#!/home/asiimwe/anaconda3/bin/python
#Running STAR 
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_path = "/scratch/asiimwe/STAR-WASP_forRebecca/FASTQ/"

base_dir = "/home/asiimwe/projects/run_env/alpha_star_wasp_comparison"
os.chdir(base_dir)
star_dir = "STAR_Runs"
shutil.rmtree(star_dir)
mkdir(star_dir)
os.chdir(star_dir)
base_code = base_dir + "/BaseCode_STAR_Runs.sh"

sub_directories = ["8threads", "16threads", "32threads"]

for path, dirs, files in os.walk(samples_path):
	for dir in dirs:
		#print(dir) #sample dirs
		for sub_directory in sub_directories:
			os.makedirs(os.path.join(dir, sub_directory))
			full_path = os.path.join(base_dir, star_dir, dir, sub_directory)
			#print(full_path)
			#/home/asiimwe/projects/run_env/alpha_star_wasp_comparison/STAR_WASP_Runs/HG00732/32_threads

			for i in os.walk(full_path):
				if i[0].split("/")[-1] == "8threads":
					#print(i[0])
					thread_dir = i[0]
					line = thread_dir + "/8threads_resource_log.txt"
					#print(line)
					subprocess.call(["touch", line]) #include sample_id
					shutil.copy(base_code, thread_dir)
					run_code = thread_dir + "/BaseCode_STAR_Runs.sh"
					st = os.stat(run_code)
					os.chmod(run_code, st.st_mode | stat.S_IEXEC)
					#y=i[0].split("_")
					#print("this is y ", y)

					if i[0].split("_")[5] == "Runs/NA12878":
						#path.split("_")[:8] 6th item
						#print(i[0])
						#print()
						xthreads = 8
						sample_id = i[0].split("/")[7]
						sample_snp_dir = "NA12878" #we want to maintain the same snp dir for all NA12878 samples to avoid having multiple copies of the same as 1 vcf files applies to all NA12878 associated samples
						#print(sample_id)
						#print(xthreads)
						base_code_path = i[0] + "/BaseCode_STAR_Runs.sh"
						#print("base is ",base_code_path)
	
						#Replacing sections of base code to represent sample specific paths and threads being run
						with fileinput.FileInput(base_code_path, inplace=True) as file: #alternative argument to create a file backup: backup='.bak'
							for line in file:
								print(line.replace("xthreads", "8threads"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("runThreadN x", "runThreadN 8"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("sample_id", sample_id), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("ssd", sample_snp_dir), end='')

					else:
						# /home/asiimwe/projects/run_env/alpha_star_wasp_comparison/STAR_WASP_Runs/HG00512/8threads
						sample_id = i[0].split("/")[7]
						#print("search is ", sample_id)
						base_code_path = i[0] + "/BaseCode_STAR_Runs.sh"

						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("xthreads", "8threads"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("runThreadN x", "runThreadN 8"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("sample_id", sample_id), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("ssd", sample_id), end='')

				elif i[0].split("/")[-1] == "16threads":
					#print(i[0])
					thread_dir = i[0]
					line = thread_dir + "/16threads_resource_log.txt"
					#print(line)
					subprocess.call(["touch", line])
					shutil.copy(base_code, thread_dir)
					run_code = thread_dir + "/BaseCode_STAR_Runs.sh"
					st = os.stat(run_code)
					os.chmod(run_code, st.st_mode | stat.S_IEXEC)

	
					if i[0].split("_")[5] == "Runs/NA12878":
						#path.split("_")[:8] 6th item
						#print(i[0])
						#print()
						xthreads = 16
						sample_id = i[0].split("/")[7]
						sample_snp_dir = "NA12878" #we want to maintain the same snp dir for all NA12878 samples to avoid having multiple copies of the same as 1 vcf files applies to all NA12878 associated samples
						#print(sample_id)
						#print(xthreads)
						base_code_path = i[0] + "/BaseCode_STAR_Runs.sh"
						#print("base is ",base_code_path)

						#Replacing sections of base code to represent sample specific paths and threads being run
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("xthreads", "16threads"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("runThreadN x", "runThreadN 16"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("sample_id", sample_id), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("ssd", sample_snp_dir), end='')

					else:
						# /home/asiimwe/projects/run_env/alpha_star_wasp_comparison/STAR_WASP_Runs/HG00512/8threads
						sample_id = i[0].split("/")[7]
						#print("search is ", sample_id)
						base_code_path = i[0] + "/BaseCode_STAR_Runs.sh"

						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("xthreads", "16threads"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("runThreadN x", "runThreadN 16"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("sample_id", sample_id), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("ssd", sample_id), end='')


				elif i[0].split("/")[-1] == "32threads":
					#print(i[0])
					thread_dir = i[0]
					line = thread_dir + "/32threads_resource_log.txt"
					#print(line)
					subprocess.call(["touch", line])
					shutil.copy(base_code, thread_dir)
					run_code = thread_dir + "/BaseCode_STAR_Runs.sh"
					st = os.stat(run_code)
					os.chmod(run_code, st.st_mode | stat.S_IEXEC)


					if i[0].split("_")[5] == "Runs/NA12878":
						#path.split("_")[:8] 6th item
						#print(i[0])
						#print()
						xthreads = 32
						sample_id = i[0].split("/")[7]
						sample_snp_dir = "NA12878" #we want to maintain the same snp dir for all NA12878 samples to avoid having multiple copies of the same as 1 vcf files applies to all NA12878 associated samples
						#print(sample_id)
						#print(xthreads)
						base_code_path = i[0] + "/BaseCode_STAR_Runs.sh"
						#print("base is ",base_code_path)
	
						#Replacing sections of base code to represent sample specific paths and threads being run
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("xthreads", "32threads"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("runThreadN x", "runThreadN 32"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("sample_id", sample_id), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("ssd", sample_snp_dir), end='')

					else:
						# /home/asiimwe/projects/run_env/alpha_star_wasp_comparison/STAR_WASP_Runs/HG00512/8threads
						sample_id = i[0].split("/")[7]
						#print("search is ", sample_id)
						base_code_path = i[0] + "/BaseCode_STAR_Runs.sh"
	
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("xthreads", "32threads"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("runThreadN x", "runThreadN 32"), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("sample_id", sample_id), end='')
						with fileinput.FileInput(base_code_path, inplace=True) as file:
							for line in file:
								print(line.replace("ssd", sample_id), end='')


#Once all files are created in their respective directories, run the following for each sample respectively: /usr/bin/time -v -o /home/asiimwe/projects/run_env/alpha_star_wasp_comparison/STAR_WASP_Runs/NA12878_Nucleus_nonPolyA/32threads_resource_log.txt ./BaseCode_STAR_Runs.sh