Metadata-Version: 1.1
Name: inheritance
Version: 0.1.2
Summary: inheritance models for mendelian genetics
Home-page: UNKNOWN
Author: Brent Pedersen
Author-email: bpederse@gmail.com
License: UNKNOWN
Description: inheritance models for mendelian diseases
        -----------------------------------------
        
        [![Build Status](https://travis-ci.org/brentp/inheritance.svg?branch=master)](https://travis-ci.org/brentp/inheritance)
        
        This module is a general-purpose framework for evaluating if a family exihibits, for example, and autosomal dominant pattern.
        The logic for this was tuned in [gemini](https://github.com/arq5x/gemini) but we make it available here as a more general purpose library to encourage:
        1. community driven improvements
        2. use outside of gemini
        3. more comprehensive testing
        
        Finding variants that match autosomal dominance in a trio, for example is very simple to find,
        however, after considering multiple generations, arbitrary family sizes, depth cutoffs, and unknown
        genotypes and phenotypes to support to real-world datasets it becomes tedious and error-prone.
        
        Supported inheritance tests
        ===========================
        
        + autosomal dominant
        + autosomal recessive
        + de novo
        + X-linked dominant, recessive, and de novo
        + compound heterozygote
        + mendelian violation
        
        Usage
        =====
        
        For now, the use is via api only. Users can look at the tests to see how to use. Most functions have a signature like:
        
        ```Python
         auto_dom(self, min_depth=0, gt_ll=False, strict=True, only_affected=True)
        ```
        
        where the arguments enforce a minimum depth, a maximum genotype likelihood, strictness (mostly related to parent-offspring requirements)
        and wether to allow unaffecteds to have the variant (or be homozygous alt).
        
        ToDo
        ====
        1. add support for X-linked soon.
        2. add a simple example of running on a VCF+PED
        3. code coverage
        4. code documentation
        
        Testing
        =======
        
        Tests can be run as:
        
        ```
        nosetests --with-coverage -x --with-doctest --cover-package inheritance
        ```
        
        Overview
        ========
        
        the generic code is in `inheritance/inheritance.py` and a specific implementation that we use in gemini is in `inheritance/pyeval.py`.
        To make this available for a new resource, for example to `bcftools` we would look at the implementation of Filter in `inheritance/pyval.py`
        and make the generated strings match those expected by `bcftools`.
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
