snip
A utility package handling Single Nucleotide polymorphism data in Python
Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (17.8%) to scientific vocabulary
Keywords
Repository
A utility package handling Single Nucleotide polymorphism data in Python
Basic Info
- Host: GitHub
- Owner: KennethEnevoldsen
- License: mit
- Language: Python
- Default Branch: main
- Homepage: https://kennethenevoldsen.github.io/snip/
- Size: 22.4 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 16
- Releases: 1
Topics
Metadata Files
README.md
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:
bash
snip convert sample.bed sample.zarr
or equivalently:
bash
python -m snip convert sample.bed sample.zarr
Learn more
To see a list of possible commands:
bash
snip --help
To find out more about each command:
bash
snip convert --help
Slurm
This project uses slurm.
Slurm quick guide
**To run a job:** ```bash 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:** ```bash 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](https://docs.rc.fas.harvard.edu/kb/convenient-slurm-commands).
💬 Where to ask questions
| Type | | | ------------------------------ | ---------------------- | | 🚨 Bug Reports | GitHub Issue Tracker | | 🎁 Feature Requests & Ideas | GitHub Issue Tracker | | 👩💻 Usage Questions | GitHub Discussions | | 🗯 General Discussion | GitHub Discussions |
Owner
- Name: Kenneth Enevoldsen
- Login: KennethEnevoldsen
- Kind: user
- Location: Aarhus
- Company: Center for Humanities Computing Aarhus
- Website: kennethEnevoldsen.com
- Twitter: KCEnevoldsen
- Repositories: 9
- Profile: https://github.com/KennethEnevoldsen
Interdisciplinary PhD Student on representation learning in Clinical NLP and Genetics at Aarhus University and Interacting Minds Centre
Citation (citation.cff)
cff-version: 1.2.0 message: "If you use this package, please cite it as below." authors: - family-names: "Enevoldsen" given-names: "Kenneth" orcid: "https://orcid.org/0000-0001-8733-0966" title: "Snip: A package for analysing Single Nucleotide polymorphisms In Python" year: 2022 url: "https://github.com/KennethEnevoldsen/snip" date-released: 2022-04-07
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 22
- Total pull requests: 40
- Average time to close issues: 22 days
- Average time to close pull requests: 2 days
- Total issue authors: 2
- Total pull request authors: 3
- Average comments per issue: 0.36
- Average comments per pull request: 0.6
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 35
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- KennethEnevoldsen (21)
- Cherished-l (1)
Pull Request Authors
- dependabot[bot] (33)
- KennethEnevoldsen (5)
- pre-commit-ci[bot] (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
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- actions/setup-python v4 composite
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- actions/checkout v3 composite
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- schneegans/dynamic-badges-action v1.4.0 composite
- snok/install-poetry v1.3.1 composite
- snok/install-poetry v1 composite
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