This package provides functionality to read and write the NEXUS file format as specified in
Maddison, Swofford, and Maddison (1997). "NEXUS: An extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. doi:10.1093/sysbio/46.4.590
Rather than trying to rip out relevant portions of a NEXUS file as quickly as possible, the implementation
in commonnexus tries to do "the right thing" according to the specification, i.e. parse a file token by
token. Thus, we sacrifice speed for correctness and the ability to support weird edge cases like
Comments do not break tokens. Thus,
AssuMP[comment]TiONSis processed asASSUMPTIONS.
Install commonnexus from PyPI:
pip install commonnexuscommonnexus provides a Python API as well as a shell command
to manipulate (the data in) NEXUS files.
In particular, it allows reading NEXUS
>>> from commonnexus import Nexus
>>> nex = Nexus.from_file('docs/characters.nex')
>>> nex.CHARACTERS.get_matrix()['t1'].values()
odict_values(['1', '0', '0', '1', '0', '1', '0', '0', '0', '0'])and writing NEXUS
>>> from commonnexus import Nexus
>>> from commonnexus.blocks import Data
>>> nex = Nexus.from_file('docs/characters.nex')
>>> print(Nexus.from_blocks(Data.from_data(nex.CHARACTERS.get_matrix())))
#NEXUS
BEGIN DATA;
DIMENSIONS NCHAR=10;
FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS="01";
MATRIX
t1 1001010000
t2 0101000100
t3 0011101010
t4 0001100001
t5 0001100001
;
END;Installing the commonnexus package will also install a command line interface commonnexus, which provides several
sub-commands to manipulate NEXUS files.
Run commonnexus -h to get an overview of available sub-commands or find detailed documentation
with examples on ReadTheDocs.
The Python API tries to convert NEXUS constructs to appropriate Python objects, e.g.
- NEXUS content is a
listofCommandobjects, - missing states in a CHARACTERS MATRIX are conveyed as
Nonevalues, etc.
This allows for dealing with NEXUS data in a way that is abstracted from the NEXUS formatting conventions
For a detailed documentation of the Python API, refer to the docs on ReadTheDocs.