{"id":42794382,"url":"https://github.com/qbicsoftware/mtb-parser-lib","last_synced_at":"2026-01-30T00:26:24.574Z","repository":{"id":57443772,"uuid":"115500842","full_name":"qbicsoftware/mtb-parser-lib","owner":"qbicsoftware","description":"A simple module for diagnostic variant information parsing","archived":false,"fork":false,"pushed_at":"2018-12-02T13:18:06.000Z","size":89,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-12-01T23:54:15.902Z","etag":null,"topics":["cnv","other","parser","python","snv","tumor"],"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/qbicsoftware.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}},"created_at":"2017-12-27T08:45:15.000Z","updated_at":"2018-12-02T13:18:08.000Z","dependencies_parsed_at":"2022-09-10T22:01:06.975Z","dependency_job_id":null,"html_url":"https://github.com/qbicsoftware/mtb-parser-lib","commit_stats":null,"previous_names":["qbicsoftware/qbic.mtbparser"],"tags_count":8,"template":false,"template_full_name":null,"purl":"pkg:github/qbicsoftware/mtb-parser-lib","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/qbicsoftware%2Fmtb-parser-lib","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/qbicsoftware%2Fmtb-parser-lib/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/qbicsoftware%2Fmtb-parser-lib/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/qbicsoftware%2Fmtb-parser-lib/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/qbicsoftware","download_url":"https://codeload.github.com/qbicsoftware/mtb-parser-lib/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/qbicsoftware%2Fmtb-parser-lib/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28891436,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-29T21:06:44.224Z","status":"ssl_error","status_checked_at":"2026-01-29T21:06:42.160Z","response_time":59,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["cnv","other","parser","python","snv","tumor"],"created_at":"2026-01-30T00:26:23.749Z","updated_at":"2026-01-30T00:26:24.568Z","avatar_url":"https://github.com/qbicsoftware.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# qbic.mtbparser\n\n[![GitHub top language](https://img.shields.io/github/languages/top/qbicsoftware/qbic.mtbparser.svg)]()\n[![Build status](https://travis-ci.org/qbicsoftware/mtb-parser-lib.svg?branch=master)](https://travis-ci.org/qbicsoftware/mtb-parser-lib.svg?branch=master)\n[![codecov](https://codecov.io/gh/qbicsoftware/mtb-parser-lib/branch/master/graph/badge.svg)](https://codecov.io/gh/qbicsoftware/mtb-parser-lib)\n[![GitHub tag](https://img.shields.io/github/release/qbicsoftware/qbic.mtbparser/all.svg)](https://github.com/qbicsoftware/qbic.mtbparser/releases)\n[![PyPI](https://img.shields.io/pypi/v/mtbparser.svg)](https://pypi.python.org/pypi/mtbparser/0.2)\n[![license](https://img.shields.io/github/license/qbicsoftware/qbic.mtbparser.svg)]() \n\nA simple module that provides parser for different diagnostic variant information as part of the Molecular Tumor Board data provisioning in Tübingen.\n\n## Documentation\n\nFile formats for\n* [Somatic SNVs](./docs/somatic_snvs.md)\n* [Somatic CNVs](./docs/cnvs.md)\n* [Somatic structural variants](./docs/structural_variants.md)\n* [Germline SNVs](./docs/germline_snvs.md)\n* [Germline CNVs](./docs/cnvs.md)\n* [Metadata](./docs/metadata.md)\n\nPython class info\n* SnvParser\n\n### How to use the SnvParser class\n\nParsing a SNV file following the formats described above is fairly simple. Just create an ``SnvParser`` object with the path to the ``tsv``-file and specify its type by providing the correct header (``SSnvHeader, GSnvHeader, ...``).\n\n```python\nfrom mtbparser.snv_parser import SnvParser\nfrom mtbparser.snv_utils import SSnvHeader\n\n# Path to a valid SNV tsv file, as specified in\n# the file format documentation.\nsomatic_snv_file = \"/path/to/mySSnv.tsv\"\n\n# Create parser object for somatic SNVs\nparser = SnvParser(somatic_snv_file, SSnvHeader)\n\n# Iterate through parsed SNV items and get the gene name\nfor snv_item in parser.getSNVs():\n    print(snv_item.get_snv_info(SSnvHeader.GENE.name))\n    \n```\n\n## Author\nThis code implementation was done at the [Quantitative Biology Center](http://qbic.life). Please contact the author [@sven1103](https://github.com/sven1103) for more information.\n\n\n## Changelog\n\n### v0.2.7\nRename enums, so their names and values are equal.\n\n### v0.2.6\nYou can now extract a copy of the complete SNV Item information as dictionary.\n\n### v0.2.5\nBugfix: parsing of empty first columns failed because of the usage of strip() function. Columns can be empty, if they contain no information, so trimming whitespaces leads to a wrong total column number. We use rstrip() now, to remove escape characters and trailing whitespaces.\n\n### v0.2.4\nFixed typo in 'tumor_content' definition in the metadata section.\n\n### v0.2.3\nJust v0.2.2, but had to rename the version on PyPi\n\n### v0.2.2\nReading of files failed, because Python expects ACII encoding by default. Now, files are explicitely opened with utf-8 encoding.\n\n### v0.2.1\nInstallation with ``pip`` failed, because the DESCRIPTION.rst for the module description was not provided in the sdist package.\n\n### v0.2\nThe first _production-ready_ version of ``mtbparser``, that is also deployed on PyPI. Only updated documentation and proper formatting for PyPI deployment.\n\n### v0.1dev\nA first develeopment version, should work, tests are good, coverage \u003e 90%.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fqbicsoftware%2Fmtb-parser-lib","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fqbicsoftware%2Fmtb-parser-lib","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fqbicsoftware%2Fmtb-parser-lib/lists"}