Metadata-Version: 1.1
Name: geneimpacts
Version: 0.3.7
Summary: normalize effects from variant annotation tools (snpEff, VEP)
Home-page: UNKNOWN
Author: Brent Pedersen
Author-email: bpederse@gmail.com
License: UNKNOWN
Description: Given multiple snpEff or VEP or BCFTools consequence annotations for a single variant, get an orderable python object for each annotation.
        
        [![Build Status](https://travis-ci.org/brentp/geneimpacts.svg?branch=master)](https://travis-ci.org/brentp/geneimpacts)
        
        This is to provide a consistent interface to
        different 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).
        and the [BCFTools consequence field](http://biorxiv.org/content/early/2016/12/01/090811)
        
        This will be used in [gemini](http://gemini.rtfd.org/) but should also be of
        general utility.
        
        Design
        ======
        
        There is an effect base-class and then a sub-class for `snpEff`, one for `VEP`, and one for `BCFT`
        
        `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.
        
        Given 2 effects objects, `a` and `b`: `a < b == True` iff the *severity* of `b` is greater than `a`.
        
        We will have a classmethod: `Effect.top_severity([eff1, ... effn]) that will return the single highest serverity if that exists or
        a list of the ties for highest
        
        Rules for severity:
        ===================
        
        Given 2 annotations, *a* and *b*
        *a* is more severe than *b* if:
        
        1. *b* is a pseudogene and *a* is not
        2. *a* is coding and *b* is not
        3. *a* has higher severity than *b* ( see below)
        4. polyphen, then sift
        5. ??? transcript length? (we dont have access to this).
        
        severity
        --------
        
        Severity is based on the [impacts from VEP](http://uswest.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick)
        and the [impacts from snpEff](http://snpeff.sourceforge.net/VCFannotationformat_v1.0.pdf). We reduce from the 4 categories HIGH, MEDIUM, LOW, MODIFIER to 3 by renaming MEDIUM to MED and renaming MODIFIER to LOW.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
