commonnexus 2.0.0

A nexus (phylogenetics) file reader and writer (.nex, .trees)

commonnexus

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]TiONS is processed as ASSUMPTIONS.

Install

Install commonnexus from PyPI:

pip install commonnexus

Overview

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;

Command line usage

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.

Python API

The Python API tries to convert NEXUS constructs to appropriate Python objects, e.g.

• NEXUS content is a list of Command objects,
• missing states in a CHARACTERS MATRIX are conveyed as 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.

See also

• https://doi.org/10.1093/sysbio/46.4.590
• https://github.com/dlce-eva/python-nexus
• http://wiki.christophchamp.com/index.php?title=NEXUS_file_format