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 commonnexus
commonnexus 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.
list of Command objects,None values, 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.
FAQs
A nexus (phylogenetics) file reader and writer (.nex, .trees)
We found that commonnexus demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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