https://github.com/zsailer/phylopandas
Pandas DataFrames for phylogenetics
https://github.com/zsailer/phylopandas
biopython pandas phylogenetics python
Last synced: 4 months ago
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Pandas DataFrames for phylogenetics
- Host: GitHub
- URL: https://github.com/zsailer/phylopandas
- Owner: Zsailer
- License: bsd-3-clause
- Created: 2017-10-24T19:38:59.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2021-06-06T13:21:02.000Z (about 4 years ago)
- Last Synced: 2025-02-27T09:46:23.430Z (4 months ago)
- Topics: biopython, pandas, phylogenetics, python
- Language: Python
- Homepage:
- Size: 982 KB
- Stars: 73
- Watchers: 6
- Forks: 21
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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**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!
## 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.display(
height=500,
)
```
## 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).