Ensembl_converter

The Ensembl_converter package is a Python library that allows you to convert Ensembl IDs to gene symbols. It provides a simple and convenient way to retrieve gene symbols for a given list of Ensembl IDs using the Ensembl REST API.

Installation

You can install Ensembl_converter using pip:

pip install Ensembl_converter

Usage

To convert Ensembl IDs to gene symbols, follow these steps:

1. Import the EnsemblConverter class from the Ensembl_converter package.
2. Create an instance of EnsemblConverter
3. Call the convert_ids method with a list of Ensembl IDs as input.

Here's an example:

from Ensembl_converter import EnsemblConverter

# Create an instance of EnsemblConverter
converter = EnsemblConverter()

# Provide a list of Ensembl IDs
ensembl_ids = ['ENSG00000000457', 'ENSG00000273486', 'ENSG00000273493']

# Convert Ensembl IDs to gene symbols
result = converter.convert_ids(ensembl_ids)

# Print the resulting DataFrame
print(result)

This will output a DataFrame with two columns: ENSG (Ensembl IDs) and Symbol (gene symbols).

The Ensembl_converter package can also be run directly from command line. To do this download the ensembl_converter_cli.py file. The pacakge can then be run in command line using the following command:

python ensembl_converter_cli.py ENSG00000000457 ENSG00000273486 ENSG00000273493 --output result.csv --progress

This command will convert the provided Ensembl gene IDs and save the result to the specified output file (result.csv). If the --output option is omitted, the result will be printed to the console instead. The --progress option enables the progress bar during conversion.

You can also provide the Ensembl gene IDs in a text file, with each ID on a separate line, and pass the file path instead of the IDs directly. For example:

python ensembl_converter_cli.py ids.txt --output result.csv --progress

Replace ids.txt with the path to your text file containing the Ensembl gene IDs.

Options

The EnsemblConverter class supports the following options:

• use_progress_bar (default=False): Set this to True to display a progress bar during the conversion process. This can be useful for larger gene lists.

Dependencies

The Ensembl_converter package depends on the following libraries:

• requests
• pandas
• tqdm

These dependencies will be automatically installed when you install the Ensembl_converter package (If you don't already have these installed).

Contributing

Contributions to Ensembl_converter are welcome! If you find any issues or have suggestions for improvements, feel free to open an issue or submit a pull request.

License

This project is licensed under the MIT License. See the LICENSE file for details.