Skip to content
No description, website, or topics provided.
Python HTML CSS
Branch: master
Clone or download
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
css
templates Modified not found color + correction on description Dec 13, 2016
.gitignore
LICENSE
README.md
SNPs_public.csv
console.py
csv_snp_manipulation.py
genotype.py Splitted the functions into smaller chunks and added a different meth… Oct 26, 2016
phenotype.py Modified not found color + correction on description Dec 13, 2016
requirements.txt requires texttable Nov 22, 2016
run.py Prints out a nice table in the console Nov 22, 2016
trait.py version 1 Aug 8, 2013
web.py

README.md

Genotype-Phenotype Mapping

This program will interpret a 23andme OR VCF datafile as a predicted phenotype profile
It is a work in progress!
I am in the process of adding more info, traits, ancestry, etc. It also needs to take account of SNP interactions with each other (I would love some help working on this) This is the underlying idea behind Stranger Visions, an artwork which imagines what strangers might look like from their DNA. http://deweyhagborg.com/projects/stranger-visions

Originally designed for 23andme style data it works with VCF files now too. You can generate a larger imputed genotype file from your 23andme results over at DNA Land https://dna.land/

This program works with Python 2.7

If you are having trouble with dependencies you might want to consider running this program in a virtual environment. See: http://docs.python-guide.org/en/latest/dev/virtualenvs/

Installation

$ pip install -r requirements.txt

Running the program

From commandline

Programs runs with 2 cmdline arguments:

  • a 23andMe datafile or a VCF file
  • the included SNPS database CSV file, ie.

$ python run.py "/Users/name/Documents/SNP_files/genome_NAME.txt" "/Users/name/Documents/workspace/genotype-phenotype/src/SNPs_public.csv"

For the web app

$ python web.py

Then open a browser and navigate to http://localhost:8080

Notes

For an example 23andme data file see:

You can’t perform that action at this time.