{"id":20371802,"url":"https://github.com/biosustain/genomediff-python","last_synced_at":"2025-04-12T06:30:32.183Z","repository":{"id":16978616,"uuid":"19741344","full_name":"biosustain/genomediff-python","owner":"biosustain","description":"GenomeDiff (*.gd) file parser for Python","archived":false,"fork":false,"pushed_at":"2019-10-11T20:51:06.000Z","size":16,"stargazers_count":2,"open_issues_count":3,"forks_count":7,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-04-06T10:44:49.529Z","etag":null,"topics":["breseq","genomediff","genomics","parser"],"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/biosustain.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}},"created_at":"2014-05-13T14:03:59.000Z","updated_at":"2023-09-06T09:14:58.000Z","dependencies_parsed_at":"2022-09-19T08:31:01.493Z","dependency_job_id":null,"html_url":"https://github.com/biosustain/genomediff-python","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fgenomediff-python","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fgenomediff-python/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fgenomediff-python/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosustain%2Fgenomediff-python/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biosustain","download_url":"https://codeload.github.com/biosustain/genomediff-python/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248529117,"owners_count":21119449,"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":["breseq","genomediff","genomics","parser"],"created_at":"2024-11-15T01:09:51.111Z","updated_at":"2025-04-12T06:30:32.122Z","avatar_url":"https://github.com/biosustain.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"genomediff-python\n=================\n\n**genomediff-python** parses files in the\n`GenomeDiff format \u003chttp://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/gd_format.html\u003e`_\ngenerated by the `breseq \u003chttp://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/index.html\u003e`_\nvariant caller for haploid microbial organisms.\n\n\nInstallation\n------------\n\n::\n    \n    pip3 install genomediff\n\n\nOnly Python 3.x is tested.\n\nUsage\n-----\n\nGenomeDiff files are read using ``GenomeDiff.read(file)``. The ``GenomeDiff`` object contains a ``metadata`` dict with\nthe meta data, as well as ``mutations``, ``evidence`` and ``validation`` lists—each containing records of that type.\nRecords can be accessed through this list or by id. ``GenomeDiff`` is iterable and iterating will return all records of all types.\n\n::\n\n    \u003e\u003e\u003e from genomediff import *\n    \u003e\u003e\u003e document = GenomeDiff.read(open('MyDiff.gd', 'r', encoding='utf-8'))\n    \u003e\u003e\u003e document.metadata\n    {'GENOME_DIFF': '1.0', 'AUTHOR': ''}\n    \u003e\u003e\u003e document.mutations[0]\n    Record('SNP', 1, [191], new_seq='A', seq_id='NC_000913', snp_type='intergenic',  position=12346)\n    \u003e\u003e\u003e document.mutations[0].parent_ids\n    [191]\n    \u003e\u003e\u003e document[191]         \n    Record('RA', 191, None, tot_cov='46/42', new_base='A', insert_position=0, ref_base='G', seq_id='NC_000913', quality=252.9, position=12345)\n    \u003e\u003e\u003e document.mutations[0].parents\n    [Record('RA', 191, None, tot_cov='46/42', new_base='A', insert_position=0, ref_base='G', seq_id='NC_000913', quality=252.9, position=12345)]\n\nContribution\n------------\n\nContribution to this project is welcomed. Wishlist:\n\n- Writing GD files\n- Python 2.x support\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Fgenomediff-python","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosustain%2Fgenomediff-python","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosustain%2Fgenomediff-python/lists"}