#! /usr/bin/python
# output directory 
# : ${output_directory=`basename $foreground`_`basename $background`}
# directory to store our counts and sorted counts
# : ${counts_directory=$output_directory/.counts}
# temp directory 
# : ${tmp_directory=$output_directory/.tmp}
# range of mers, min and max 
# : ${min_mer_range=6}
#: ${max_mer_range=10}
# max mer distance, the distance between two mers in our selected outputs
#: ${max_mer_distance=5000}
# min/maximum kmer meling point
# : ${max_melting_temp=30}
# : ${min_melting_temp=0}
# minimum mer count
# : ${min_mer_count=0}
# maximum mers to pick
# : ${max_select=15}
# mers to specifically IGNORE, space delimited
# ${ignore_mers=''}

# ${foreground=''}
# ${background=''}

foreground = ""
background = ""

yes_no = {'Y': True, 'y': True,'n': False, 'N': False, 'yes': True, 'no': False, '': '' }

variables = {}

questions = [
	{ 'question' : "Where would you like your output directory to be?", 
	  'default_str': 'current directory',
	  'variable': 'output_directory'
	 },
	{'question': "Where would you like to temporary files to be stored?",
	 'default_str': '$output_directory/.tmp',
	 'variable': "temp_directory" },
	{ 'question': 'What is the maximum mer size you would like to pick?',
	  'default_str': '12',
	  'variable': 'max_mer_range' },
	{ 'question': 'What is the minimum mer size you would like to pick?',
	  'default_str': '6',
	  'variable': 'min_mer_range' },
	{ 'question': 'What is the minimum mer count you want to have for your selected mer?',
	  'default_str': 'None',
	  'variable': 'min_mer_count' },
	{ 'question': 'What is the maximum number of mers you want to search and select?',
	  'default_str': '15',
	  'variable': 'max_select' },
	{'question': 'Do you want to specifically ignore any mers? (space seperated)',
	 'default_str': "None",
	 'variable': 'ignore_mers' }

]

def bool_ask(ask_string, default):
	ans = ""

	ask_string = ask_string + " (Y/N/Default=" + str(default) + ")" + ": "

	ans = raw_input(ask_string)
	while ans not in yes_no.keys():
		ans = raw_input(ask_string)
	if ans is '':
		ans = default

	return yes_no[ans]

def ask(question_dict):
	question = question_dict['question']
	default_str = question_dict['default_str']

	ask_string = question + " (Y/N/Default=" + str(default_str) + ")" + ": "

	ans = raw_input(ask_string)
	return ans 

def variables_to_string(variables):
	ret = ""
	for variable in variables:
		ret = ret + variable + "=\"" + variables[variable] + "\" "
	ret = ret + "foreground=\"" + foreground + "\" "
	ret = ret + "background=\"" + foreground + "\" "
	return ret

def run(variables_as_a_string):

	import subprocess
	subprocess.check_call(variables_as_a_string + " " + "SelectGenomeAmplification " + foreground + " " + background, shell=True)

if(bool_ask("would you like to input all your variables at once?", "n")):
	variables = raw_input("Please paste in your variables (space delimited):")
	print variables
	run(variables)
else:
	for q in questions:
		if 'bool' in q:
			res = ask_bool(q['question'], q['default'])
		else:
			res = ask(q)

		variables[q['variable']] = res 

	foreground = raw_input("Input the path to your foreground file:")
	background = raw_input("Input the path to your background file:")

	if(bool_ask("Would you like to output your inserted variables to a string you can later paste?", "y")):
		print variables_to_string(variables)

	if(bool_ask("Run SelectiveGenomeAmplification?", "y")):
		run(variables_to_string(variables))

# SelectGenomeAmplification

# export ignore_mers
# export min_mer_range
# export max_mer_range

# export max_select

# export min_mer_count
# export max_mer_distance

# export max_melting_temp 
#export min_melting_temp