{"id":34077891,"url":"https://github.com/rnajena/read5_ont","last_synced_at":"2025-12-30T08:05:33.407Z","repository":{"id":209049907,"uuid":"723107256","full_name":"rnajena/read5_ont","owner":"rnajena","description":"Wrapper to read fast5 and pod5 files.","archived":false,"fork":false,"pushed_at":"2025-04-05T20:27:25.000Z","size":834,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-29T10:28:21.102Z","etag":null,"topics":["fast5","ont","oxford-nanopore","oxford-nanopore-data","pod5","raw-data"],"latest_commit_sha":null,"homepage":"https://jannessp.github.io/read5.github.io/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/rnajena.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-11-24T17:48:25.000Z","updated_at":"2025-09-05T12:06:05.000Z","dependencies_parsed_at":"2023-11-27T13:28:39.051Z","dependency_job_id":"961bf7a0-d259-407c-827b-230b3392903e","html_url":"https://github.com/rnajena/read5_ont","commit_stats":null,"previous_names":["jannessp/read5_ont","rnajena/read5_ont"],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/rnajena/read5_ont","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rnajena%2Fread5_ont","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rnajena%2Fread5_ont/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rnajena%2Fread5_ont/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rnajena%2Fread5_ont/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/rnajena","download_url":"https://codeload.github.com/rnajena/read5_ont/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/rnajena%2Fread5_ont/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":27726731,"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","status":"online","status_checked_at":"2025-12-14T02:00:11.348Z","response_time":56,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["fast5","ont","oxford-nanopore","oxford-nanopore-data","pod5","raw-data"],"created_at":"2025-12-14T10:56:17.516Z","updated_at":"2025-12-14T10:56:18.222Z","avatar_url":"https://github.com/rnajena.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ![Alt text](figures/logo.png)\n\n- [**Read5**](https://github.com/JannesSP/read5) is a python wrapper to read fast5, slow5/blow5 and pod5 files using the same overloaded functions from different APIs. ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/read5)\n- [**Read5_ont**](https://github.com/JannesSP/read5_ont) is a python wrapper to read fast5 and pod5 files using the same overloaded functions from different APIs. ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/read5_ont)\n\n[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-teal.svg)](https://www.gnu.org/licenses/gpl-3.0)\n\n[![PyPI](https://img.shields.io/pypi/v/read5) ![PyPI - Downloads](https://img.shields.io/pypi/dm/read5_ont) ![PyPI - Status](https://img.shields.io/pypi/status/read5_ont)](https://pypi.org/project/read5_ont/)\n\n\n[![Anaconda-Server Badge](https://anaconda.org/jannessp/read5/badges/version.svg)](https://anaconda.org/jannessp/read5_ont) ![Conda](https://img.shields.io/conda/dn/jannessp/read5_ont) [![Conda package](https://anaconda.org/jannessp/read5_ont/badges/latest_release_date.svg)](https://anaconda.org/jannessp/read5_ont) [![Conda package](https://anaconda.org/jannessp/read5_ont/badges/platforms.svg)](https://anaconda.org/jannessp/read5_ont)\n \n[![DOI](https://zenodo.org/badge/633012569.svg)](https://zenodo.org/badge/latestdoi/633012569)\n\n[![Twitter Follow](https://img.shields.io/twitter/follow/Ja_Spangenberg)](https://twitter.com/Ja_Spangenberg)\n___\n## Table of Content\n1.  [Installation](#installation)\n2.  [Usage](#usage)\n3.  [Full Documentation](https://jannessp.github.io/read5.github.io/)\n___\n## Installation\n\n### Pypi/pip\n```bash\npip install read5_ont\n```\n### Conda\nPod5 is now available via [conda](https://anaconda.org/jannessp/pod5) (19.07.2023).\n\n```bash\nconda create -n read5_ont -c jannessp read5_ont\nconda activate read5_ont\n```\n___\n## Usage\n\n[Click here to see a full documentation about the classes and function.](https://jannessp.github.io/read5.github.io/)\n\n*my_file* can be a fast5 or pod5 file. The wrapper detects the file format depending on the file extension.\n\n\u003cspan style=\"color:red\"\u003eYou might encounter errors with python 3.13. AFAIK there is some dependency problem with pyarrow and other libraries for python 3.13, but I could not fix it.\u003c/span\u003e.\n\n### Small example:\n\n```python\nfrom read5 import read # or from read5.Reader import read\n\nr5 = read(my_file) # file with one of these extensions: .fast5, .pod5\nfor readid in r5:\n    signal = r5.getSignal(readid) # returns raw integer values stored in the file\n    pA_signal = r5.getpASignal(readid) # returns pA signal\n    norm_signal = r5.getZNormSignal(readid) # returns normalised read signal: norm_signal = (signal - median(signal)) / mad(signal)\n    polyAstdSignal = r5.getPolyAStandardizedSignal(readid, polyAstart, polyAend) # returns polyA standardized read signal\n    # default polyAMean : float = 108.901413, polyAStdev : float = 2.676522, this can be changed using the parameters\n    channel = r5.getChannelNumber(readid)\n    sampleid = r5.getSampleID(readid)\n    runid = r5.getRunID(readid)\n\nreadid_list = r5.getReads()\n```\n\n### File Reader Classes\nIf you want to use the file readers you can import the corresponding class like this:\n\n```python\nfrom read5.Fast5Reader import Fast5Reader # contains the Fast5 Reader class\nfrom read5.Slow5Reader import Slow5Reader # contains the Slow5 Reader class - !not available in read5_ont!\nfrom read5.Pod5Reader import Pod5Reader # contains the Pod5 Reader class\n```\n\n### Abstract File Reader Class\n\n```python\nfrom read5.AbstractFileReader import AbstractFileReader\n```\n\n### Possible Exceptions\n\n```python\nfrom read5.Exceptions import UnknownFileFormatException, UnknownNormalizationMode\n```\n\n- UnknownFileFormatException: is raised, when the file extension does not match one of ['.fast5', '.slow5', '.blow5', '.pod5'] (or ['.fast5', '.pod5'] in **read5_ont**)\n- UnknownNormalizationMode: is raised, when an unknown mode is provided for the signal normalization function\n\n## Full Documentation\nCreated with [pdoc3](https://pdoc3.github.io/pdoc/).\nCan be found [here](https://jannessp.github.io/read5.github.io/).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frnajena%2Fread5_ont","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frnajena%2Fread5_ont","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frnajena%2Fread5_ont/lists"}