#! /bin/bash

# This mini-script copies txt files from each analysed barcode folder to the 'forR' directory.
# The pre-requisite is to have empty directories of the same name in 'forR', which can easily be made with mkdir {dir1,dir2,etc.} .
# Once done, 'forR' can be compressed to .zip which can then be easily transferred to Macbook for R analysis. 

cd /home/jankatalinic/hdd/RciVariants/Orthogonality_repl2


for folder in *;  do 
	cp $folder/Mapped/Filtered/*.txt forR/"$folder"
	echo "done with folder "$folder" !"
    done