Belval / AlphaMissenseCheck

See how pathogenic your mutations are according to AlphaMissense based on your 23andme raw data

AlphaMissenseCheck

How to use

1. Clone the repository git clone https://github.com/Belval/AlphaMissenseCheck.git
2. Download the AlphaMissense_hg19.tsv.gz file
3. Download your genome data from 23andme
4. Un-gzip both and rename your genome file as "genome.txt"
5. Install dependencies pip install -r requirements.txt
6. Run python check.py

Output

The script will print all your mutations with their classification and then print a small summary. Here is mine for reference:

Report:
        % Mutated genes: 1.97%
        % Mutated genes with at least 1 allele classified as benign: 93.98%
        % Mutated genes with at least 1 allele classified as ambiguous: 3.94%
        % Mutated genes with at least 1 allele classified as pathogenic: 2.08%
        % Mutated genes with 2 alleles classified as benign: 31.11%
        % Mutated genes with 2 alleles classified as ambiguous: 0.88%
        % Mutated genes with 2 alleles classified as pathogenic: 0.33%