GSEA_merge.sh

#!/bin/bash

# Author: Daniel Guevara
# dgdiaz011202@gmail.com
# June 23rd, 2024

# Use this script to merge and rename GSEA results data.

# ------------- #
# Define routes #
# ------------- #

main_dir=/path_to_home_directory
output_dir=$main_dir/C2_CGP    

# Iterate over each subdirectory in the main directory
for dir in "$output_dir"/*/; do
	# Extract the comparison and collection from the directory name
	dir_name=$(basename "$dir")
	comparison=${dir_name#C2_CGP_}
	comparison=${comparison%.Gsea*}
	collection="C2_CGP"
	
	# Define the output file name
	output_file="$output_dir/${collection}_${comparison}_merged.tsv"
	
	# Initialize a flag to track the header
	header_included=false
	
	# Find and merge all matching files within the subdirectory
	for file in "$dir"gsea_report_for*.tsv; do
		if [ "$header_included" = false ]; then
			# Include the header for the first file
			cat "$file" >> "$output_file"
			header_included=true
		else
			# Skip the header for subsequent files
			tail -n +2 "$file" >> "$output_file"
		fi
	done
	
	echo "Merged files from $dir into $output_file"
done