Make Summary Excel Files from Frequency Files

Clone and Run the project

1. Clone the repository locally

   git clone https://github.com/pbashyal-nmdp/make-summary-freqs.git
   cd urban-potato

2. Make a virtual environment by running make venv

    > make venv
    uv venv --prompt make-summary-freqs-venv
    Using CPython 3.13.0
    Creating virtual environment at: .venv
    Activate with: source .venv/bin/activate

3. Source the virtual environment

   source .venv/bin/activate

4. Install dependencies

   make install

Make commands

Development workflow is driven through Makefile. Use make to list show all targets.

> make
clean                remove all build and other Python artifacts
clean-build          remove build artifacts
clean-pyc            remove Python file artifacts
lint                 check style with ruff
install              install packages
local                Make local environment editable
run                  Run main script
venv                 Create a Python3 virtualenv environment in .venv
activate             Activating the virtual environment. Run `make venv` before activating.
bump-dry             Bump up the patch version (dry-run)

Copy/Link frequency data folder to freqs folder

main.py

Method

For each haplotype, sum all the frequencies for all populations to calculate total frequency for that haplotype. Once you do this for all haplotypes across all populations (All 26 popularions: 21 detailed and 5 broad) then sort by that total frequency.

When doing it for fewer locus, reduce to those combination first (need to renormalize) from 9-locus and then apply the above method. When you reduce by collapsing loci, the freqs should still add to 1.