<p align="center">
<img src="https://raw.githubusercontent.com/luanrabelo/SynGenes/stable/docs/assets/SynGenes.png" alt="SynGenes Logo" width="50%">
</p>
<h1 align="center">
<b>Syn</b><i>Genes</i>
</h1>
<h2 align="center">
Welcome to the <b>Syn</b><i>Genes</i> Documentation!
</h2>
<p align="center">
<img src="https://img.shields.io/github/license/luanrabelo/SynGenes?style=for-the-badge&label=License&labelColor=191919&color=647E68" alt="License"/>
<img src="https://img.shields.io/github/v/release/luanrabelo/SynGenes?style=for-the-badge&label=Release&labelColor=191919&color=647E68" alt="Release"/>
<img src="https://img.shields.io/github/stars/luanrabelo/SynGenes?style=for-the-badge&label=Stars&labelColor=191919&color=647E68" alt="Stars"/>
<img src="https://img.shields.io/github/forks/luanrabelo/SynGenes?style=for-the-badge&label=Forks&labelColor=191919&color=647E68" alt="Forks"/>
<img src="https://img.shields.io/github/downloads/luanrabelo/SynGenes/total?style=for-the-badge&label=Downloads&labelColor=191919&color=647E68" alt="Downloads"/>
<img src="https://img.shields.io/github/languages/top/luanrabelo/SynGenes?style=for-the-badge&label=Python&labelColor=191919&color=647E68" alt="Language"/>
<img src="https://img.shields.io/github/commit-activity/t/luanrabelo/SynGenes?style=for-the-badge&label=Commits&labelColor=191919&color=647E68" alt="Commits"/>
</p>
<h3 align="left">
<b>Syn</b><i>Genes</i> is a Python class designed for standardizing <b>Mitochondrial</b> or <b>Chloroplast</b> gene nomenclatures. It can recognize and convert various nomenclature variations into a standardized format.
</h3>
## License
**SynGenes** is **released** under the **MIT License**. This license permits reuse within proprietary software provided that all copies of the licensed software include a copy of the MIT License terms and the copyright notice.
For more details, please see the **MIT License**.
## Getting Started
### Prerequisites
Before installing **SynGenes**, ensure that you have the following prerequisites installed:
- Python Environment
- Python 3.6 or higher
- conda (optional)
- Dependencies (automatically installed with pip)
- `requests`
- `pandas`
- `openpyxl`
***
### Installation
There are tree ways to install **SynGenes**:
1. **Through pip**: Install **SynGenes** directly using pip:
```bash
pip install SynGenes
```
- This will install SynGenes and its dependencies in your Python environment.
2. **By cloning the GitHub repository**: Clone the source code of **SynGenes** from GitHub:
```bash
git clone https://github.com/luanrabelo/SynGenes.git
cd SynGenes
pip install -r requirements.txt
```
- This command will **clone the repository**, and then you should **navigate to the cloned directory** to **install SynGenes and its dependencies** using pip.
3. Installation via **conda**: You can also install **SynGenes** using conda with the following commands:
```bash
conda create -n SynGenes -c conda-forge -c bioconda SynGenes
conda activate SynGenes
```
- This method will set up **SynGenes** along with its **dependencies** in a **new conda environment**.
***
## Functions
### `__init__(self, **kwargs)`
Initializes the **SynGenes** class. This function is the constructor of the class and is called when a new instance of the **SynGenes** class is created.
When an instance of the **SynGenes** class is created, the constructor checks if the `SynGenes.xlsx` database exists at the specified path.
If it does not exist, it will attempt to create the **SynGenes directory** and **download the database from the GitHub repository**.
If verbose is **True**, status messages will be printed in the terminal to inform the user about the progress of these operations.
#### Parameters:
- `verbose (bool)`: If `True`, messages will be printed during execution. The default is `True`.
#### Returns:
- `None`
#### Notes:
- This function requires the `requests` library to be imported.
- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.
#### Usage Example:
```python
from SynGenes import SynGenes
sg = SynGenes(verbose=True)
```
### `updateSynGenes(self, **kwargs)`
Updates the **SynGenes** database by **downloading it from the GitHub repository's stable branch**. If an existing database is found, it is removed before downloading the new one.
The `updateSynGenes` function checks if the `SynGenes.xlsx` database file exists in the user’s computer.
If it does, the file is removed.
Then, the function attempts to **download the latest version of the database from the specified GitHub repository URL**.
If the verbose parameter is set to **True**, the function will print messages to the console to inform the user of the progress, including the removal of the old database and the download of the new one.
#### Parameters:
- `verbose (bool)`: If `True`, messages will be printed during execution. The default is `True`.
#### Returns:
- The updated `SynGenes` database saved in the `SynGenes` folder.
#### Notes:
- This function requires the `requests` library to be imported.
- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.
#### Usage Example:
```python
from SynGenes import SynGenes
sg = SynGenes()
sg.updateSynGenes()
```
### `fixGeneName(self, **kwargs)`
Corrects the gene name according to the **SynGenes** database, ensuring it adheres to the standardized nomenclature.
The `fixGeneName` function takes a gene name and corrects it based on the entries in the **SynGenes** database.
It supports both **mitochondrial (mt)** and **chloroplast (cp)** genes.
If the provided **gene name is found in the database**, **it is replaced with the standardized short name**.
**If not found**, **the original name is returned, and a log entry is created**.
The function provides verbose output if the verbose parameter is set to **True**.
#### Parameters:
- `geneName (str)`: The gene name to be corrected.
- `type (str)`: The type of gene (`mt` for Mitochondrial, `cp` for Chloroplast). The default is `mt`.
- `verbose (bool)`: If set to `True`, messages will be printed during execution. The default is `True`.
#### Returns:
- `ShortName (str)`: The corrected gene name.
#### Notes:
- This function requires the `pandas` library to be imported.
- The `SynGenes` database can be found at github.com/luanrabelo/SynGenes.
#### Usage Example:
```python
from SynGenes import SynGenes
sg = SynGenes()
# Mitocondrial
_geneName = sg.fixGeneName(geneName='cytochrome c oxidase subunit I', type='mt')
print(_geneName)
# Output: 'COI'
# Chloroplast
_geneName = sg.fixGeneName(geneName='ATPsynthaseCF1 alpha subunit', type='cp')
print(_geneName)
# Output: 'atpA'
```
### `buildQuery(self, **kwargs)`
Builds a query for Entrez search in **GenBank** or **PubMed** using the *SynGenes* database.
The `buildQuery` function constructs a query string that can be used for searching specific gene information in **GenBank** or **PubMed** databases.
It ensures that the **gene name is in the correct format** by referencing the predefined lists for **mitochondrial** and **chloroplast** genes.
The **search type** is also validated against a **list of acceptable formats**.
If the verbose parameter is **True**, the function will print informative messages during the query construction process.
#### Parameters:
- `geneName (str)`: The gene name to search. The gene name must be in the correct format; use the `fixGeneName()` function to correct the gene name.
- `type (str)`: The type of gene (`mt` for Mitochondrial, `cp` for Chloroplast). The default is `mt`.
- `searchType (str)`: The type of search (Title, Abstract, All Fields, MeSH Terms). The default is All Fields.
- `verbose (bool)`: If `True`, messages will be printed during execution. The default is `True`.
#### Returns:
- `query (str)`: The query for Entrez search in GenBank or PubMed.
#### Notes:
- This function requires the `pandas` library to be imported.
- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.
- Predefined lists `_listGenes_mt` and `_listGenes_cp` contain the correct formats for mitochondrial and chloroplast genes, respectively.
- The `_listTypes` contains the valid formats for the search type.
#### Usage Example:
```python
from SynGenes import SynGenes
sg = SynGenes()
query = sg.buildQuery(geneName='COI', type='mt', searchType='Title')
print(query)
# Output: '"COI"[Title] OR "cytochrome c oxidase subunit I"[Title] OR "cytochrome c oxidase subunit 1"[Title] OR "chytochrome c oxidase subunit I"[Title]...'
```
### `buildJson(self, **kwargs)`
Creates a JSON file containing the data from the **SynGenes** database.
The `buildJson` function generates a **JSON file** that encapsulates the **SynGenes database’s data**.
It takes the name of the file and the path where it should be saved as parameters.
If the file already exists, it is removed, and a new one is created.
The function provides verbose output if the verbose parameter is set to **True**, informing the user about the file creation process.
During the creation of the **JSON file**, the function writes the data for **mitochondrial** and **chloroplast** genes into separate objects within the file.
It also records the date when the file was updated. The verbose output will notify the user when the **JSON file** is being created and once it has been successfully created.
#### Parameters:
- `fileName (str)`: The name of the JSON file. The default is `SynGenes.js`.
- `pathSaveFile (str)`: The path where the JSON file will be saved. The default is the `SynGenes` folder in the current working directory.
- `verbose (bool)`: If set to `True`, messages will be printed during execution. The default is `True`.
#### Returns:
- A `SynGenes.js` file in the `SynGenes` folder.
#### Notes:
- This function requires the `pandas` library to be imported.
- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.
- The function checks if the specified JSON file already exists and removes it before creating a new one.
#### Usage Example:
```python
from SynGenes import SynGenes
sg = SynGenes()
sg.buildJson()
```
### `citeSynGenes(self)`
Provides the citation format for the **SynGenes** database.
The `citeSynGenes` function outputs the correct citation format for referencing the **SynGenes database** in **academic work** or **publications**.
It does not take any parameters and does not return any value. Instead, it prints the citation instructions directly to the console.
#### Parameters:
- None
#### Returns:
- None
#### Notes:
- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.
#### Usage Example:
```python
from SynGenes import SynGenes
sg = SynGenes()
howCite = sg.citeSynGenes()
print(howCite)
# Output: Please, cite the SynGenes database as: ...
```
### `versionSynGenes(self)`
Displays the current version of the **SynGenes** database.
The `versionSynGenes` function outputs the version number of the **SynGenes database**. It does not take any parameters and does not return any value. Instead, it prints the version number directly to the console.
#### Parameters:
- None
#### Returns:
- None
#### Notes:
- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.
#### Usage Example:
```python
from SynGenes import SynGenes
sg = SynGenes()
version = sg.versionSynGenes()
print(version)
# Output: '1.0'
```
***
## Web Form for SynGenes
We have developed a user-friendly web form available at (https://luanrabelo.github.io/SynGenes) for researchers who wish to perform individual searches using various names associated with the same gene. This web form generates a command that incorporates multiple names, enabling precise searches on platforms such as the National Center for Biotechnology Information (NCBI) - GenBank and PubMed Central.
***
## Developers
- Luan Rabelo
- Marcelo Vallinoto
- Iracilda Sampaio
Raw data
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"description": "<p align=\"center\">\r\n <img src=\"https://raw.githubusercontent.com/luanrabelo/SynGenes/stable/docs/assets/SynGenes.png\" alt=\"SynGenes Logo\" width=\"50%\">\r\n</p>\r\n\r\n<h1 align=\"center\">\r\n <b>Syn</b><i>Genes</i>\r\n</h1>\r\n\r\n<h2 align=\"center\">\r\n Welcome to the <b>Syn</b><i>Genes</i> Documentation!\r\n</h2>\r\n\r\n<p align=\"center\">\r\n <img src=\"https://img.shields.io/github/license/luanrabelo/SynGenes?style=for-the-badge&label=License&labelColor=191919&color=647E68\" alt=\"License\"/>\r\n <img src=\"https://img.shields.io/github/v/release/luanrabelo/SynGenes?style=for-the-badge&label=Release&labelColor=191919&color=647E68\" alt=\"Release\"/>\r\n <img src=\"https://img.shields.io/github/stars/luanrabelo/SynGenes?style=for-the-badge&label=Stars&labelColor=191919&color=647E68\" alt=\"Stars\"/>\r\n <img src=\"https://img.shields.io/github/forks/luanrabelo/SynGenes?style=for-the-badge&label=Forks&labelColor=191919&color=647E68\" alt=\"Forks\"/>\r\n <img src=\"https://img.shields.io/github/downloads/luanrabelo/SynGenes/total?style=for-the-badge&label=Downloads&labelColor=191919&color=647E68\" alt=\"Downloads\"/>\r\n <img src=\"https://img.shields.io/github/languages/top/luanrabelo/SynGenes?style=for-the-badge&label=Python&labelColor=191919&color=647E68\" alt=\"Language\"/>\r\n <img src=\"https://img.shields.io/github/commit-activity/t/luanrabelo/SynGenes?style=for-the-badge&label=Commits&labelColor=191919&color=647E68\" alt=\"Commits\"/>\r\n</p>\r\n\r\n<h3 align=\"left\">\r\n <b>Syn</b><i>Genes</i> is a Python class designed for standardizing <b>Mitochondrial</b> or <b>Chloroplast</b> gene nomenclatures. It can recognize and convert various nomenclature variations into a standardized format.\r\n</h3>\r\n\r\n## License\r\n\r\n**SynGenes** is **released** under the **MIT License**. This license permits reuse within proprietary software provided that all copies of the licensed software include a copy of the MIT License terms and the copyright notice.\r\n\r\nFor more details, please see the **MIT License**.\r\n\r\n## Getting Started\r\n### Prerequisites\r\nBefore installing **SynGenes**, ensure that you have the following prerequisites installed:\r\n- Python Environment\r\n - Python 3.6 or higher\r\n - conda (optional)\r\n- Dependencies (automatically installed with pip)\r\n - `requests`\r\n - `pandas`\r\n - `openpyxl`\r\n*** \r\n### Installation\r\nThere are tree ways to install **SynGenes**:\r\n\r\n1. **Through pip**: Install **SynGenes** directly using pip: \r\n ```bash \r\n pip install SynGenes\r\n ```\r\n - This will install SynGenes and its dependencies in your Python environment.\r\n \r\n2. **By cloning the GitHub repository**: Clone the source code of **SynGenes** from GitHub:\r\n ```bash\r\n git clone https://github.com/luanrabelo/SynGenes.git\r\n cd SynGenes \r\n pip install -r requirements.txt\r\n ```\r\n - This command will **clone the repository**, and then you should **navigate to the cloned directory** to **install SynGenes and its dependencies** using pip.\r\n \r\n3. Installation via **conda**: You can also install **SynGenes** using conda with the following commands: \r\n ```bash\r\n conda create -n SynGenes -c conda-forge -c bioconda SynGenes\r\n conda activate SynGenes \r\n ```\r\n - This method will set up **SynGenes** along with its **dependencies** in a **new conda environment**.\r\n \r\n***\r\n## Functions \r\n### `__init__(self, **kwargs)` \r\nInitializes the **SynGenes** class. This function is the constructor of the class and is called when a new instance of the **SynGenes** class is created. \r\n \r\nWhen an instance of the **SynGenes** class is created, the constructor checks if the `SynGenes.xlsx` database exists at the specified path.\r\nIf it does not exist, it will attempt to create the **SynGenes directory** and **download the database from the GitHub repository**.\r\nIf verbose is **True**, status messages will be printed in the terminal to inform the user about the progress of these operations.\r\n\r\n#### Parameters:\r\n- `verbose (bool)`: If `True`, messages will be printed during execution. The default is `True`.\r\n\r\n#### Returns:\r\n- `None`\r\n\r\n#### Notes:\r\n- This function requires the `requests` library to be imported.\r\n- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.\r\n\r\n#### Usage Example:\r\n```python\r\nfrom SynGenes import SynGenes\r\nsg = SynGenes(verbose=True)\r\n```\r\n \r\n### `updateSynGenes(self, **kwargs)` \r\nUpdates the **SynGenes** database by **downloading it from the GitHub repository's stable branch**. If an existing database is found, it is removed before downloading the new one. \r\n\r\nThe `updateSynGenes` function checks if the `SynGenes.xlsx` database file exists in the user\u00e2\u20ac\u2122s computer.\r\nIf it does, the file is removed.\r\nThen, the function attempts to **download the latest version of the database from the specified GitHub repository URL**.\r\nIf the verbose parameter is set to **True**, the function will print messages to the console to inform the user of the progress, including the removal of the old database and the download of the new one.\r\n\r\n#### Parameters:\r\n- `verbose (bool)`: If `True`, messages will be printed during execution. The default is `True`.\r\n\r\n#### Returns:\r\n- The updated `SynGenes` database saved in the `SynGenes` folder.\r\n\r\n#### Notes:\r\n- This function requires the `requests` library to be imported.\r\n- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.\r\n\r\n#### Usage Example:\r\n```python\r\nfrom SynGenes import SynGenes\r\nsg = SynGenes()\r\nsg.updateSynGenes()\r\n```\r\n \r\n### `fixGeneName(self, **kwargs)`\r\nCorrects the gene name according to the **SynGenes** database, ensuring it adheres to the standardized nomenclature. \r\n\r\nThe `fixGeneName` function takes a gene name and corrects it based on the entries in the **SynGenes** database.\r\nIt supports both **mitochondrial (mt)** and **chloroplast (cp)** genes.\r\nIf the provided **gene name is found in the database**, **it is replaced with the standardized short name**.\r\n**If not found**, **the original name is returned, and a log entry is created**.\r\nThe function provides verbose output if the verbose parameter is set to **True**.\r\n\r\n#### Parameters:\r\n- `geneName (str)`: The gene name to be corrected.\r\n- `type (str)`: The type of gene (`mt` for Mitochondrial, `cp` for Chloroplast). The default is `mt`.\r\n- `verbose (bool)`: If set to `True`, messages will be printed during execution. The default is `True`.\r\n\r\n#### Returns:\r\n- `ShortName (str)`: The corrected gene name.\r\n\r\n#### Notes:\r\n- This function requires the `pandas` library to be imported.\r\n- The `SynGenes` database can be found at github.com/luanrabelo/SynGenes.\r\n\r\n#### Usage Example:\r\n```python\r\nfrom SynGenes import SynGenes\r\nsg = SynGenes()\r\n\r\n# Mitocondrial\r\n_geneName = sg.fixGeneName(geneName='cytochrome c oxidase subunit I', type='mt')\r\nprint(_geneName)\r\n# Output: 'COI'\r\n\r\n# Chloroplast\r\n_geneName = sg.fixGeneName(geneName='ATPsynthaseCF1 alpha subunit', type='cp')\r\nprint(_geneName)\r\n# Output: 'atpA'\r\n```\r\n \r\n### `buildQuery(self, **kwargs)`\r\nBuilds a query for Entrez search in **GenBank** or **PubMed** using the *SynGenes* database. \r\n\r\nThe `buildQuery` function constructs a query string that can be used for searching specific gene information in **GenBank** or **PubMed** databases.\r\nIt ensures that the **gene name is in the correct format** by referencing the predefined lists for **mitochondrial** and **chloroplast** genes.\r\nThe **search type** is also validated against a **list of acceptable formats**.\r\nIf the verbose parameter is **True**, the function will print informative messages during the query construction process.\r\n\r\n#### Parameters:\r\n- `geneName (str)`: The gene name to search. The gene name must be in the correct format; use the `fixGeneName()` function to correct the gene name.\r\n- `type (str)`: The type of gene (`mt` for Mitochondrial, `cp` for Chloroplast). The default is `mt`.\r\n- `searchType (str)`: The type of search (Title, Abstract, All Fields, MeSH Terms). The default is All Fields.\r\n- `verbose (bool)`: If `True`, messages will be printed during execution. The default is `True`.\r\n\r\n#### Returns:\r\n- `query (str)`: The query for Entrez search in GenBank or PubMed.\r\n\r\n#### Notes:\r\n- This function requires the `pandas` library to be imported.\r\n- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.\r\n- Predefined lists `_listGenes_mt` and `_listGenes_cp` contain the correct formats for mitochondrial and chloroplast genes, respectively.\r\n- The `_listTypes` contains the valid formats for the search type.\r\n\r\n#### Usage Example:\r\n```python\r\nfrom SynGenes import SynGenes\r\nsg = SynGenes()\r\nquery = sg.buildQuery(geneName='COI', type='mt', searchType='Title')\r\nprint(query)\r\n# Output: '\"COI\"[Title] OR \"cytochrome c oxidase subunit I\"[Title] OR \"cytochrome c oxidase subunit 1\"[Title] OR \"chytochrome c oxidase subunit I\"[Title]...'\r\n```\r\n \r\n### `buildJson(self, **kwargs)`\r\nCreates a JSON file containing the data from the **SynGenes** database. \r\n\r\nThe `buildJson` function generates a **JSON file** that encapsulates the **SynGenes database\u00e2\u20ac\u2122s data**.\r\nIt takes the name of the file and the path where it should be saved as parameters.\r\nIf the file already exists, it is removed, and a new one is created.\r\nThe function provides verbose output if the verbose parameter is set to **True**, informing the user about the file creation process. \r\n\r\nDuring the creation of the **JSON file**, the function writes the data for **mitochondrial** and **chloroplast** genes into separate objects within the file.\r\nIt also records the date when the file was updated. The verbose output will notify the user when the **JSON file** is being created and once it has been successfully created.\r\n\r\n#### Parameters:\r\n- `fileName (str)`: The name of the JSON file. The default is `SynGenes.js`.\r\n- `pathSaveFile (str)`: The path where the JSON file will be saved. The default is the `SynGenes` folder in the current working directory.\r\n- `verbose (bool)`: If set to `True`, messages will be printed during execution. The default is `True`.\r\n\r\n#### Returns:\r\n- A `SynGenes.js` file in the `SynGenes` folder.\r\n\r\n#### Notes:\r\n- This function requires the `pandas` library to be imported.\r\n- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.\r\n- The function checks if the specified JSON file already exists and removes it before creating a new one.\r\n\r\n#### Usage Example:\r\n```python\r\nfrom SynGenes import SynGenes\r\nsg = SynGenes()\r\nsg.buildJson()\r\n```\r\n \r\n### `citeSynGenes(self)`\r\nProvides the citation format for the **SynGenes** database. \r\n\r\nThe `citeSynGenes` function outputs the correct citation format for referencing the **SynGenes database** in **academic work** or **publications**.\r\nIt does not take any parameters and does not return any value. Instead, it prints the citation instructions directly to the console.\r\n\r\n#### Parameters:\r\n- None\r\n\r\n#### Returns:\r\n- None\r\n\r\n#### Notes:\r\n- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.\r\n\r\n#### Usage Example:\r\n```python\r\nfrom SynGenes import SynGenes\r\nsg = SynGenes()\r\nhowCite = sg.citeSynGenes()\r\nprint(howCite)\r\n# Output: Please, cite the SynGenes database as: ...\r\n```\r\n \r\n### `versionSynGenes(self)`\r\nDisplays the current version of the **SynGenes** database. \r\n\r\nThe `versionSynGenes` function outputs the version number of the **SynGenes database**. It does not take any parameters and does not return any value. Instead, it prints the version number directly to the console.\r\n\r\n#### Parameters:\r\n- None\r\n\r\n#### Returns:\r\n- None\r\n\r\n#### Notes:\r\n- The `SynGenes` database is available at github.com/luanrabelo/SynGenes.\r\n\r\n#### Usage Example:\r\n```python\r\nfrom SynGenes import SynGenes\r\nsg = SynGenes()\r\nversion = sg.versionSynGenes()\r\nprint(version)\r\n# Output: '1.0'\r\n```\r\n \r\n***\r\n## Web Form for SynGenes\r\nWe have developed a user-friendly web form available at (https://luanrabelo.github.io/SynGenes) for researchers who wish to perform individual searches using various names associated with the same gene. This web form generates a command that incorporates multiple names, enabling precise searches on platforms such as the National Center for Biotechnology Information (NCBI) - GenBank and PubMed Central. \r\n***\r\n## Developers\r\n- Luan Rabelo\r\n- Marcelo Vallinoto\r\n- Iracilda Sampaio\r\n",
"bugtrack_url": null,
"license": "MIT License",
"summary": "SynGenes is a Python class for standardizing Mitochondrial or Chloroplast gene nomenclatures, this class is capable of recognizing and converting the different nomenclature variations into a standardized form.",
"version": "1.0.2",
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