rghilduta / human-chromosome-data-generator

Human Chromosome Data Generator

This bash script generates a specified number of rows of DNA sequence data from a selected human chromosome using the art_illumina tool from the art-nextgen-simulation-tools package.

Prerequisites

• Linux operating system (tested on Ubuntu)
• wget command-line utility
• art-nextgen-simulation-tools package

Installation

1. Clone this repository: git clone https://github.com/yourusername/human-chromosome-data-generator.git

2. Navigate to the cloned directory: cd human-chromosome-data-generator

3. Make the script executable: chmod +x generate_chromosome_data.sh

Usage

Run the script with the following command: ./generate_chromosome_data.sh -c <chromosome> -l <line_length> -r <num_rows>

• -c <chromosome>: Specify the chromosome number (1-22) or X or Y. Default is 11.
• -l <line_length>: Specify the length of each row in the output file. Default is 800.
• -r <num_rows>: Specify the number of rows to generate in the output file. Default is 1200.

Example: ./generate_chromosome_data.sh -c 1 -l 1000 -r 500 This command will generate 500 rows of length 1000 from chromosome 1.

Output

The script will generate a file named generate_out.csv containing the specified number of rows of DNA sequence data from the selected chromosome. The file will be created in the same directory as the script.

Dependencies

The script relies on the following dependencies:

• art-nextgen-simulation-tools: This package provides the art_illumina tool used for generating the DNA sequence data. The script will automatically install this package if it is not already installed.

• wget: This command-line utility is used for downloading the chromosome reference files from the UCSC Genome Browser. It is assumed to be already installed on the system.

Notes

• The script performs MD5 checksum verification of the downloaded chromosome reference files to ensure data integrity.
• If the chromosome reference file is already downloaded and the MD5 checksum matches, the script will skip the download step to save time.
• The script uses a fixed random seed (--rndSeed 42) for reproducibility of the generated data.
• The generated output file (generate_out.csv) will contain the specified number of rows, with each row having the specified length of DNA sequence data.

License

This script is open-source and available under the MIT License.