This Python script automates the search and retrieval of biological sequences from the NCBI Entrez database using the eSearch and eFetch services.
Requirements
Note: This script may not work properly on Windows due to the use of wget. It is recommended to run it on a Linux system for the best experience.
Python 3.x
Internet connection
wget installed on the system
Warnings
This script only accepts precise inputs. Incorrect database names, incorrect organism names, or running the script with arguments that do not follow the provided examples may cause execution failures or return unexpected outputs.
Installation
Clone this repository:
git clone https://github.com/AceSCav/Fasta-Entrez-Loader
cd Fasta-Entrez-Loader
Ensure wget is installed:
sudo apt install wget
Usage Run the script with the following arguments:
python3 Script.py "database" "organism" x
database: Name of the NCBI database (nucleotide, protein)
organism: Name of the target organism (Homo sapiens)
x: Maximum number of sequences to display
Example Execution:
python3 Script.py "nucleotide" "Homo sapiens" 10
License This project is licensed under the GNU General Public License Version 3, 29 June 2007. You are free to use, modify, and distribute it under the terms of this license.