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)
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-0.7.1.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 28494e1e89d812634a8adda9870231f392eb8e03a0abdf6969002b2282ab1745 |
|
MD5 | 7abdd9d27bbf27ae5fac7ebbad642eb8 |
|
BLAKE2b-256 | 79c65b4439a191f09b72f9195e703004d2c63b01c627aff3f29d6455f1e5ff73 |
Hashes for alifedata_phyloinformatics_convert-0.7.1-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b71cfa3b5e3b0f25d48383be9f18c85936034c61d90c89ba042b492b2da00188 |
|
MD5 | 65762683b6e0613e6db15ede58e629d0 |
|
BLAKE2b-256 | da310a89bec26a934f4da89d36b5cd99e4cdacc08687dbf18f842bbc3b240f12 |