This repository contains some of the script I wrote for 580.488 Foundations of Computational Biology and Bioinformatics to simplify data collection and processing.
This script allows the user to grab all 23andme genomes for a given phenotype. It is assumed that the given phenotype is valid. The script also performs a simple validation check and moves files that fail to a separate directory.
This tool saves phenotypes into a folder structure separated by variant name as shown below:
- (root)
- [phenotype#]
- [variant1]
- file1
- file2
- ...
- [variant2]
- file3
- ...
- ...
- [variant1]
- [phenotype#]
This script requires that bs4 be installed within the Python
environment you are running this script in.
This script allows the user submit all files in a directory to the Haplotype Imputer at http://hapimpute.opencravat.org/. The script will also monitor the progress of each job and automatically download the resulting imputed data file once the job is complete.
This script will open a Chrome window that is automatically controlled, which can be minimized for the duration of the run.
This script requires that tqdm and selenium be installed within the
Python environment you are running this script in. The chromedriver
executable is also needed, which can be downloaded from
https://chromedriver.chromium.org/downloads. Download the
version corresponding to the version of Chrome that is installed on
your system.