Metadata-Version: 2.1
Name: alifedata-phyloinformatics-convert
Version: 0.7.1
Summary: alifedata-phyloinformatics-convert helps apply traditional phyloinformatics software to alife standardized data
Home-page: https://github.com/mmore500/alifedata-phyloinformatics-convert
Author: Matthew Andres Moreno
Author-email: m.more500@gmail.com
License: MIT license
Keywords: alifedata-phyloinformatics-convert
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.6
Requires-Dist: biopython (>=1.79)
Requires-Dist: click (>=7.0)
Requires-Dist: dendropy (>=4.5.2)
Requires-Dist: iterpop (>=0.4.0)
Requires-Dist: lyncs-utils (>=0.3.2)
Requires-Dist: nanto (>=0.1.1)
Requires-Dist: numpy (>=1.21.5)
Requires-Dist: opytional (>=0.1.0)
Requires-Dist: pandas (>=1.1.0)
Requires-Dist: sortedcontainers (>=2.4.0)

==================================
alifedata-phyloinformatics-convert
==================================


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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 :code:`dendropy` library.

Use it as a command line tool to convert to alife standard phylogenetics data

.. code-block::

  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

.. code-block::

  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

.. code-block:: python3

  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

.. code-block:: bash

  pip3 install alifedata-phyloinformatics-convert


Credits
-------

This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.

.. _Cookiecutter: https://github.com/audreyr/cookiecutter
.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage


=======
History
=======

0.0.0 (2022-03-22)
------------------

* First release on PyPI.


