This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
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Project Description
Given multiple snpEff or VEP 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)

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` and one for `VEP`

`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.
Release History

Release History

0.2.0

This version

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0.1.3

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0.1.2

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0.1.1

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0.1.0

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0.0.9

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0.0.8

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0.0.7

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0.0.6

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0.0.5

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0.0.4

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0.0.3

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0.0.2

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0.0.1

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Download Files

Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
geneimpacts-0.2.0.tar.gz (28.8 kB) Copy SHA256 Checksum SHA256 Source Nov 8, 2016

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