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
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README.rst | 203 +++++++++++++++++++++++++++++++++++++++++++++++++++++
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-
-
-[![Stargazers][stars-shield]][stars-url]
-[![Commits][commits-shield]][commits-url]
-[![Issues][issues-shield]][issues-url]
-[![MIT License][license-shield]][license-url]
-[![LinkedIn][linkedin-shield]][linkedin-url]
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PyNCBI
-
-
- Simple API for Python Integration with NCBI .
-
- Explore the docs »
-
-
- View Demo
- ·
- Report Bug
- ·
- Request Feature
-
-
-
-
-
-
-## 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
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--- /dev/null
+++ b/README.rst
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+.. 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/