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Description:

alifedataphyloinformaticsconvert 0.16.3

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 apc’s RosettaTree interface for flexible conversion between phylogenetic data structures and schemas.
First, create a RosettaTree object from any supported structure/schema
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)

# 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
# ... converter created as above
converter.as_alife # pandas DataFrame
converter.as_biopython
converter.as_dendropy
converter.as_ete
converter.as_networkx
converter.as_phylotrack

# 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 apc’s functional interface to convert between alife format other libraries’ tree objects
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)

# partial support is also included for,
# - adjacency lists
# - anytree trees
# - scipy linkage matrices
# ... see API documentation for details

Command Line Interface
Use apc’s CLI toalifedata command to convert newick, nexml, and nexus data to alife standard phylogenetics data
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 fromalifedata command to convert to other formats from alife standard phylogenetics data
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
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

@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.