From caea6165a913d7ad688754f85e5602d6ef15503f Mon Sep 17 00:00:00 2001 From: Thomas Konstantinovsky <56339082+MuteJester@users.noreply.github.com> Date: Fri, 20 May 2022 10:23:29 +0300 Subject: [PATCH] Added GSM Class Functionality --- README.md | 161 ------------------------------------------ README.rst | 203 +++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 203 insertions(+), 161 deletions(-) delete mode 100644 README.md create mode 100644 README.rst diff --git a/README.md b/README.md deleted file mode 100644 index 75c5916..0000000 --- a/README.md +++ /dev/null @@ -1,161 +0,0 @@ -

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PyNCBI

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- Simple API for Python Integration with NCBI . -
- Explore the docs » -
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- View Demo - · - Report Bug - · - Request Feature -

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- - - - -## Table of Contents - -* [About the Project](#about-the-project) -* [Usage](#usage) -* [Roadmap](#roadmap) -* [Contributing](#contributing) -* [License](#license) -* [Contact](#contact) - - - - -## About The Project -Here's Why PyNCBI :dna: : - -When working with methylation data, NCBI might be one of the most extensive open source databases that provide the methylation data and the information around it. -When working with NCBI on a day-to-day basis, searching, querying, and extracting information may prove to be a time-consuming and headache-producing challenge. -PyNCBI strives to answer all needs a researcher might need when communicating with NCBI using a straightforward python API that allows to quickly test, extract, analyze and download relevant data. - - - -### Installation -``` -pip install PyNCBI -``` - - -## Usage - - -#### GSE Wise Info Retrival -```py -from PyNCBI import GEOReader -# Create Reader Instance -reader= GEOReader() -# Extact all GSM info associated to GSE99624 (Saved csv will appear in your downloads folder) -reader.extract_gse_sample_info('GSE99624') -``` - - -#### GSE Wise Data Retrival -```py -from PyNCBI import GEOReader -# Create Reader Instance -reader= GEOReader() -# Extact all GSM methylation data associated to GSE142512 (Saved files will appear in your downloads folder per GSM depending on page data status) -reader.download_gse_data('GSE142512') -``` - -#### Single GSM Data Retrival -```py -from PyNCBI import GEOReader -# Create Reader Instance -reader= GEOReader() -# Extact GSM methylation data associated to GSE142512 (Saved file will appear in your downloads folder per GSM depending on page data status) -reader.download_gsm_data('GSM1518180') -``` - -#### Parsing IDAT files - -```py -from PyNCBI import parse_idat_files - -# Beta Values will be stored in a parquet file in path -parse_idat_files("Path_To_IDAT_FILES/", 'array_type') -``` - -### Currently Supported Data Features - * __GSE Wise Card Information Extraction__ - * __GSM Card Information Extraction__ - * __GSE Wise Methylation Data Extraction__ - * __GSM Card Methylation Data Extraction__ - * __IDAT File Parsing Management Based on methylprep__ - - - - - -## Roadmap - -See the [open issues](https://github.com/MuteJester/PyNCBI/issues) for a list of proposed features (and known issues). - - -## Contributing - - -Contributions are what make the open-source community such a powerful place to create new ideas, inspire, and make progress. Any contributions you make are **greatly appreciated**. - -1. Fork the Project -2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`) -3. Commit your changes (`git commit -m 'Add some AmazingFeature'`) -4. Push to the Branch (`git push origin feature/AmazingFeature`) -5. Open a Pull Request - - - -## License - -Distributed under the MIT license. See `LICENSE` for more information. - - - - -## Contact - -[Thomas Konstantinovsky]() - thomaskon90@gmail.com - -Project Link: [https://github.com/MuteJester/PyNCBI](https://github.com/MuteJester/PyNCBI) - - - - - - -[stars-shield]: https://img.shields.io/github/stars/MuteJester/PyNCBI.svg?style=flat-square -[stars-url]: https://github.com/MuteJester/PyNCBI/stargazers -[issues-shield]: https://img.shields.io/github/issues/MuteJester/PyNCBI.svg?style=flat-square -[issues-url]: https://github.com/MuteJester/PyNCBI/issues -[license-shield]: https://img.shields.io/github/license/MuteJester/PyNCBI.svg?style=flat-square -[license-url]: https://github.com/MuteJester/PyNCBI/blob/master/LICENSE -[commits-shield]: https://img.shields.io/github/commit-activity/m/MuteJester/PyNCBI?style=flat-square -[commits-url]: https://github.com/MuteJester/PyNCBI -[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=flat-square&logo=linkedin&colorB=555 -[linkedin-url]: https://www.linkedin.com/in/thomas-konstantinovsky-56230117b/ diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..6871d46 --- /dev/null +++ b/README.rst @@ -0,0 +1,203 @@ +.. raw:: html + +

+ +|Stargazers| |Commits| |Issues| |MIT License| |LinkedIn| + +.. raw:: html + +

+ +.. raw:: html + + + +.. raw:: html + +

+ +.. raw:: html + +

+ +PyNCBI + +.. raw:: html + +

+ +.. raw:: html + +

+ +Simple API for Python Integration with NCBI . Explore the docs » View +Demo · Report Bug · Request Feature + +.. raw:: html + +

+ +.. raw:: html + +

+ +.. raw:: html + + + +Table of Contents +----------------- + +- `About the Project <#about-the-project>`__ +- `Usage <#usage>`__ +- `Roadmap <#roadmap>`__ +- `Contributing <#contributing>`__ +- `License <#license>`__ +- `Contact <#contact>`__ + +.. raw:: html + + + +About The Project +----------------- + +Here’s Why PyNCBI :dna: : + +When working with methylation data, NCBI might be one of the most +extensive open source databases that provide the methylation data and +the information around it. When working with NCBI on a day-to-day basis, +searching, querying, and extracting information may prove to be a +time-consuming and headache-producing challenge. PyNCBI strives to +answer all needs a researcher might need when communicating with NCBI +using a straightforward python API that allows to quickly test, extract, +analyze and download relevant data. + +Installation +~~~~~~~~~~~~ + +:: + + pip install PyNCBI + +.. raw:: html + + + +Usage +----- + +GSE Wise Info Retrival +^^^^^^^^^^^^^^^^^^^^^^ + +.. code:: py + + from PyNCBI import GEOReader + # Create Reader Instance + reader= GEOReader() + # Extact all GSM info associated to GSE99624 (Saved csv will appear in your downloads folder) + reader.extract_gse_sample_info('GSE99624') + +GSE Wise Data Retrival +^^^^^^^^^^^^^^^^^^^^^^ + +.. code:: py + + from PyNCBI import GEOReader + # Create Reader Instance + reader= GEOReader() + # Extact all GSM methylation data associated to GSE142512 (Saved files will appear in your downloads folder per GSM depending on page data status) + reader.download_gse_data('GSE142512') + +Single GSM Data Retrival +^^^^^^^^^^^^^^^^^^^^^^^^ + +.. code:: py + + from PyNCBI import GEOReader + # Create Reader Instance + reader= GEOReader() + # Extact GSM methylation data associated to GSE142512 (Saved file will appear in your downloads folder per GSM depending on page data status) + reader.download_gsm_data('GSM1518180') + +Parsing IDAT files +^^^^^^^^^^^^^^^^^^ + +.. code:: py + + from PyNCBI import parse_idat_files + + # Beta Values will be stored in a parquet file in path + parse_idat_files("Path_To_IDAT_FILES/", 'array_type') + +Currently Supported Data Features +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +- **GSE Wise Card Information Extraction** +- **GSM Card Information Extraction** +- **GSE Wise Methylation Data Extraction** +- **GSM Card Methylation Data Extraction** +- **IDAT File Parsing Management Based on methylprep** + +.. raw:: html + + + +Roadmap +------- + +See the `open issues `__ +for a list of proposed features (and known issues). + +.. raw:: html + + + +Contributing +------------ + +Contributions are what make the open-source community such a powerful +place to create new ideas, inspire, and make progress. Any contributions +you make are **greatly appreciated**. + +1. Fork the Project +2. Create your Feature Branch + (``git checkout -b feature/AmazingFeature``) +3. Commit your changes (``git commit -m 'Add some AmazingFeature'``) +4. Push to the Branch (``git push origin feature/AmazingFeature``) +5. Open a Pull Request + +.. raw:: html + + + +License +------- + +Distributed under the MIT license. See ``LICENSE`` for more information. + +.. raw:: html + + + +Contact +------- + +`Thomas Konstantinovsky <>`__ - thomaskon90@gmail.com + +Project Link: https://github.com/MuteJester/PyNCBI + +.. raw:: html + + + +.. |Stargazers| image:: https://img.shields.io/github/stars/MuteJester/PyNCBI.svg?style=flat-square + :target: https://github.com/MuteJester/PyNCBI/stargazers +.. |Commits| image:: https://img.shields.io/github/commit-activity/m/MuteJester/PyNCBI?style=flat-square + :target: https://github.com/MuteJester/PyNCBI +.. |Issues| image:: https://img.shields.io/github/issues/MuteJester/PyNCBI.svg?style=flat-square + :target: https://github.com/MuteJester/PyNCBI/issues +.. |MIT License| image:: https://img.shields.io/github/license/MuteJester/PyNCBI.svg?style=flat-square + :target: https://github.com/MuteJester/PyNCBI/blob/master/LICENSE +.. |LinkedIn| image:: https://img.shields.io/badge/-LinkedIn-black.svg?style=flat-square&logo=linkedin&colorB=555 + :target: https://www.linkedin.com/in/thomas-konstantinovsky-56230117b/