https://github.com/holmrenser/picea

lightweight python library for working with trees and sequence collections
https://github.com/holmrenser/picea

Last synced: 3 months ago
JSON representation

lightweight python library for working with trees and sequence collections

• Host: GitHub
• URL: https://github.com/holmrenser/picea
• Owner: holmrenser
• License: mit
• Created: 2019-06-07T12:45:52.000Z (over 5 years ago)
• Default Branch: master
• Last Pushed: 2024-06-05T09:41:29.000Z (8 months ago)
• Last Synced: 2024-10-15T03:52:14.839Z (3 months ago)
• Language: Python
• Homepage: https://holmrenser.github.io/picea
• Size: 7.34 MB
• Stars: 4
• Watchers: 1
• Forks: 1
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

Awesome Lists containing this project

README

        
# _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)

```