Metadata-Version: 2.1
Name: phylopandas
Version: 0.7.3
Summary: Pandas for phylogenetics
Home-page: https://github.com/Zsailer/phylopandas
Author: Zachary Sailer
Author-email: zachsailer@gmail.com
License: MIT
Description: 
        <img src="docs/_logo/banner.png">
        
        [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/phylopandas/Lobby)
        [![Documentation Status](http://readthedocs.org/projects/phylopandas/badge/?version=latest)](http://phylopandas.readthedocs.io/en/latest/?badge=latest)
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        [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/Zsailer/phylopandas/master?filepath=examples%2Fintro-notebook.ipynb)
        
        **Bringing the [Pandas](https://github.com/pandas-dev/pandas) `DataFrame` to phylogenetics.**
        
        
        PhyloPandas provides a Pandas-like interface for reading sequence and phylogenetic tree data into pandas DataFrames. This enables easy manipulation of phylogenetic data using familiar Python/Pandas functions. Finally, phylogenetics for humans!
        
        <img src='docs/_images/jlab.png' align="middle">
        
        ## How does it work?
        
        Don't worry, we didn't reinvent the wheel. **PhyloPandas** is simply a [DataFrame](https://github.com/pandas-dev/pandas)
        (great for human-accessible data storage) interface on top of [Biopython](https://github.com/biopython/biopython) (great for parsing/writing sequence data) and [DendroPy](https://github.com/jeetsukumaran/DendroPy) (great for reading tree data).
        
        PhyloPandas does two things:
        1. It offers new `read` functions to read sequence/tree data directly into a DataFrame.
        2. It attaches a new `phylo` **accessor** to the Pandas DataFrame. This accessor provides writing methods for sequencing/tree data (powered by Biopython and dendropy).
        
        ## Basic Usage
        
        **Sequence data:**
        
        Read in a sequence file.
        ```python
        import phylopandas as ph
        
        df1 = ph.read_fasta('sequences.fasta')
        df2 = ph.read_phylip('sequences.phy')
        ```
        
        Write to various sequence file formats.
        
        ```python
        df1.phylo.to_clustal('sequences.clustal')
        ```
        
        Convert between formats.
        
        ```python
        # Read a format.
        df = ph.read_fasta('sequences.fasta')
        
        # Write to a different format.
        df.phylo.to_phylip('sequences.phy')
        ```
        
        **Tree data:**
        
        Read newick tree data
        ```python
        df = ph.read_newick('tree.newick')
        ```
        
        Visualize the phylogenetic data (powered by [phylovega](https://github.com/Zsailer/phylovega)).
        ```python
        df.phylo.show(
            height=500,
        )
        ```
        
        <img src='docs/_images/tree.png' align="middle" height="200">
        
        ## Contributing
        
        If you have ideas for the project, please share them on the project's [Gitter chat](https://gitter.im/phylopandas/Lobby).
        
        It's *easy* to create new read/write functions and methods for PhyloPandas. If you
        have a format you'd like to add, please submit PRs! There are many more formats
        in Biopython that I haven't had the time to add myself, so please don't be afraid
        to add them! I thank you ahead of time!
        
        ## Testing
        
        PhyloPandas includes a small [pytest](https://docs.pytest.org/en/latest/) suite. Run these tests from base directory.
        ```
        $ cd phylopandas
        $ pytest
        ```
        
        ## Install
        
        Install from PyPI:
        ```
        pip install phylopandas
        ```
        
        Install from source:
        ```
        git clone https://github.com/Zsailer/phylopandas
        cd phylopandas
        pip install -e .
        ```
        
        ## Dependencies
        
        - [BioPython](https://github.com/biopython/biopython): Library for managing and manipulating biological data.
        - [DendroPy](https://github.com/jeetsukumaran/DendroPy): Library for phylogenetic scripting, simulation, data processing and manipulation
        - [Pandas](https://github.com/pandas-dev/pandas): Flexible and powerful data analysis / manipulation library for Python
        - [pandas_flavor](https://github.com/Zsailer/pandas_flavor): Flavor pandas objects with new accessors using pandas' new register API (with backwards compatibility).
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Python: >=3.0
Description-Content-Type: text/markdown
