# SuperSeeker Pipeline
The SuperSeeker pipeline is a Python library for identifying subclonal evolution in cancer. It integrates various tools and scripts to process VCF files, cluster variants using PyClone-VI, and reconstruct subclonal evolutionary trees using SuperSeeker.
## Installation
### Step 1: Install External Tools
#### Installing PyClone-VI
PyClone-VI is used for clustering genetic variants. You can install it using Conda:
```bash
conda install -c bioconda pyclone-vi
```
#### Installing SuperSeeker
SuperSeeker is used for reconstructing the evolutionary history of subclones. You can install it from its source repository:
```bash
git clone https://github.com/yiq/SuperSeeker.git
cd SuperSeeker
```
Use the `requirements.txt` file to install the necessary Python packages:
```bash
pip install -r requirements.txt
```
### Step 3: Install the SuperSeeker Python Package
Finally, install the SuperSeeker Pipeline Python package:
```bash
pip install superseeker_pipeline
```
## Usage
To use the SuperSeeker pipeline, you can run the `run_pipeline` function from the `superseeker.pipeline` module. Here's an example:
```python
from superseeker.pipeline import run_pipeline
run_pipeline(
patient='patient1',
vcf_file='input_file.vcf',
patient_sex='M',
restarts=100,
clusters=10,
cn_neutral=True
)
```
## License
This project is licensed under the MIT License - see the [LICENSE.txt](LICENSE.txt) file for details.
Raw data
{
"_id": null,
"home_page": "https://github.com/gageblack/superseeker_pipeline",
"name": "superseeker-pipeline",
"maintainer": null,
"docs_url": null,
"requires_python": ">=3.6",
"maintainer_email": null,
"keywords": null,
"author": "Your Name",
"author_email": "your.email@example.com",
"download_url": "https://files.pythonhosted.org/packages/3d/9d/650fb768556d05e755d207706ff192e4886d759a688fd160479945fac5e7/superseeker_pipeline-0.1.tar.gz",
"platform": null,
"description": "\n# SuperSeeker Pipeline\n\nThe SuperSeeker pipeline is a Python library for identifying subclonal evolution in cancer. It integrates various tools and scripts to process VCF files, cluster variants using PyClone-VI, and reconstruct subclonal evolutionary trees using SuperSeeker.\n\n## Installation\n\n### Step 1: Install External Tools\n\n#### Installing PyClone-VI\n\nPyClone-VI is used for clustering genetic variants. You can install it using Conda:\n\n```bash\nconda install -c bioconda pyclone-vi\n```\n\n#### Installing SuperSeeker\n\nSuperSeeker is used for reconstructing the evolutionary history of subclones. You can install it from its source repository:\n\n```bash\ngit clone https://github.com/yiq/SuperSeeker.git\ncd SuperSeeker\n```\n\nUse the `requirements.txt` file to install the necessary Python packages:\n\n```bash\npip install -r requirements.txt\n```\n\n### Step 3: Install the SuperSeeker Python Package\n\nFinally, install the SuperSeeker Pipeline Python package:\n\n```bash\npip install superseeker_pipeline\n```\n## Usage\n\nTo use the SuperSeeker pipeline, you can run the `run_pipeline` function from the `superseeker.pipeline` module. Here's an example:\n\n```python\nfrom superseeker.pipeline import run_pipeline\n\nrun_pipeline(\n patient='patient1',\n vcf_file='input_file.vcf',\n patient_sex='M',\n restarts=100,\n clusters=10,\n cn_neutral=True\n)\n```\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE.txt](LICENSE.txt) file for details.\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "SuperSeeker_Pipeline is a Python library for identifying subclonal evolution in cancer.",
"version": "0.1",
"project_urls": {
"Homepage": "https://github.com/gageblack/superseeker_pipeline"
},
"split_keywords": [],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "b818fee0e20ca5c6a8e061cd997349c53d4db958fa8086497d728dca028b7db7",
"md5": "211bd707c5a3331307bb81bf9022ef69",
"sha256": "d7071bdf85f0020ad05ab49937a938dadcb6708b898e28f36d9e5bb3c6f376bd"
},
"downloads": -1,
"filename": "superseeker_pipeline-0.1-py3-none-any.whl",
"has_sig": false,
"md5_digest": "211bd707c5a3331307bb81bf9022ef69",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.6",
"size": 9974,
"upload_time": "2024-05-30T19:25:33",
"upload_time_iso_8601": "2024-05-30T19:25:33.655078Z",
"url": "https://files.pythonhosted.org/packages/b8/18/fee0e20ca5c6a8e061cd997349c53d4db958fa8086497d728dca028b7db7/superseeker_pipeline-0.1-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "3d9d650fb768556d05e755d207706ff192e4886d759a688fd160479945fac5e7",
"md5": "2bf6b8fa406e8ba62a62c164626ef438",
"sha256": "5bf5aa73ddfa9c74988186ff1ffc8dcc1260c273b838157f8426cccd3d4aee90"
},
"downloads": -1,
"filename": "superseeker_pipeline-0.1.tar.gz",
"has_sig": false,
"md5_digest": "2bf6b8fa406e8ba62a62c164626ef438",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.6",
"size": 9377,
"upload_time": "2024-05-30T19:25:35",
"upload_time_iso_8601": "2024-05-30T19:25:35.527461Z",
"url": "https://files.pythonhosted.org/packages/3d/9d/650fb768556d05e755d207706ff192e4886d759a688fd160479945fac5e7/superseeker_pipeline-0.1.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-05-30 19:25:35",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "gageblack",
"github_project": "superseeker_pipeline",
"travis_ci": false,
"coveralls": false,
"github_actions": false,
"requirements": [
{
"name": "numpy",
"specs": []
},
{
"name": "pandas",
"specs": []
}
],
"lcname": "superseeker-pipeline"
}
JSON
