https://github.com/brentp/inheritance
inheritance models for mendelian diseases
https://github.com/brentp/inheritance
Last synced: 4 months ago
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inheritance models for mendelian diseases
- Host: GitHub
- URL: https://github.com/brentp/inheritance
- Owner: brentp
- License: mit
- Created: 2015-10-28T22:53:37.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2019-01-16T19:33:31.000Z (over 6 years ago)
- Last Synced: 2024-05-01T22:46:29.835Z (about 1 year ago)
- Language: Python
- Size: 74.2 KB
- Stars: 7
- Watchers: 3
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
inheritance models for mendelian diseases
-----------------------------------------
[](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`.