KennethEnevoldsen / snip

A utility package handling Single Nucleotide polymorphism data in Python

Snip: A package for data handling and model training using Single Nucleotide polymorphism data

A package for data handling and model training using Single Nucleotide polymorphism data. Implemented in Python and PyTorch.

🔧 Installation

To get started using this package install it using pip by running the following line in your terminal:

pip install git+https://github.com/KennethEnevoldsen/snip

For more detailed instructions on installing see the installation instructions.

Development Setup

To set up the project for development:

conda create -n snip python=3.9
conda activate snip
conda install poetry
peotry install

👩‍💻 Getting started

Convert

To convert .bed files to .zarr simply run from your terminal:

snip convert sample.bed sample.zarr

or equivalently:

python -m snip convert sample.bed sample.zarr

Learn more

To see a list of possible commands:

snip --help

To find out more about each command:

snip convert --help

Slurm

This project uses slurm.

Slurm quick guide

To run a job:

sbatch {filename}.sh -A NLPPred

Where A stands for account and NLPPred is the account.

Check the status of submitted queue:

squeue -u {username}

See available nodes:

gnodes

SSH to node:

ssh {node id}

Run an interactive window:

srun --pty -c 4 --mem=16g bash -A NLPPred

Using 4 cores and 16GB memory.

For more on slurm please check out this site.

💬 Where to ask questions

Type
🚨 Bug Reports	GitHub Issue Tracker
🎁 Feature Requests & Ideas	GitHub Issue Tracker
👩‍💻 Usage Questions	GitHub Discussions
🗯 General Discussion	GitHub Discussions