SynGenes 1.0.2

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.

SynGenes

Welcome to the SynGenes Documentation!

SynGenes is a Python class designed for standardizing Mitochondrial or Chloroplast gene nomenclatures. It can recognize and convert various nomenclature variations into a standardized format.

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

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Installation

There are tree ways to install SynGenes:

1. Through pip: Install SynGenes directly using pip:

   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:

   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:

   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.  

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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:

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:

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:

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:

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:

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:

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:

from SynGenes import SynGenes
sg = SynGenes()
version = sg.versionSynGenes()
print(version)
# Output: '1.0'

 

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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.

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Developers

• Luan Rabelo
• Marcelo Vallinoto
• Iracilda Sampaio