{"id":15359671,"url":"https://github.com/jhsmit/dont-fret","last_synced_at":"2025-07-02T20:07:25.781Z","repository":{"id":255444141,"uuid":"447536253","full_name":"Jhsmit/dont-fret","owner":"Jhsmit","description":"Don't FRET: A python webserver for confocal smFRET burst search","archived":false,"fork":false,"pushed_at":"2025-04-10T13:46:54.000Z","size":20564,"stargazers_count":3,"open_issues_count":8,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-07-02T20:07:24.083Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","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/Jhsmit.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,"zenodo":null}},"created_at":"2022-01-13T09:19:58.000Z","updated_at":"2025-05-15T11:25:14.000Z","dependencies_parsed_at":"2025-01-15T15:52:50.262Z","dependency_job_id":"6ca942d4-1e8c-4019-bcf4-7096c2e1f5f3","html_url":"https://github.com/Jhsmit/dont-fret","commit_stats":{"total_commits":8,"total_committers":1,"mean_commits":8.0,"dds":0.0,"last_synced_commit":"5b94ba51d94c7e424d37866e56ea4a4caa33c323"},"previous_names":["jhsmit/dont-fret"],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/Jhsmit/dont-fret","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2Fdont-fret","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2Fdont-fret/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2Fdont-fret/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2Fdont-fret/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Jhsmit","download_url":"https://codeload.github.com/Jhsmit/dont-fret/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Jhsmit%2Fdont-fret/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263208051,"owners_count":23430676,"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":[],"created_at":"2024-10-01T12:45:38.665Z","updated_at":"2025-07-02T20:07:25.750Z","avatar_url":"https://github.com/Jhsmit.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"Don't FRET\n============\n\n\nDon't FRET! is a python package featuring a web application for performing burst search on confocal smFRET data. \n\n```\npip install dont-fret\n```\n\n![screenshot](assets/screenshot.png)\n\n## Process photon files\n\n```\ndont-fret process filename.ptu\n```\n\nWill process the file. It will perform burst search as specified in the configuration file. Output (default) are burst photons and bursts as .pq files. \n\n## Run the web application\n\nTo launch with the default configuration file:\n\n```\ndont-fret serve\n```\n\nTo create a local default configuration file:\n\n```\ndont-fret config\n```\n\nThen you can edit the created config file. To launch the web application with a specific config file:\n\n```\ndont-fret serve --config config.yaml\n```\n\n## Configuration\n\nConfiguration for channels, photon streams and (default) burst search settings is done from the config .yaml file. \n\nFirst, define your channels:\n\n```yaml\nchannels: # refactor channels in code to channel_identifiers\n  laser_D:\n    target: nanotimes\n    value: [ 0, 1000 ]\n  laser_A:\n    target: nanotimes\n    value: [ 1000, 2000 ] # intervals are inclusive, exclusive\n  det_D:\n    target: detectors\n    value: 1\n  det_A:\n    target: detectors\n    value: 0\n```\n\nCurrently supported targets are `nanotimes`, `detectors` and `timestamps`. These are as read from the file and not converted to seconds. Modulo is supported (untested) for us-ALEX:\n```yaml\nchannels: # refactor channels in code to channel_identifiers\n  laser_D:\n    target: timestamps\n    value: [ 0, 100 ]\n    modulo: 200\n```\n\nThis will assign photons with a timestamp modulo 200 in the range from 0 up to 100 to \"laser_D\".\n\nNext, define your photon streams. Photons streams are combinations of channels (\"AND\"):\n\n```yaml\nstreams:\n  DD: [laser_D, det_D]\n  DA: [laser_D, det_A]\n  AA: [laser_A, det_A]\n  AD: [laser_A, det_D]\n```\n\n!IMPORTANT\nThe notation used here is excitation then emission, thus the FRET stream is 'DA' while in literature the FRET photon stream is often written as `A|D` (Acceptor emission during donor excitation). \n\n\n!IMPORTANT  \nAt the moment apparent FRET and stoichiometry are calculated from the defined photon streams and it is required the following streams are defined: 'AA', 'DD', 'DA' (=FRET). This is expected to be changed in future updates.\n\n## Development\n\nDownload a test file:\n\n```sh\nwget https://kuleuven-my.sharepoint.com/:u:/g/personal/jochem_smit_kuleuven_be/Efy7ur779ARNiBlP05Ki7NMBabKX3auswj30xmpRLaIfPg?e=E6wWoZ\u0026download=1\n```\n\n\nIf autoreload (refresh web application upon code changes) doesnt work, run from:\nsolara run dont_fret\\tmp.py -- --config default_testing.yaml\n\n### Create a new release\n\n- Create a new release on github. Create a new tag with the version (format: v0.1.0)\n- github actions creates release on pypi\n- done!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjhsmit%2Fdont-fret","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjhsmit%2Fdont-fret","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjhsmit%2Fdont-fret/lists"}