{"id":22632337,"url":"https://github.com/lmdu/pytrf","last_synced_at":"2025-07-01T10:37:44.766Z","repository":{"id":57471821,"uuid":"281266819","full_name":"lmdu/pytrf","owner":"lmdu","description":"a python package for finding tandem repeats from genomic sequences","archived":false,"fork":false,"pushed_at":"2025-03-19T15:17:17.000Z","size":1538,"stargazers_count":26,"open_issues_count":3,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-06-21T02:18:44.394Z","etag":null,"topics":["microsatellite","minisatellite","repeats","ssr","str","tandem","vntr"],"latest_commit_sha":null,"homepage":"https://pytrf.readthedocs.io","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lmdu.png","metadata":{"files":{"readme":"README.rst","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,"zenodo":null}},"created_at":"2020-07-21T01:41:16.000Z","updated_at":"2025-06-16T13:36:43.000Z","dependencies_parsed_at":"2023-12-25T08:47:03.371Z","dependency_job_id":"f4132d57-0937-4904-8c26-6f1c0fac5d18","html_url":"https://github.com/lmdu/pytrf","commit_stats":{"total_commits":78,"total_committers":2,"mean_commits":39.0,"dds":0.08974358974358976,"last_synced_commit":"2860f72323c98ac7e8de07edf5ded596fa9b0702"},"previous_names":["lmdu/stria"],"tags_count":17,"template":false,"template_full_name":null,"purl":"pkg:github/lmdu/pytrf","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lmdu%2Fpytrf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lmdu%2Fpytrf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lmdu%2Fpytrf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lmdu%2Fpytrf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lmdu","download_url":"https://codeload.github.com/lmdu/pytrf/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lmdu%2Fpytrf/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262945039,"owners_count":23388874,"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":["microsatellite","minisatellite","repeats","ssr","str","tandem","vntr"],"created_at":"2024-12-09T02:17:08.533Z","updated_at":"2025-07-01T10:37:44.720Z","avatar_url":"https://github.com/lmdu.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"Pytrf\n#####\n\n.. image:: https://github.com/lmdu/pytrf/actions/workflows/wheel.yml/badge.svg\n   :target: https://github.com/lmdu/pytrf/actions/workflows/wheel.yml\n   :alt: Github Action\n\n.. image:: https://readthedocs.org/projects/pytrf/badge/?version=latest\n   :target: https://pytrf.readthedocs.io/en/latest/?badge=latest\n   :alt: Readthedocs\n\n.. image:: https://img.shields.io/pypi/v/pytrf.svg\n   :target: https://pypi.org/project/pytrf\n   :alt: PyPI\n\n.. image:: https://img.shields.io/pypi/pyversions/pytrf\n\t:target: https://pypi.org/project/pytrf\n\t:alt: PyPI\n\n.. image:: https://app.codacy.com/project/badge/Grade/bbe59e55f686465ca5824c69583e9718\n\t:target: https://app.codacy.com/gh/lmdu/pytrf/dashboard?utm_source=gh\u0026utm_medium=referral\u0026utm_content=\u0026utm_campaign=Badge_grade\n\n*a fast Python package for finding tandem repeat sequences*\n\nIntroduction\n============\n\nA Tandem repeat (TR) in genomic sequence is a set of adjacent short DNA\nsequence repeated consecutively. The pytrf is a lightweight Python C extension for identification of tandem repeats. The pytrf enables to fastly identify both exact\nor perfect SSRs. It also can find generic tandem repeats with any size of motif,\nsuch as with maximum motif length of 100 bp. Additionally, it has capability of finding approximate or imperfect tandem repeats. Furthermore, the pytrf not only can be used as Python package but also provides command line interface for users to facilitate the identification of tandem repeats.\n\nNote: pytrf is not a Python binding to common used tool `TRF \u003chttps://tandem.bu.edu/trf/trf.html\u003e`_.\n\nUsage\n=====\n\nThe pytrf can be used as Python package. It requires `pyfastx \u003chttps://github.com/lmdu/pyfastx\u003e`_ to parse FASTA or FASTQ file.\n\n.. code:: python\n\n\t\u003e\u003e\u003e import pytrf\n\t\u003e\u003e\u003e import pyfastx\n\t\u003e\u003e\u003e fa = pyfastx.Fastx('test.fa', uppercase=True):\n\t\u003e\u003e\u003e for name, seq in fa:\n\t\u003e\u003e\u003e \tfor ssr in STRFinder(name, seq):\n\t\u003e\u003e\u003e \t\tprint(ssr.as_string())\n\nCommand line\n============\n\nThe pytrf also provides command line tools for you to find tandem repeats from given FASTA or FASTQ file.\n\n.. code:: sh\n\n\tpytrf -h\n\n\tusage: pytrf command [options] fastx\n\n\ta python package for finding tandem repeats from genomic sequences\n\n\toptions:\n\t  -h, --help     show this help message and exit\n\t  -v, --version  show program's version number and exit\n\n\tcommands:\n\n\t    findstr      find exact or perfect short tandem repeats\n\t    findgtr      find exact or perfect generic tandem repeats\n\t    findatr      find approximate or imperfect tandem repeats\n\t    extract      get tandem repeat sequence and flanking sequence\n\nFor example:\n\n.. code:: sh\n\n\tpytrf findstr test.fa\n\nDocumentation\n=============\n\nFor more detailed usage, see our manual: `https://pytrf.readthedocs.io \u003chttps://pytrf.readthedocs.io\u003e`_\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flmdu%2Fpytrf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flmdu%2Fpytrf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flmdu%2Fpytrf/lists"}