{ "info": { "author": "Brent Pedersen", "author_email": "bpederse@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Given multiple snpEff or VEP or BCFTools consequence annotations for a single variant, get an orderable python object for each annotation.\n\n[![Build Status](https://travis-ci.org/brentp/geneimpacts.svg?branch=master)](https://travis-ci.org/brentp/geneimpacts)\n\nThis is to provide a consistent interface to\ndifferent variant annotations such as from [snpEff ANN field](http://snpeff.sourceforge.net/) and the [VEP CSQ field](http://www.ensembl.org/info/docs/tools/vep/index.html).\nand the [BCFTools consequence field](http://biorxiv.org/content/early/2016/12/01/090811)\n\nThis will be used in [gemini](http://gemini.rtfd.org/) but should also be of\ngeneral utility.\n\nDesign\n======\n\nThere is an effect base-class and then a sub-class for `snpEff`, one for `VEP`, and one for `BCFT`\n\n`Effect` objects are orderable (via \\_\\_le\\_\\_ ) and should have an \\_\\_eq\\_\\_ method so that we can use [functools.total_ordering](https://docs.python.org/2/library/functools.html#functools.total_ordering) to provide the other comparison operators.\n\nGiven 2 effects objects, `a` and `b`: `a < b == True` iff the *severity* of `b` is greater than `a`.\n\nWe will have a classmethod: `Effect.top_severity([eff1, ... effn]) that will return the single highest serverity if that exists or\na list of the ties for highest\n\nRules for severity:\n===================\n\nGiven 2 annotations, *a* and *b*\n*a* is more severe than *b* if:\n\n1. *b* is a pseudogene and *a* is not\n2. *a* is coding and *b* is not\n3. *a* has higher severity than *b* ( see below)\n4. polyphen, then sift\n5. ??? transcript length? 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