py-cdhit 0.5.0

A Python interface for CD-HIT package.

py-cdhit

A Python interface for CD-HIT package.

Description

This package provides a Python interface for CD-HIT (Cluster Database at High Identity with Tolerance), which has programs for clustering biological sequences with a very fast speed. Specifically, it contains functions that run commands and read the output files, thus reducing the overhead of switching between languages and writing parsing code when using Python in the data analysis workflows.

Usage

A simple example on Linux is provided below. See the notebook for more details.

from pycdhit import cd_hit, read_clstr

res = cd_hit(
    i="./docs/examples/apd.fasta",
    o="./docs/examples/out",
    c=0.7,
    d=0,
    sc=1,
)

df_clstr = read_clstr("./docs/examples/out.clstr")

Please visit CD-HIT's documentations for its installation and the options of commands.

Installation

Install

First Install CD-HIT. Then install this package as follows.

Install from PyPI:

pip install py-cdhit

Develop

Install from source after git clone:

cd py-cdhit
pip install -e '.[dev,doc]'
python -m pytest --cov-report term-missing --cov=pycdhit tests/