<p align="center">
<h1 align="center">
ngsderive
</h1>
<p align="center">
<a href="https://actions-badge.atrox.dev/stjudecloud/ngsderive/goto" target="_blank">
<img alt="Actions: CI Status"
src="https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2Fstjudecloud%2Fngsderive%2Fbadge&style=flat" />
</a>
<a href="https://pypi.org/project/ngsderive/" target="_blank">
<img alt="PyPI"
src="https://img.shields.io/pypi/v/ngsderive?color=orange">
</a>
<a href="https://pypi.python.org/pypi/ngsderive/" target="_blank">
<img alt="PyPI: Downloads"
src="https://img.shields.io/pypi/dm/ngsderive?color=orange">
</a>
<a href="https://pypi.python.org/pypi/ngsderive/" target="_blank">
<img alt="PyPI: Downloads"
src="https://img.shields.io/pypi/pyversions/ngsderive?color=orange">
</a>
<a href="https://github.com/stjudecloud/ngsderive/blob/master/LICENSE.md" target="_blank">
<img alt="License: MIT"
src="https://img.shields.io/badge/License-MIT-blue.svg" />
</a>
</p>
<p align="center">
Forensic analysis tool useful in backwards computing information from next-generation sequencing data and annotating splice junctions.
<br />
<a href="https://stjudecloud.github.io/ngsderive/"><strong>Explore the docs »</strong></a>
<br />
<br />
<a href="https://github.com/stjudecloud/ngsderive/issues/new?assignees=&labels=&template=feature_request.md&title=Descriptive%20Title&labels=enhancement">Request Feature</a>
·
<a href="https://github.com/stjudecloud/ngsderive/issues/new?assignees=&labels=&template=bug_report.md&title=Descriptive%20Title&labels=bug">Report Bug</a>
·
⭐ Consider starring the repo! ⭐
<br />
</p>
</p>
> Notice: `ngsderive` is largely a forensic analysis tool useful in backwards computing information
> from next-generation sequencing data. Notably, most results are provided as a 'best guess' —
> the tool does not claim 100% accuracy and results should be considered with that understanding.
> An exception would be the `junction-annotation` tool which analyzes more concrete evidence than the other tools.
## 🎨 Features
The following attributes can be guessed using ngsderive:
* <b>Illumina Instrument.</b> Infer which Illumina instrument was used to generate the data by matching against known instrument and flowcell naming patterns. Each guess comes with a confidence score.
* <b>RNA-Seq Strandedness.</b> Infer from the data whether RNA-Seq data was generated using a Stranded-Forward, Stranded-Reverse, or Unstranded protocol.
* <b>Pre-trimmed Read Length.</b> Compute the distribution of read lengths in the file and attempt to guess what the original read length of the experiment was.
* <b>PHRED Score Encoding.</b> Infers which encoding scheme was used to store PHRED scores as ASCII characters.
* <b>Junction Annotation.</b> Annotates splice junctions as novel, partial novel, or known in comparison to a reference gene model.
## 📚 Getting Started
### Installation
You can install ngsderive using the Python Package Index ([PyPI](https://pypi.org/)).
```bash
pip install ngsderive
```
## 🖥️ Development
If you are interested in contributing to the code, please first review our [CONTRIBUTING.md][contributing-md] document.
To bootstrap a development environment, please use the following commands.
```bash
# Clone the repository
git clone git@github.com:stjudecloud/ngsderive.git
cd ngsderive
# Install the project using poetry
poetry install
```
## 🚧️ Tests
ngsderive provides a (currently patchy) set of tests — both unit and end-to-end.
```bash
py.test
```
## 🤝 Contributing
Contributions, issues and feature requests are welcome!<br />Feel free to check [issues page](https://github.com/stjudecloud/ngsderive/issues). You can also take a look at the [contributing guide][contributing-md].
## 📝 License
This project is licensed as follows:
* All code related to the `instrument` subcommand is licensed under the [AGPL v2.0][agpl-v2]. This is not due to any strict requirement, but out of deference to some [code][10x-inspiration] I drew inspiration from (and copied patterns from), the decision was made to license this code consistently.
* The rest of the project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details.
Copyright © 2020 [St. Jude Cloud Team](https://github.com/stjudecloud).<br />
[10x-inspiration]: https://github.com/10XGenomics/supernova/blob/master/tenkit/lib/python/tenkit/illumina_instrument.py
[agpl-v2]: http://www.affero.org/agpl2.html
[contributing-md]: https://github.com/stjudecloud/ngsderive/blob/master/CONTRIBUTING.md
[license-md]: https://github.com/stjudecloud/ngsderive/blob/master/LICENSE.md
Raw data
{
"_id": null,
"home_page": "https://github.com/claymcleod/ngsderive",
"name": "ngsderive",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.8,<4.0",
"maintainer_email": "",
"keywords": "bioinformatics,genomics,sam,bam,fastq",
"author": "Clay McLeod",
"author_email": "Clay.McLeod@STJUDE.org",
"download_url": "https://files.pythonhosted.org/packages/a8/2d/5cd92e2f05188a46b270ee5227cc391ce86f783459d1d25582b96e810530/ngsderive-4.0.0.tar.gz",
"platform": null,
"description": "<p align=\"center\">\n <h1 align=\"center\">\n ngsderive\n </h1>\n\n <p align=\"center\">\n <a href=\"https://actions-badge.atrox.dev/stjudecloud/ngsderive/goto\" target=\"_blank\">\n <img alt=\"Actions: CI Status\"\n src=\"https://img.shields.io/endpoint.svg?url=https%3A%2F%2Factions-badge.atrox.dev%2Fstjudecloud%2Fngsderive%2Fbadge&style=flat\" />\n </a>\n <a href=\"https://pypi.org/project/ngsderive/\" target=\"_blank\">\n <img alt=\"PyPI\"\n src=\"https://img.shields.io/pypi/v/ngsderive?color=orange\">\n </a>\n <a href=\"https://pypi.python.org/pypi/ngsderive/\" target=\"_blank\">\n <img alt=\"PyPI: Downloads\"\n src=\"https://img.shields.io/pypi/dm/ngsderive?color=orange\">\n </a>\n <a href=\"https://pypi.python.org/pypi/ngsderive/\" target=\"_blank\">\n <img alt=\"PyPI: Downloads\"\n src=\"https://img.shields.io/pypi/pyversions/ngsderive?color=orange\">\n </a>\n <a href=\"https://github.com/stjudecloud/ngsderive/blob/master/LICENSE.md\" target=\"_blank\">\n <img alt=\"License: MIT\"\n src=\"https://img.shields.io/badge/License-MIT-blue.svg\" />\n </a>\n </p>\n\n\n <p align=\"center\">\n Forensic analysis tool useful in backwards computing information from next-generation sequencing data and annotating splice junctions.\n <br />\n <a href=\"https://stjudecloud.github.io/ngsderive/\"><strong>Explore the docs \u00bb</strong></a>\n <br />\n <br />\n <a href=\"https://github.com/stjudecloud/ngsderive/issues/new?assignees=&labels=&template=feature_request.md&title=Descriptive%20Title&labels=enhancement\">Request Feature</a>\n \u00b7\n <a href=\"https://github.com/stjudecloud/ngsderive/issues/new?assignees=&labels=&template=bug_report.md&title=Descriptive%20Title&labels=bug\">Report Bug</a>\n \u00b7\n \u2b50 Consider starring the repo! \u2b50\n <br />\n </p>\n</p>\n\n> Notice: `ngsderive` is largely a forensic analysis tool useful in backwards computing information\n> from next-generation sequencing data. Notably, most results are provided as a 'best guess' \u2014\n> the tool does not claim 100% accuracy and results should be considered with that understanding.\n> An exception would be the `junction-annotation` tool which analyzes more concrete evidence than the other tools.\n\n## \ud83c\udfa8 Features\n\nThe following attributes can be guessed using ngsderive:\n\n* <b>Illumina Instrument.</b> Infer which Illumina instrument was used to generate the data by matching against known instrument and flowcell naming patterns. Each guess comes with a confidence score.\n* <b>RNA-Seq Strandedness.</b> Infer from the data whether RNA-Seq data was generated using a Stranded-Forward, Stranded-Reverse, or Unstranded protocol.\n* <b>Pre-trimmed Read Length.</b> Compute the distribution of read lengths in the file and attempt to guess what the original read length of the experiment was.\n* <b>PHRED Score Encoding.</b> Infers which encoding scheme was used to store PHRED scores as ASCII characters.\n* <b>Junction Annotation.</b> Annotates splice junctions as novel, partial novel, or known in comparison to a reference gene model.\n\n## \ud83d\udcda Getting Started\n\n### Installation\n\nYou can install ngsderive using the Python Package Index ([PyPI](https://pypi.org/)).\n\n```bash\npip install ngsderive\n```\n\n## \ud83d\udda5\ufe0f Development\n\nIf you are interested in contributing to the code, please first review our [CONTRIBUTING.md][contributing-md] document. \n\nTo bootstrap a development environment, please use the following commands.\n\n```bash\n# Clone the repository\ngit clone git@github.com:stjudecloud/ngsderive.git\ncd ngsderive\n\n# Install the project using poetry\npoetry install\n```\n\n## \ud83d\udea7\ufe0f Tests\n\nngsderive provides a (currently patchy) set of tests \u2014 both unit and end-to-end.\n\n```bash\npy.test\n```\n\n## \ud83e\udd1d Contributing\n\nContributions, issues and feature requests are welcome!<br />Feel free to check [issues page](https://github.com/stjudecloud/ngsderive/issues). You can also take a look at the [contributing guide][contributing-md].\n\n## \ud83d\udcdd License\n\nThis project is licensed as follows:\n\n* All code related to the `instrument` subcommand is licensed under the [AGPL v2.0][agpl-v2]. This is not due to any strict requirement, but out of deference to some [code][10x-inspiration] I drew inspiration from (and copied patterns from), the decision was made to license this code consistently.\n* The rest of the project is licensed under the MIT License - see the [LICENSE.md](LICENSE.md) file for details.\n\nCopyright \u00a9 2020 [St. Jude Cloud Team](https://github.com/stjudecloud).<br />\n\n[10x-inspiration]: https://github.com/10XGenomics/supernova/blob/master/tenkit/lib/python/tenkit/illumina_instrument.py\n[agpl-v2]: http://www.affero.org/agpl2.html\n[contributing-md]: https://github.com/stjudecloud/ngsderive/blob/master/CONTRIBUTING.md\n[license-md]: https://github.com/stjudecloud/ngsderive/blob/master/LICENSE.md\n\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Forensic analysis tool useful in backwards computing information from next-generation sequencing data.",
"version": "4.0.0",
"project_urls": {
"Homepage": "https://github.com/claymcleod/ngsderive",
"Repository": "https://github.com/claymcleod/ngsderive"
},
"split_keywords": [
"bioinformatics",
"genomics",
"sam",
"bam",
"fastq"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "2f8e13e17561491a7ff810f6d51f6e4253a7cc4e025dad361cb392d037ee7aa6",
"md5": "408b0f603a7532817f19c748f16af124",
"sha256": "afef89cde8fd7d61c432b5b1911365afdc10a735541a71b563686f7db6eae714"
},
"downloads": -1,
"filename": "ngsderive-4.0.0-py3-none-any.whl",
"has_sig": false,
"md5_digest": "408b0f603a7532817f19c748f16af124",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.8,<4.0",
"size": 23363,
"upload_time": "2023-10-04T16:19:23",
"upload_time_iso_8601": "2023-10-04T16:19:23.136687Z",
"url": "https://files.pythonhosted.org/packages/2f/8e/13e17561491a7ff810f6d51f6e4253a7cc4e025dad361cb392d037ee7aa6/ngsderive-4.0.0-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "a82d5cd92e2f05188a46b270ee5227cc391ce86f783459d1d25582b96e810530",
"md5": "a9634e41f0f660eb86b0aeb88df487dd",
"sha256": "1e55f7bed3dfe1ecf4b3955636bd6fc7b1c1bd7c5685c539c0e248abfc47bf97"
},
"downloads": -1,
"filename": "ngsderive-4.0.0.tar.gz",
"has_sig": false,
"md5_digest": "a9634e41f0f660eb86b0aeb88df487dd",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.8,<4.0",
"size": 20780,
"upload_time": "2023-10-04T16:19:25",
"upload_time_iso_8601": "2023-10-04T16:19:25.281785Z",
"url": "https://files.pythonhosted.org/packages/a8/2d/5cd92e2f05188a46b270ee5227cc391ce86f783459d1d25582b96e810530/ngsderive-4.0.0.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-10-04 16:19:25",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "claymcleod",
"github_project": "ngsderive",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"lcname": "ngsderive"
}
JSON
