{"id":22313719,"url":"https://github.com/ctb/sourmash_plugin_load_from_fasta","last_synced_at":"2025-03-26T02:41:44.740Z","repository":{"id":187729504,"uuid":"677424826","full_name":"ctb/sourmash_plugin_load_from_fasta","owner":"ctb","description":"An experimental plugin to load sketches from a FASTA/FASTQ file with lazy sketching.","archived":false,"fork":false,"pushed_at":"2023-08-11T16:46:58.000Z","size":91,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-30T23:47:24.237Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ctb.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}},"created_at":"2023-08-11T14:39:22.000Z","updated_at":"2023-09-11T02:22:04.000Z","dependencies_parsed_at":"2023-08-11T23:45:21.279Z","dependency_job_id":null,"html_url":"https://github.com/ctb/sourmash_plugin_load_from_fasta","commit_stats":null,"previous_names":["ctb/sourmash_plugin_load_from_fasta"],"tags_count":0,"template":false,"template_full_name":"sourmash-bio/sourmash_plugin_template","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2Fsourmash_plugin_load_from_fasta","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2Fsourmash_plugin_load_from_fasta/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2Fsourmash_plugin_load_from_fasta/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctb%2Fsourmash_plugin_load_from_fasta/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ctb","download_url":"https://codeload.github.com/ctb/sourmash_plugin_load_from_fasta/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245579416,"owners_count":20638675,"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":"2024-12-03T22:07:59.609Z","updated_at":"2025-03-26T02:41:44.702Z","avatar_url":"https://github.com/ctb.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# sourmash_plugin_load_from_fasta\n\n**This is an experimental plugin. Do not use for real work :).**\n\nThis is a sourmash plugin that will directly load a FASTA/FASTQ file as a\nsketch. It does so in a \"lazy\" manner: the file is not sketched until\na specific ksize/moltype/scaled is requested.\n\nFor example, the following command is run directly on FASTA files!\n```\n% sourmash search examples/{47,63}.head.fa\n\nselect query k=31 automatically.\nloaded query: NC_009665.1 Shewanella baltica... (k=31, DNA)\nReturning ScreedFileIndex.head.fa'...\ncreating ScreedFileIndex('examples/63.head.fa')\n--\nloaded 1 total signatures from 1 locations.\nafter selecting signatures compatible with search, 1 remain.\n\n1 matches above threshold 0.080:\nsimilarity   match\n----------   -----\n 29.6%       NC_011663.1 Shewanella baltica OS223, complete genome\n```\n\nThis means that you can immediately do comparisons with any k-mer\nsize, moltype, scaled, etc.\n\nIn exchange, the file is sketched each time.\n\nAmusingly, this also lets you replace `sourmash sketch` calls with\n`sig cat`:\n```\nsourmash sig cat examples/47.head.fa -k 12 -o 47.head.zip\n```\n\n(There's no real immediate purpose to this other than to explore the concept!)\n\n## Installation\n\n```\npip install sourmash_plugin_load_from_fasta\n```\n\n## Usage\n\nMore info goes here :).\n\n## Support\n\nWe suggest filing issues in [the main sourmash issue tracker](https://github.com/dib-lab/sourmash/issues) as that receives more attention!\n\n## Dev docs\n\n`sourmash_plugin_load_from_fasta` is developed at\nhttps://github.com/ctb/sourmash_plugin_load_from_fasta\n\n### Generating a release\n\nBump version number in `pyproject.toml` and push.\n\nMake a new release on github.\n\nThen pull, and:\n\n```\npython -m build\n```\n\nfollowed by `twine upload dist/...`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctb%2Fsourmash_plugin_load_from_fasta","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fctb%2Fsourmash_plugin_load_from_fasta","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctb%2Fsourmash_plugin_load_from_fasta/lists"}