{"id":17060640,"url":"https://github.com/ahwagner/pymvld","last_synced_at":"2025-03-23T08:14:37.837Z","repository":{"id":147729749,"uuid":"142964259","full_name":"ahwagner/pymvld","owner":"ahwagner","description":"A Python implementation of the Minimum Variant Level Data standard","archived":false,"fork":false,"pushed_at":"2018-08-25T05:36:38.000Z","size":15,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-01-28T14:47:55.036Z","etag":null,"topics":["genomics","standards","variant-interpretation"],"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/ahwagner.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}},"created_at":"2018-07-31T04:59:15.000Z","updated_at":"2018-08-25T05:36:39.000Z","dependencies_parsed_at":"2023-06-15T03:30:12.338Z","dependency_job_id":null,"html_url":"https://github.com/ahwagner/pymvld","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ahwagner%2Fpymvld","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ahwagner%2Fpymvld/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ahwagner%2Fpymvld/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ahwagner%2Fpymvld/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ahwagner","download_url":"https://codeload.github.com/ahwagner/pymvld/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245072268,"owners_count":20556353,"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":["genomics","standards","variant-interpretation"],"created_at":"2024-10-14T10:44:51.894Z","updated_at":"2025-03-23T08:14:37.828Z","avatar_url":"https://github.com/ahwagner.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pyMVLD\npyMVLD is a Python implementation of the Minimum Variant Level Data framework of standardized data elements, first defined by the ClinGen Somatic Working Group in 2016 ([paper](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0367-z)).\n\n![MVLD Figure](https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs13073-016-0367-z/MediaObjects/13073_2016_367_Fig3_HTML.gif)\n\n## Why use pyMVLD\npyMVLD is an implementation of the MVLD framework for ensuring compliance. Use of this module provides:\n* Validation of correct data types and values when generating MVLD objects\n* Immutable, standardized objects for downstream applications\n* Framework versioning\n\n## How to use pyMVLD\nCreating an MVLD object first requires construction of three sub-objects corresponding to the three field sets described by the framework: _AlleleDescriptive_, _AlleleInterpretive_, and _SomaticInterpretive_.\n\n### Allele Descriptive Fields\nThe Allele Descriptive fields are expected to conform to the following rules:\n\n#### Genome Version\nThe Genome Version must be in the GRCh37/GRCh38 format, preferably with the build version (e.g. GRCh38.p12). pyMVLD explicitly limits the values to a `str` describing GRCh37 or GRCh38, the two major GRC assemblies that are currently available. The assembly version, if provided, is checked only for syntactic correctness, not that it corresponds to a published version.\n\n#### Gene\nGenes must be provided as HGNC Approved Gene Symbols. The `Gene` field is checked to be a `str`, and is compared against the current HGNC list of approved symbols. If not HGNC Approved, the raised error describes the use of a known alias or retired symbol, if applicable.\n\n### Examples\n```\nkwargs = {\n        'genome_version': 'GRCh37',\n        'gene': 'BRAF',\n        'chromosome': 'chr7',\n        'dna_position': 'NC_000007.13:g.140453136A\u003eT',\n        'refseq_transcript': 'NM_004333.4',\n        'refseq_protein': 'NP_004324.2'\n}\nad = AlleleDescriptive(**kwargs)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fahwagner%2Fpymvld","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fahwagner%2Fpymvld","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fahwagner%2Fpymvld/lists"}