{"id":19478170,"url":"https://github.com/yuanx749/py-cdhit","last_synced_at":"2025-08-09T19:34:52.862Z","repository":{"id":169362141,"uuid":"645297821","full_name":"yuanx749/py-cdhit","owner":"yuanx749","description":"A Python package for CD-HIT, clustering protein or nucleotide sequences.","archived":false,"fork":false,"pushed_at":"2024-11-22T03:31:05.000Z","size":58,"stargazers_count":121,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-03-28T14:09:34.876Z","etag":null,"topics":["bioinformatics","package","sequence-analysis","tool"],"latest_commit_sha":null,"homepage":"https://yuanx749.github.io/py-cdhit/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/yuanx749.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-05-25T10:49:37.000Z","updated_at":"2025-02-20T03:00:09.000Z","dependencies_parsed_at":"2024-05-28T14:28:30.704Z","dependency_job_id":"e03a4d97-80a1-462b-9c1a-305445ad0891","html_url":"https://github.com/yuanx749/py-cdhit","commit_stats":{"total_commits":23,"total_committers":1,"mean_commits":23.0,"dds":0.0,"last_synced_commit":"ddc92c1b74aa4cbfc818dcf6f65424b10bf5ebfe"},"previous_names":["yuanx749/py-cdhit"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yuanx749%2Fpy-cdhit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yuanx749%2Fpy-cdhit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yuanx749%2Fpy-cdhit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/yuanx749%2Fpy-cdhit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/yuanx749","download_url":"https://codeload.github.com/yuanx749/py-cdhit/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247198446,"owners_count":20900079,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","package","sequence-analysis","tool"],"created_at":"2024-11-10T19:47:26.089Z","updated_at":"2025-04-04T15:05:18.740Z","avatar_url":"https://github.com/yuanx749.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# py-cdhit\n\n[![PyPI version](https://badge.fury.io/py/py-cdhit.svg)](https://badge.fury.io/py/py-cdhit)\n[![Downloads](https://static.pepy.tech/badge/py-cdhit/month)](https://pepy.tech/project/py-cdhit)\n[![Codacy Badge](https://app.codacy.com/project/badge/Grade/197a0be6dcd14961b919e666a0de39eb)](https://app.codacy.com/gh/yuanx749/py-cdhit/dashboard?utm_source=gh\u0026utm_medium=referral\u0026utm_content=\u0026utm_campaign=Badge_grade)\n\nA Python package for CD-HIT, clustering protein or nucleotide sequences.\n\nThis 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.\n\nRead the documentation [here](https://yuanx749.github.io/py-cdhit/).\n\n## Usage\n\nA simple example on Linux is provided below. See the [notebook](docs/examples/examples.ipynb) for more details.\n\n```Python\nfrom pycdhit import cd_hit, read_clstr\n\nres = cd_hit(\n    i=\"./docs/examples/apd.fasta\",\n    o=\"./docs/examples/out\",\n    c=0.7,\n    d=0,\n    sc=1,\n)\n\ndf_clstr = read_clstr(\"./docs/examples/out.clstr\")\n```\n\nPlease visit CD-HIT's [documentations](https://github.com/weizhongli/cdhit/wiki) for its installation and the options of commands.\n\n## Installation\n\nFirst Install CD-HIT. [Mamba](https://mamba.readthedocs.io/) is recommended. For example, to create an environment and install:\n\n```bash\nmamba create -n myenv python=3.10\nmamba activate myenv\n```\n\n```bash\nmamba install -c bioconda cd-hit cd-hit-auxtools\n```\n\nThen install this package from PyPI:\n\n```bash\npip install py-cdhit\n```\n\n## Development\n\nInstall from source after git clone:\n\n```bash\ncd py-cdhit\npip install -e '.[dev]'\npip install -r docs/requirements.txt\npython -m pytest --cov-report term-missing --cov=pycdhit tests/\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fyuanx749%2Fpy-cdhit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fyuanx749%2Fpy-cdhit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fyuanx749%2Fpy-cdhit/lists"}