Metadata-Version: 1.2
Name: alifedata-phyloinformatics-convert
Version: 0.2.0
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
Description: ==================================
        alifedata-phyloinformatics-convert
        ==================================
        
        
        .. image:: https://img.shields.io/pypi/v/alifedata-phyloinformatics-convert.svg
                :target: https://pypi.python.org/pypi/alifedata-phyloinformatics-convert
        
        .. image:: https://img.shields.io/travis/mmore500/alifedata-phyloinformatics-convert.svg
                :target: https://travis-ci.com/mmore500/alifedata-phyloinformatics-convert
        
        .. image:: https://readthedocs.org/projects/alifedata-phyloinformatics-convert/badge/?version=latest
                :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
            --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
          import dendropy
          import pandas as pd
        
          alife_df = pd.read_csv('alifedata.csv')
        
          # get a dendropy Tree from alife-standardized phylogeny dataframe
          tree = apc.alife_dataframe_to_dendropy_tree(converted_df)
        
          # get a alife-standardized phylogeny dataframe from a dendropy Tree
          reconverted_alife_df = apc.dendropy_tree_to_alife_dataframe(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.
        
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
