https://github.com/zeqianli/carbonutilization
Code for the carbon utilization project.
https://github.com/zeqianli/carbonutilization
Last synced: 3 months ago
JSON representation
Code for the carbon utilization project.
- Host: GitHub
- URL: https://github.com/zeqianli/carbonutilization
- Owner: zeqianli
- Created: 2022-12-26T17:46:57.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-03-25T06:50:46.000Z (about 1 year ago)
- Last Synced: 2024-03-25T07:51:38.126Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 42.2 MB
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Predict microbial metabolic traits from genomes
Zeqian Li, Ahmed Selim, Seppe Kuehn
Last update: Mar 24th, 2024
## Files
- `snakemake`: snakemake pipeline for bioinformatic pipeline and fba simulation. See `snakemake/README`.
- `organize_data.ipynb`: organize the three datasets
- `figures.ipynb`: Jupyter notebook to generate figures
- `figures_*.ipynb:` Jupyter notebook to generate specific panels
- `figures_SI.ipynb`: code to generate SI figures
- `workflows/gapfill`: snakemake pipelines to study the effects of gap-filled carbons.
## Data
Data files are deposited to the [Open Science Framework (OSF)](https://osf.io/jwkr7/)
## Setup
1. If you use conda environments or pyenv, create and switch to a new environment.
2. Install packages
```
pip install -r requirements.txt
```
3. Download data
```
mkdir data && cd data
osf -p jwkr7 clone
mv -v data/jwkr7/osfstorage/* .
rm -rf jwkr7
```
`figure_data.zip` contains pre-trained data saved in pickle.
## Citation
[Li, Zeqian, Ahmed Selim, and Seppe Kuehn. "Statistical prediction of microbial metabolic traits from genomes." PLOS Computational Biology 19, no. 12 (2023): e1011705.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011705)
## Contact
Zeqian Li ([email protected])