A utility package handling Single Nucleotide polymorphism data in Python
MIT License
A package for data handling and model training using Single Nucleotide polymorphism data. Implemented in Python and PyTorch.
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.
To set up the project for development:
conda create -n snip python=3.9
conda activate snip
conda install poetry
peotry install
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
To see a list of possible commands:
snip --help
To find out more about each command:
snip convert --help
This project uses slurm.
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.
Type | |
---|---|
🚨 Bug Reports | GitHub Issue Tracker |
🎁 Feature Requests & Ideas | GitHub Issue Tracker |
👩💻 Usage Questions | GitHub Discussions |
🗯 General Discussion | GitHub Discussions |