https://github.com/yuanx749/py-cdhit

A Python package for CD-HIT, clustering protein or nucleotide sequences.
https://github.com/yuanx749/py-cdhit

bioinformatics package sequence-analysis tool

Last synced: 10 months ago
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A Python package for CD-HIT, clustering protein or nucleotide sequences.

• Host: GitHub
• URL: https://github.com/yuanx749/py-cdhit
• Owner: yuanx749
• License: gpl-2.0
• Created: 2023-05-25T10:49:37.000Z (about 3 years ago)
• Default Branch: main
• Last Pushed: 2024-11-22T03:31:05.000Z (over 1 year ago)
• Last Synced: 2025-03-28T14:09:34.876Z (about 1 year ago)
• Topics: bioinformatics, package, sequence-analysis, tool
• Language: Python
• Homepage: https://yuanx749.github.io/py-cdhit/
• Size: 56.6 KB
• Stars: 121
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# py-cdhit

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A Python package for CD-HIT, clustering protein or nucleotide sequences.

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, this package 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.

Read the documentation [here](https://yuanx749.github.io/py-cdhit/).

## Usage

A simple example on Linux is provided below. See the [notebook](docs/examples/examples.ipynb) for more details.

```Python

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](https://github.com/weizhongli/cdhit/wiki) for its installation and the options of commands.

## Installation

First Install CD-HIT. [Mamba](https://mamba.readthedocs.io/) is recommended. For example, to create an environment and install:

```bash

mamba create -n myenv python=3.10

mamba activate myenv

```

```bash

mamba install -c bioconda cd-hit cd-hit-auxtools

```

Then install this package from PyPI:

```bash

pip install py-cdhit

```

## Development

Install from source after git clone:

```bash

cd py-cdhit

pip install -e '.[dev]'

pip install -r docs/requirements.txt

python -m pytest --cov-report term-missing --cov=pycdhit tests/

```