==================================
alifedata-phyloinformatics-convert
==================================
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:alt: PyPI Status
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.. 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 <https://github.com/mmore500/alifedata-phyloinformatics-convert/stargazers>`__!
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
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"description": "==================================\nalifedata-phyloinformatics-convert\n==================================\n\n\n.. image:: https://img.shields.io/pypi/v/alifedata-phyloinformatics-convert.svg\n :target: https://pypi.python.org/pypi/alifedata-phyloinformatics-convert\n :alt: PyPI Status\n\n.. image:: https://github.com/mmore500/alifedata-phyloinformatics-convert/actions/workflows/CI.yml/badge.svg\n :target: https://github.com/mmore500/alifedata-phyloinformatics-convert/actions/workflows/CI.yml\n :alt: CI Status\n\n.. image:: https://readthedocs.org/projects/alifedata-phyloinformatics-convert/badge/?version=latest\n :target: https://alifedata-phyloinformatics-convert.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://zenodo.org/badge/466241441.svg\n :target: https://zenodo.org/doi/10.5281/zenodo.10701178\n\n\nalifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data\n\n\n* Free software: MIT license\n* Documentation: https://alifedata-phyloinformatics-convert.readthedocs.io.\n\nUsage\n-----\n\nUse :code:`apc`'s :code:`RosettaTree` interface for flexible conversion between phylogenetic data structures and schemas.\nFirst, create a :code:`RosettaTree` object from any supported structure/schema\n\n.. code-block:: python3\n\n import io\n import pathlib\n\n import alifedata_phyloinformatics_convert as apc\n import anytree\n import Bio\n import dendropy\n import ete3 as ete\n import networkx\n import pandas\n import phylotrackpy\n import treeswift\n\n newickstr = \"((A,B),(C,D));\"\n\n for obj in [\n anytree.AnyNode(),\n Bio.Phylo.read(io.StringIO(newickstr), \"newick\"),\n dendropy.Tree.get(data=newickstr, schema=\"newick\"),\n ete.Tree(newickstr),\n treeswift.Tree.read_tree_newick(newickstr),\n networkx.DiGraph(),\n pandas.DataFrame({\"id\": [0], \"ancestor_list\": \"[None]\"}), # alife standard\n phylotrackpy.systematics.Systematics(lambda x: x),\n ]:\n converter = apc.RosettaTree(obj)\n\n # from phyloinformatics schema\n # ... nexml and nexus also supported!\n converter = apc.RosettaTree.from_newick(newickstr)\n converter = apc.RosettaTree.from_newick(pathlib.Path(\"read.newick\"))\n with open(\"read.newick\", \"r\") as fp:\n converter = apc.RosettaTree.from_newick(fp)\n\n # from alife standard data via Pandas\n converter = apc.RosettaTree(pandas.read_csv(\"read-alifestd.csv\"))\n\nThen, convert or serialize data\n\n.. code-block:: python3\n\n # ... converter created as above\n converter.as_alife # pandas DataFrame\n converter.as_biopython\n converter.as_dendropy\n converter.as_ete\n converter.as_networkx\n converter.as_phylotrack\n converter.as_treeswift\n\n # serialization, nexml and nexus schemata also supported\n converter.to_newick() # returns newick string\n converter.to_newick(pathlib.Path(\"write.newick\")) # writes to path\n with open(\"write.newick\", \"w\") as fp: # writes to file object\n converter.to_newick(fp)\n\n # alifestd serialization\n converter.as_alife.to_csv(\"write-alifestd.csv\", index=False)\n\nUse :code:`apc`'s functional interface to convert between alife format other libraries' tree objects\n\n.. code-block:: python3\n\n import alifedata_phyloinformatics_convert as apc\n import pandas\n\n alife_df = pandas.read_csv('alifedata.csv')\n\n # biopython\n tree = apc.alife_dataframe_tobiopython_tree(alife_df)\n frame = apc.biopython_tree_to_alife_dataframe(tree)\n\n # dendropy\n tree = apc.alife_dataframe_to_dendropy_tree(alife_df)\n frame = apc.dendropy_tree_to_alife_dataframe(tree)\n\n # ete\n ete_tree = apc.alife_dataframe_to_ete_tree(alife_df)\n frame = apc.ete_tree_to_alife_dataframe(tree)\n\n # networkx\n digraph = apc.alife_dataframe_to_networkx_digraph(alife_df)\n frame = apc.networkx_digraph_to_alife_dataframe(digraph)\n\n # phylotrackpy\n systematics = apc.alife_dataframe_to_phylotrack_systematics(alife_df)\n frame = apc.phylotrack_systematics_to_alife_dataframe(systematics)\n\n # treeswift\n treeswift_tree = apc.alife_dataframe_to_treeswift_tree(alife_df)\n frame = apc.treeswift_tree_to_alife_dataframe(tree)\n\n # partial support is also included for,\n # - adjacency lists\n # - anytree trees\n # - scipy linkage matrices\n # ... see API documentation for details\n\nCommand Line Interface\n----------------------\n\nUse :code:`apc`'s CLI :code:`toalifedata` command to convert newick, nexml, and nexus data to alife standard phylogenetics data\n\n.. code-block:: bash\n\n Usage: alifedata-phyloinformatics-convert toalifedata [OPTIONS]\n\n convert standard alife phylogeny data to phloinformatics format\n\n Options:\n --input-file FILENAME phyloinformatics data file path; default\n stdin\n --input-schema TEXT phyloinformatics data format schema; options\n include newick, nexml, and nexus [required]\n --output-file FILENAME alife data file path; default stdout\n --output-format TEXT alife data file format; default csv\n --suppress-unifurcations / --keep-unifurcations\n Compress sequences of nodes with single\n descendants\n --help Show this message and exit.\n\n\n\nUse the :code:`fromalifedata` command to convert to other formats from alife standard phylogenetics data\n\n.. code-block:: bash\n\n Usage: alifedata-phyloinformatics-convert fromalifedata [OPTIONS]\n\n convert phloinformatics data to standard alife phylogeny format\n\n Options:\n --input-file FILENAME alife data file path; default stdin\n --input-format TEXT alife data file format; default csv\n --output-file FILENAME phyloinformatics data file path; default\n stdout\n --output-schema TEXT phyloinformatics data format schema; options\n include newick, nexml, and nexus [required]\n --suppress-unifurcations / --keep-unifurcations\n Compress sequences of nodes with single\n descendants\n --help Show this message and exit.\n\nInstallation\n------------\n\nInstall from PyPi\n\n.. code-block:: bash\n\n pip3 install alifedata-phyloinformatics-convert\n\nCiting\n------\n\nIf alifedata-phyloinformatics-convert is used in scientific publication, please cite it as\n\n Matthew Andres Moreno and Santiago Rodriguez Papa. 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