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alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data
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
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), networkx.DiGraph(), pandas.DataFrame({"id": [0], "ancestor_list": "[None]"}), # alife standard phylotrackpy.systematics.Systematics(lambda x: x), ]: converter = apc.RosettaTree(obj)
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)
converter = apc.RosettaTree(pandas.read_csv("read-alifestd.csv"))
Then, convert or serialize data
.. code-block:: python3
converter.as_alife # pandas DataFrame converter.as_biopython converter.as_dendropy converter.as_ete converter.as_networkx converter.as_phylotrack
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)
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')
tree = apc.alife_dataframe_tobiopython_tree(alife_df) frame = apc.biopython_tree_to_alife_dataframe(tree)
tree = apc.alife_dataframe_to_dendropy_tree(alife_df) frame = apc.dendropy_tree_to_alife_dataframe(tree)
ete_tree = apc.alife_dataframe_to_ete_tree(alife_df) frame = apc.ete_tree_to_alife_dataframe(tree)
digraph = apc.alife_dataframe_to_networkx_digraph(alife_df) frame = apc.networkx_digraph_to_alife_dataframe(digraph)
systematics = apc.alife_dataframe_to_phylotrack_systematics(alife_df) frame = apc.phylotrack_systematics_to_alife_dataframe(systematics)
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 formatOptions: --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 formatOptions: --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.
Install from PyPi
.. code-block:: bash
pip3 install alifedata-phyloinformatics-convert
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>__!
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