picea


Namepicea JSON
Version 0.0.31 PyPI version JSON
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home_pagehttps://github.com/holmrenser/picea
SummaryA lightweight python library for working with trees and biological sequence collections
upload_time2024-06-05 09:39:51
maintainerNone
docs_urlNone
authorRens Holmer
requires_python<3.13,>=3.10
licenseMIT
keywords
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls. 
            # _picea_

Sprucing up bioinformatics analysis

[![CI](https://github.com/holmrenser/picea/actions/workflows/ci.yml/badge.svg)](https://github.com/holmrenser/picea/actions/workflows/ci.yml)
![docs](https://github.com/holmrenser/picea/workflows/docs/badge.svg?branch=master)
[![Coverage Status](https://coveralls.io/repos/github/holmrenser/picea/badge.svg?branch=master)](https://coveralls.io/github/holmrenser/picea?branch=master)

[![PyPI version](https://badge.fury.io/py/picea.svg)](https://badge.fury.io/py/picea)
[![PyPI pyversions](https://img.shields.io/pypi/pyversions/picea.svg)](https://pypi.python.org/pypi/ansicolortags/)
[![PyPI status](https://img.shields.io/pypi/status/picea.svg)](https://pypi.python.org/pypi/ansicolortags/)

![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)

```
pip install picea
```

_picea_ has datastructures and methods to perform common bioinformatics tasks. Currently sequences, sequence annotations, trees, and ontologies are supported.

Example:

```python
from picea import Tree, treeplot
import matplotlib.pyplot as plt

newick = '(((a,b),(c,d)),e)'
tree = Tree.from_newick(newick)

fig, (ax1, ax2) = plt.subplots(ncols = 2, figsize = (10, 4))

#left-to-right layout with direct links
treeplot(tree, style='rectangular', ltr=True, ax=ax1)

#right-to-left layout with square links
treeplot(tree, style='square', ltr=False, ax=ax2)
```

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Rens Holmer
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