alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data
Project description
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.
Built using the dendropy
library.
Use it as a command line tool to convert 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 it as a command line tool to convert 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.
Use it as a Python module
import alifedata_phyloinformatics_convert as apc
alife_df = pd.read_csv('alifedata.csv')
# get a dendropy Tree from alife-standardized phylogeny pandas dataframe
dendropy_tree = apc.alife_dataframe_to_dendropy_tree(alife_df)
# get an alife-standardized phylogeny pandas dataframe from a dendropy Tree
reconverted_alife_df = apc.dendropy_tree_to_alife_dataframe(dendropy_tree)
# get an ete Tree from alife-standardized phylogeny pandas dataframe
ete_tree = apc.alife_dataframe_to_ete_tree(alife_df)
# get an alife-standardized phylogeny pandas dataframe from an ete Tree
reconverted_alife_df = apc.ete_tree_to_alife_dataframe(ete_tree)
# get a biopython Tree from alife-standardized phylogeny pandas dataframe
biopython_tree = apc.alife_dataframe_to_biopython_tree(alife_df)
# get an alife-standardized phylogeny pandas dataframe from a biopython Tree
reconverted_alife_df = apc.dendropy_tree_to_alife_dataframe(biopython_tree)
# get a networkx DiGraph from alife-standardized phylogeny pandas dataframe
networkx_digraph = apc.alife_dataframe_to_networkx_digraph(alife_df)
# get adjacency lists from alife-standardized phylogeny pandas dataframe
adjacency_lists = apc.alife_dataframe_to_dict_of_lists(alife_df)
Install from PyPi
pip3 install alifedata-phyloinformatics-convert
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.0.0 (2022-03-22)
First release on PyPI.
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