Metadata-Version: 2.1
Name: alifedata-phyloinformatics-convert
Version: 0.14.0
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: anytree >=2.8.0
Requires-Dist: biopython >=1.79
Requires-Dist: click >=7.0
Requires-Dist: dendropy >=4.5.2
Requires-Dist: ete3 >=3.0.0
Requires-Dist: iterpop >=0.4.0
Requires-Dist: lyncs-utils >=0.3.2
Requires-Dist: nanto >=0.1.1
Requires-Dist: networkx >=2.5
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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        :target: https://alifedata-phyloinformatics-convert.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status




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
    --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

.. 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]
    --suppress-unifurcations / --keep-unifurcations
                                    Compress sequences of nodes with single
                                    descendants
    --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)

  # 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

.. 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.


