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
--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]
--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 a alife-standardized phylogeny pandas dataframe from a dendropy Tree
reconverted_alife_df = apc.dendropy_tree_to_alife_dataframe(dendropy_tree)
# get a biopython Tree from alife-standardized phylogeny pandas dataframe
biopython_tree = apc.alife_dataframe_to_biopython_tree(alife_df)
# get a 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
adjjacency_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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for alifedata-phyloinformatics-convert-0.8.1.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 38db69155b8d09d7a258b25e6cbed0f2d5078aa0b9caeb12793cb61b33140815 |
|
MD5 | 650979241ecb10eb6b1235be76bfcf1d |
|
BLAKE2b-256 | ec88d65effebdb7efdf8f4703fd8508afbe3117cc0627d2ca563c0c1490aaa30 |
Hashes for alifedata_phyloinformatics_convert-0.8.1-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 02c6db9520e1178a2289fd8de58777c55ed03aaefed79d9442a1e0d12529d148 |
|
MD5 | 12890369224b353ccc5508b828acc0b4 |
|
BLAKE2b-256 | 6aae4c04e0ac84ae3776b64a9cca5ae28ebf0dba22d5e9775d5fb76c957947a5 |