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Description:

phylopandas 0.8.0

Bringing the 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!

How does it work?
Don't worry, we didn't reinvent the wheel. PhyloPandas is simply a DataFrame
(great for human-accessible data storage) interface on top of Biopython (great for parsing/writing sequence data) and DendroPy (great for reading tree data).
PhyloPandas does two things:

It offers new read functions to read sequence/tree data directly into a DataFrame.
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.
import phylopandas as ph

df1 = ph.read_fasta('sequences.fasta')
df2 = ph.read_phylip('sequences.phy')

Write to various sequence file formats.
df1.phylo.to_clustal('sequences.clustal')

Convert between formats.
# 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
df = ph.read_newick('tree.newick')

Visualize the phylogenetic data (powered by phylovega).
df.phylo.display(
height=500,
)

Contributing
If you have ideas for the project, please share them on the project's Gitter chat.
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 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: Library for managing and manipulating biological data.
DendroPy: Library for phylogenetic scripting, simulation, data processing and manipulation
Pandas: Flexible and powerful data analysis / manipulation library for Python
pandas_flavor: Flavor pandas objects with new accessors using pandas' new register API (with backwards compatibility).