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qclayssen authored Apr 5, 2021
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This project is provided with a tool to generate some naive data set. This tool fit with a logistic regression and produce a data set of given sizes with a given number of causal SNPs. This operation is performed by simu_naive.py.

### Prerequisite, generation of right virtual environment

These steps are done if installation_of_project.sh was used.

Some packages are required to run this tool. List of them is provided with needed version in environment.yml or environment.txt file. In order to generate a virtual environment where simu_naive.py can be executed please follow next steps.

For this step conda is needed, please follow instructions from anaconda documentation to get it installed. If conda is installed please execute this line to generate an environment called projet_c:

conda env create -f ./environment_to_execute_python/environment.yml

If virtualenv if prefered and is not installed. Please use following lines:

pip install virtualenv
virtualenv -p /usr/bin/python3.6 projet_c
source projet_c/bin/activate
pip install -r environment.txt
deactivate



Following this, activate this environment and execute simu_naive with arguments:

source activate projet_c
./simu_naive.py -p simu_naive -f 1 -v 28 -pa 2000 -o toy_dataset -c 2000 -s 2
source deactivate

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