#!/home/asiimwe/anaconda3/bin/python
#Extracting data for comparative analyses between STAR_WASP and WASP - Leveraging data from the 32 thread runs
import sys
import csv
import os
import string
import subprocess
from itertools import chain
import pandas as pd
from os import mkdir
import shutil
import glob
import fileinput
import stat

samples = ["HG00512", "HG00732", "NA12878_Nucleus_nonPolyA", "NA12878_Nucleus_PolyA", "NA12878_PolyA", "NA12878_RAMPAGE", "NA12878_Small", "NA12878_Total_Rep", "NA19239",
		"HG00513", "HG00731",  "HG00733",  "NA12878_Nucleus_nonPolyA_Rep",  "NA12878_Nucleus_PolyA_Rep",  "NA12878_PolyA_Rep",  "NA12878_RAMPAGE_Rep", "NA12878_Total", "NA19238","NA19240"]

#samples_path = "/scratch/asiimwe/STAR-WASP_forRebecca/FASTQ/"

base_dir = "/home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/"
#os.chdir(base_dir)
#wasp_dir = "WASP_Runs"
#shutil.rmtree(wasp_dir)
#mkdir(wasp_dir)
#os.chdir(wasp_dir)
#base_code = base_dir + "/BaseCode_WASP_Runs.sh"

file = "/home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/dataExtractions/comp_runs.sh"
run_file_name = "comp_runs.sh"

for i in samples:
	#print(i)
	path = base_dir + i +"/32threads/"
	#print(path)
	#/home/asiimwe/projects/run_env/alpha_star_wasp_benchmarking/WASP/WASP_Runs/HG00512/32threads/
	os.chdir(path)
	shutil.copy(file, path)
	run = path +  run_file_name
	#print(run)
	with fileinput.FileInput(run, inplace=True) as file2:
		for line in file2:
			print(line.replace("sample", i), end='')
	subprocess.call(run, shell = True)