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Hacking Race - Planning.pdf
README.md
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classify_HG01108_group_probabilities.csv
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gtm_config.py
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hacker.py
hacker.py~
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kenya_dig_it_2control_plot.html
kenya_dig_it_control_plot.html
kenya_dig_it_group_probabilities.csv
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kenya_dig_it_trainedMap.html
requirements.txt
standard_config.json
util.py

README.md

hacking_race

problems with "ancestry reports"

BioHacking Village

Make sure you have git, python, and pip installed

Step 0 (Optional): Make a virtual environment

This part is optional but encouraged because we're about to download files and stuff that might mess up existing dependencies you have in your dev environment. We'll be following the instructions from: https://docs.python-guide.org/dev/virtualenvs/

$ cd ~

$ sudo apt install virtualenv

$ cd <directory_path_you_work_in> ie. $ cd Downloads or something

$ virtualenv -p /usr/bin/python2.7 venv to make a virtual environment named venv

$ source venv/bin/activate to activate the virtual environment

Step 1: CLONE THIS REPO

$ cd venv

$ git clone https://github.com/herroannekim/hacking_race.git into your virtual environment

Step 2: Download the Data

$ ./download_viz.sh

Step 3: Install dependencies

Either make a virtual environment or install the dependencies to your system:

$ pip install -r requirements.txt

Step 4: Run ancestry prediction and clustering

In this example, we're running a prediction on sample HG01108, a Puerto Rican female

http://www.internationalgenome.org/data-portal/sample/HG01108

$ python2 hacker.py --model GTM --out classify_HG01108 --config ./standard_config.json --classify-id HG01108

Step 5: Hack 3:D

For the ancestry hack, we will now shift her ancestry towards Kenyan using

$ python2 hacker.py --model GTM --out kenya_dig_it --classify-id HG01108 --config ./standard_config.json --manipulate-towards "Luhya_in_Webuye,_Kenya"

Step 6: Check your work

  • Now you should be able to check the output and cluster graphs :)

Step 7 (optional): Clean up

If you used a virtual environment, you can clean up with $ deactivate

You can’t perform that action at this time.