point me in the right direction..? Thanks, --nate