alifedata-phyloinformatics-convert

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
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

# ... 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 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)

# 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 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.