arv 0.1

A fast 23andMe raw genome file parser

arv — a fast 23andMe parser for Python

Arv (Norwegian; “inheritance” or “heritage”) is a Python module for parsing raw 23andMe genome files. It lets you lookup SNPs from RSIDs.

from arv import load, unphased_match as match

genome = load("genome.txt")

print("You are a {gender} with {color} eyes and {complexion} skin.".format(
  gender     = "man" if genome.y_chromosome else "woman",
  complexion = "light" if genome["rs1426654"] == "AA" else "dark",
  eyecolor   = match(genome["rs12913832"], {"AA": "brown",
                                            "AG": "brown or green",
                                            "GG": "blue"})))

In my case, this little program produces:

You are a man with blue eyes and light skin.

It’s insanely fast: On a 2013 Xeon machine, a 24 Mb file is fully parsed and put into a hash table in less than 70 ms. Its guts are written in finely tuned C++ and is exposed to Python via Cython.

Status

> This project is currently just a work in progress! I intend to wrap dna-traits under a new name, using Cython to interface with dna-traits much more easily. For a working (but old) version, see https://github.com/cslarsen/dna-traits

Installation

The recommended way is to install from PyPi.

$ pip install arv

NOTE: PyPi/pip is not yet available!

In the meantime, you can do

$ python setup.py install

License

Copyright 2014, 2016, 2017 Christian Stigen Larsen Distributed under the GNU GPL v3 or later.

See the file COPYING for the full license text. This software makes use of open source software; see LICENSES for details.

This code is largely based on the project dna-traits, by the same author.