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Fast and optimal genome segmentation with Bayesian blocks

Project description

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Fast, mathematically optimal genome segmentation with Bayesian blocks

Installation

pip install blockify

The earliest recommended version of blockify is 0.2.1.

Usage

Blockify is available as both a Python library and a command line executable.

To use in Python:

from blockify import annotation
from blockify import segmentation
from blockify import normalization
from blockify import downsampling

To use from the command line: blockify -h

For more details, please see the documentation.

Development

To actively develop blockify, clone from GitHub and switch to the development branch:

git clone https://github.com/arnavm/blockify.git
cd blockify
git checkout dev

Unit tests are available from the top-level directory:

python -m unittest tests.test_basic

Two batteries of tests are provided: tests.test_basic and tests.test_advanced. For routine development, the basic set of tests should be sufficient. The advanced suite takes much more time and fetches several large datasets. It is best used when making major changes to the code.

Disclaimer

Not to be confused with the similarly-named Spotify plugin.

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