# LanceOTron CLI
[](https://badge.fury.io/py/lanceotron) [](https://pepy.tech/project/lanceotron) [](https://circleci.com/gh/Chris1221/lanceotron/tree/main) [](https://codecov.io/gh/Chris1221/lanceotron)
A bare-bones interface to the trained LanceOTron (LoT) model from the command line.
## Installation
```{sh}
pip install lanceotron
```
### Local installation
1. Clone the repository.
2. Install dependencies with pip.
3. Install the package.
4. Run tests to ensure that everything is working.
```{sh}
git clone git@github.com:Chris1221/lanceotron.git; cd lanceotron # Step 1
pip install -r requirements.txt # Step 2
pip install -e . # Step 3
python -m unittest
```
## Usage
To see available commands, use the `--help` flag.
```
lanceotron --help
```
## Call Peaks
To call peaks from a bigWig track, use the `callPeaks` command.
| Option | Description | Default |
|-----------------|--------------------------------------------------------|---------|
| file | BigWig Track to analyse | |
| -t, --threshold | Threshold for selecting candidate peaks | 4 |
| -w, --window | Window size for rolling mean to select candidate peaks | 400 |
| -f, --folder | Output folder | "./" |
| --skipheader | Skip writing the header | False |
## Call Peaks with Input
To call peaks from a bigWig track with an input file, use the `callPeaks_Input` command.
| Option | Description | Default |
|-----------------|--------------------------------------------------------|---------|
| file | BigWig track to analyse | |
| -i, --input | Control input track to calculate significance of peaks | |
| -t, --threshold | Threshold for selecting candidate peaks | 4 |
| -w, --window | Window size for rolling mean to select candidate peaks | 400 |
| -f, --folder | Output folder | "./" |
| --skipheader | Skip writing the header | False |
## Score a Bed file
To score the peaks in an existing Bed file, use the `scoreBed` command.
| Option | Description | Default |
|-----------------|--------------------------------------------------------|---------|
| file | BigWig Track to analyse | |
| -b, --bed | Bed file of regions to be scored | |
| -f, --folder | Output folder | "./" |
| --skipheader | Skip writing the header | False |
## Examples
There is a basic bigWig file included in the `test` subdirectory. To try out the caller, execute it on this file.
```sh
lanceotron callPeaks test/chr22.bw -f output_folder
```
## Citation
```{bibtex}
@article {Hentges2021.01.25.428108,
author = {Hentges, Lance D. and Sergeant, Martin J. and Downes, Damien J. and Hughes, Jim R. and Taylor, Stephen},
title = {LanceOtron: a deep learning peak caller for ATAC-seq, ChIP-seq, and DNase-seq},
year = {2021},
doi = {10.1101/2021.01.25.428108},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2021/01/27/2021.01.25.428108},
journal = {bioRxiv}
}
```
## Building the documentation
To serve the documentation locally, use
```
python -m mkdocs serve
```
## Bug Reports and Improvement Suggestions
Please [raise an issue](https://github.com/Chris1221/lanceotron/issues/new/choose) if there is anything you wish to ask or contribute.
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