hhk21 / salmonre2rpm

Translation of salmon and taxonomic annotation results to logRPM results

salmonRE2RPM

salmonRE2RPM is a tool for working with bioinformatics data that converts Salmon and taxonomic annotation results into log relative abundance (logRPM) results. The program is particularly suitable for research in the field of viruses and can help researchers better understand the abundance of viruses in their samples.

Installation

This script is written in Python and requires the following dependencies:

• Python 3.10
• pandas
• math

#!/bin/bash

# Define required packages
REQUIRED_PKG="pandas"

# Check if pandas is installed and install if not
if ! python -c "import pandas" &> /dev/null; then
    echo "pandas is not installed. Installing..."
    pip install pandas
else
    echo "pandas is already installed."
fi

echo "All necessary packages are installed."

Usage

The program accepts input through command line arguments. You need to provide three key parameters:

• -f: The path to the TSV format input file.
• -c: The path to the TSV format count file.
• -o: The path to the output directory.

Example:

python salmonRE2RPM.py -f path/to/input.tsv -c path/to/count.tsv -o path/to/output

The script will process the specified input file and generate processed CSV files in the specified output directory.