quantgene takes in file with relative gene expression units as a input and outputs file including converted TPM value or scatter plot of TPM values based on the user's choice.
To download this tool, clone this repository:
git clone https://github.com/kmjsm2/quantgene
Then change the current folder to quantgene by:
cd quantgene
quantgene requires the pandas, numpy, and matplotlib.pyplot libraries to be installed.
To install those libraries:
pip install pandas numpy matplotlib
After required libraries installed, install quantgene by below command:
pip install .
To run quantgene
quantgene [-h] [--x_label X_LABEL] [--y_label Y_LABEL] [--p_title P_TITLE] [--o_title O_TITLE] [--converted CONVERTED] [—input_dir INPUT_DIR]{scatter,convert} file1 [file2] out_dir
required arguments:
{scatter,convert} Mode of operation: scatter for scatter plot, convert for gene expression conversion
file1 Path to the first file, need to have column gene_id and FPKM for convert and TPM for scatter
file2 Path to the second file (not required for convert mode), need to have column TPM for scatter
out_dir Directory to save the output plot or converted files
options:
-h, --help show this help message and exit
--x_label X_LABEL Label for x-axis
--y_label Y_LABEL Label for y-axis
--p_title P_TITLE Title of the scatter plot
--o_title O_TITLE Name of the output scatter plot file
--converted CONVERTED
Name of the output file for convert mode
--input_dir INPUT_DIR
Directory containing input files for batch conversion, files must be ending with _fpkm.csv and each file have column gene_id and FPKM
Example to use convert:
quantgene convert benchmark/Chow_Rep1.genes.results ./
Above code will convert the FPKM value to TPM value. When the input already have existing column TPM like this input, it will generate new column as Calc_TPM, otherwise TPM.
Example to use scatter:
quantgene scatter benchmark/Chow_Rep1.genes.results benchmark/Chow_Rep2.genes.results ./
Takes in two files with TPM value and save the image of scatter plot of TPM values.