Code Review 10 April 2024.

This repo contains scripts to calculate Linkage Disequilibirum (LD) measures. Info on LD: https://docs.google.com/presentation/d/1I6e-q22om6AiI-cYjlJ7pJ3f5w0gQTDE/edit?usp=sharing&ouid=115928088663191390220&rtpof=true&sd=true

Requirements

• csv
• pandas
• matplotlib.pyplot
• numpy
• itertools

Scripts

1. PyLD.py - contains functions to read a VCF, obtain genotype, obtain haplotype, calculate LD measures, outputs a dictionary of LD measures for each rs ID pair, and can create a CSV file of the output.
2. heatmaps.py - contains functions to create a heatmap each of the LD measures.

Examples

• example.ipynb - An example of how to run the code.
• toy_data.vcf - Example data. This is actually a subset of the British population VCF from 1000 Genomes Project
• toy_data_output.csv - Example output from the PyLD.py script.
• r2.png, dprime.png - Example outputs from the heatmaps.py script.

PyPi scripts

• setup.py - set up code to set up as a PyPi packed - stil to do.

Things I'd like feedback/advice on

• structure of repo
• setting up a PyPi package
• any code advice - e.g my use of functions and classes?
• tests?
• poetry?
• anything else :)