https://github.com/mmore500/alifedata-phyloinformatics-convert
alifedata-phyloinformatics-conversion helps apply traditional phyloinformatics software to alife standardized data
https://github.com/mmore500/alifedata-phyloinformatics-convert
Last synced: about 1 month ago
JSON representation
alifedata-phyloinformatics-conversion helps apply traditional phyloinformatics software to alife standardized data
- Host: GitHub
- URL: https://github.com/mmore500/alifedata-phyloinformatics-convert
- Owner: mmore500
- License: mit
- Created: 2022-03-04T04:25:04.000Z (about 3 years ago)
- Default Branch: master
- Last Pushed: 2025-02-23T23:21:34.000Z (3 months ago)
- Last Synced: 2025-04-30T10:13:12.374Z (about 1 month ago)
- Language: Python
- Homepage: https://alifedata-phyloinformatics-convert.readthedocs.io.
- Size: 458 KB
- Stars: 1
- Watchers: 1
- Forks: 3
- Open Issues: 7
-
Metadata Files:
- Readme: README.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE
- Citation: CITATION.cff
- Authors: AUTHORS.rst
Awesome Lists containing this project
README
alifedata-phyloinformatics-convert
==================================
.. image:: https://img.shields.io/pypi/v/alifedata-phyloinformatics-convert.svg
:target: https://pypi.python.org/pypi/alifedata-phyloinformatics-convert
:alt: PyPI Status
.. image:: https://github.com/mmore500/alifedata-phyloinformatics-convert/actions/workflows/CI.yml/badge.svg
:target: https://github.com/mmore500/alifedata-phyloinformatics-convert/actions/workflows/CI.yml
:alt: CI Status
.. image:: https://readthedocs.org/projects/alifedata-phyloinformatics-convert/badge/?version=latest
:target: https://alifedata-phyloinformatics-convert.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://zenodo.org/badge/466241441.svg
:target: https://zenodo.org/doi/10.5281/zenodo.10701178
alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data
* Free software: MIT license
* Documentation: https://alifedata-phyloinformatics-convert.readthedocs.io.
Usage
-----
Use :code:`apc`'s :code:`RosettaTree` interface for flexible conversion between phylogenetic data structures and schemas.
First, create a :code:`RosettaTree` object from any supported structure/schema
.. code-block:: python3
import io
import pathlib
import alifedata_phyloinformatics_convert as apc
import anytree
import Bio
import dendropy
import ete3 as ete
import networkx
import pandas
import phylotrackpy
import treeswift
newickstr = "((A,B),(C,D));"
for obj in [
anytree.AnyNode(),
Bio.Phylo.read(io.StringIO(newickstr), "newick"),
dendropy.Tree.get(data=newickstr, schema="newick"),
ete.Tree(newickstr),
treeswift.Tree.read_tree_newick(newickstr),
networkx.DiGraph(),
pandas.DataFrame({"id": [0], "ancestor_list": "[None]"}), # alife standard
phylotrackpy.systematics.Systematics(lambda x: x),
]:
converter = apc.RosettaTree(obj)
# from phyloinformatics schema
# ... nexml and nexus also supported!
converter = apc.RosettaTree.from_newick(newickstr)
converter = apc.RosettaTree.from_newick(pathlib.Path("read.newick"))
with open("read.newick", "r") as fp:
converter = apc.RosettaTree.from_newick(fp)
# from alife standard data via Pandas
converter = apc.RosettaTree(pandas.read_csv("read-alifestd.csv"))
Then, convert or serialize data
.. code-block:: python3
# ... converter created as above
converter.as_alife # pandas DataFrame
converter.as_biopython
converter.as_dendropy
converter.as_ete
converter.as_networkx
converter.as_phylotrack
converter.as_treeswift
# serialization, nexml and nexus schemata also supported
converter.to_newick() # returns newick string
converter.to_newick(pathlib.Path("write.newick")) # writes to path
with open("write.newick", "w") as fp: # writes to file object
converter.to_newick(fp)
# alifestd serialization
converter.as_alife.to_csv("write-alifestd.csv", index=False)
Use :code:`apc`'s functional interface to convert between alife format other libraries' tree objects
.. code-block:: python3
import alifedata_phyloinformatics_convert as apc
import pandas
alife_df = pandas.read_csv('alifedata.csv')
# biopython
tree = apc.alife_dataframe_tobiopython_tree(alife_df)
frame = apc.biopython_tree_to_alife_dataframe(tree)
# dendropy
tree = apc.alife_dataframe_to_dendropy_tree(alife_df)
frame = apc.dendropy_tree_to_alife_dataframe(tree)
# ete
ete_tree = apc.alife_dataframe_to_ete_tree(alife_df)
frame = apc.ete_tree_to_alife_dataframe(tree)
# networkx
digraph = apc.alife_dataframe_to_networkx_digraph(alife_df)
frame = apc.networkx_digraph_to_alife_dataframe(digraph)
# phylotrackpy
systematics = apc.alife_dataframe_to_phylotrack_systematics(alife_df)
frame = apc.phylotrack_systematics_to_alife_dataframe(systematics)
# treeswift
treeswift_tree = apc.alife_dataframe_to_treeswift_tree(alife_df)
frame = apc.treeswift_tree_to_alife_dataframe(tree)
# partial support is also included for,
# - adjacency lists
# - anytree trees
# - scipy linkage matrices
# ... see API documentation for details
Command Line Interface
----------------------
Use :code:`apc`'s CLI :code:`toalifedata` command to convert newick, nexml, and nexus data to alife standard phylogenetics data
.. code-block:: bash
Usage: alifedata-phyloinformatics-convert toalifedata [OPTIONS]
convert standard alife phylogeny data to phloinformatics format
Options:
--input-file FILENAME phyloinformatics data file path; default
stdin
--input-schema TEXT phyloinformatics data format schema; options
include newick, nexml, and nexus [required]
--output-file FILENAME alife data file path; default stdout
--output-format TEXT alife data file format; default csv
--suppress-unifurcations / --keep-unifurcations
Compress sequences of nodes with single
descendants
--help Show this message and exit.
Use the :code:`fromalifedata` command to convert to other formats from alife standard phylogenetics data
.. code-block:: bash
Usage: alifedata-phyloinformatics-convert fromalifedata [OPTIONS]
convert phloinformatics data to standard alife phylogeny format
Options:
--input-file FILENAME alife data file path; default stdin
--input-format TEXT alife data file format; default csv
--output-file FILENAME phyloinformatics data file path; default
stdout
--output-schema TEXT phyloinformatics data format schema; options
include newick, nexml, and nexus [required]
--suppress-unifurcations / --keep-unifurcations
Compress sequences of nodes with single
descendants
--help Show this message and exit.
Installation
------------
Install from PyPi
.. code-block:: bash
pip3 install alifedata-phyloinformatics-convert
Citing
------
If alifedata-phyloinformatics-convert is used in scientific publication, please cite it as
Matthew Andres Moreno and Santiago Rodriguez Papa. (2024). mmore500/alifedata-phyloinformatics-convert. Zenodo. https://doi.org/10.5281/zenodo.10701178
.. code:: bibtex
@software{moreno2024apc,
author = {Matthew Andres Moreno AND Santiago {Rodriguez Papa}},
title = {mmore500/alifedata-phyloinformatics-convert},
month = feb,
year = 2024,
publisher = {Zenodo},
doi = {10.5281/zenodo.10701178},
url = {https://doi.org/10.5281/zenodo.10701178}
}
And don't forget to leave a `star on GitHub `__!
Credits
-------
Built using the `DendroPy`_ library.
This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
.. _DendroPy: https://github.com/jeetsukuruman/dendropy
.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage