#!/usr/bin/env python2.7
import os.path

foreground = ""
background = ""

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

variables = {}

questions = [
	{ 'q' : "Where would you like your output directory to be?", 
	  'def': 'current directory/foreground_background/',
	  'v': 'output_directory' },

	{'q': "Where would you like to temporary files to be stored?",
	 'def': '$output_directory/.tmp',
	 'v': "temp_directory" },

	{'q': "Where would you like to count files to be stored?",
	 'def': '$output_directory/.tmp',
	 'v': "counts_directory" },

	{ 'q': 'maximum mer size you would like to pick?',
	  'def': '12',
	  'v': 'max_mer_range' },

	{ 'q': 'minimum mer size you would like to pick?',
	  'def': '6',
	  'v': 'min_mer_range' },

	{ 'q': 'eliminate mers that appear less frequently on average than this number ?',
	  'def': '50000',
	  'v': 'min_foreground_binding_average' },

	{ 'q': 'maximum size of mer combinations you want to search and select?',
	  'def': '15',
	  'v': 'max_select' },

	{ 'q': 'maximum number of mers you want to use as possible primers?',
	  'def': '35',
	  'v': 'max_check' },

	{'q': 'enter mers to ignore? (space seperated)',
	 'def': "None",
	 'v': 'ignore_mers'},

	{'q': 'enter files to ignore all mers from? (space seperated)',
	 'def': "None",
	 'v': 'ignore_all_mers_from_files'},

	{ 'q': 'maximum distance between mers in the final selection?',
	  'def': "5000 bases",
	  'v': 'max_mer_distance' },

	{ 'q': 'minimum background ratio?',
	  'def': "None",
	  'v': 'min_bg_ratio' },

	{ 'q': 'maximum melting temperature for mers?', 'def': '30c', 'v': 'max_melting_temp' },
	{ 'q': 'minimum melting temperature for mers?', 'def': '0c',  'v': 'min_melting_temp' },
	{ 'q': 'DNA Concentration (nM)?', 'def': '5000nM',  'v': 'dna_con' },
	{ 'q': 'Salt Concentration (mM) ?', 'def': '10mM',  'v': 'na_con' },
	{ 'q': 'Magnesium Concentration (mM)?', 'def': '20mM',  'v': 'mg_con' },
	{ 'q': 'dNTPs Concentration (mM) ?', 'def': '10mM',  'v': 'dntps_con' },
	{ 'q': 'maximum number of consecutively binding mers in hetero and homodimers?', 'def': '4', 'v': 'max_consecutive_binding' },
	{ 'q': 'what extra weight do you want for highgly binding primers? (0-1)', 'def': '0', 'v': 'fg_weight' },
  { 'q': 'what extra weight do you want for sets with a higher number of primers? (0-1)', 'def': '0', 'v': 'primer_weight'},
	{ 'q': 'how many scored sets would you like in the top_scored_sets output file?', 'def':'10000', 'v': 'output_top_nb'},
	{ 'q': 'would you like to use a custom scoring function? see README.md for details', 'def':'', 'v': 'score_func'}
]

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['q']
	default = question_dict['def']

	ask_string = question + " (Default=" + str(default) + ")" + ": "

	ans = raw_input(ask_string)
	return ans 

def variables_to_string(variables):
	ret = ""
	for variable in variables:
		if variables[variable] is not '':
			ret = ret + variable + "=\"" + variables[variable] + "\" "

	ret = ret + "foreground=\"" + foreground + "\" "
	ret = ret + "background=\"" + background + "\" "
	return ret

def run(variables_as_a_string):

	import subprocess
	try:
		subprocess.check_call(variables_as_a_string + " " + "SelectiveWholeGenomeAmplification " + foreground + " " + background, shell=True)
	except:
		pass

def file_ask(query):
	response = None
	while response is None:
		response = raw_input(query)
		if os.path.isfile(response) is not True:
			print "That file doesn't exist."
			response = None

	return response


if(bool_ask("would you like to input all your variables at once?", "n")):
	variables = raw_input("Please paste in your variables (space delimited) and Run:")
	run(variables)

	raw_input("Press Enter to exit...")

else:
	for q in questions:
		if 'bool' in q:
			res = ask_bool(q['q'], q['def'])
		else:
			res = ask(q)

		variables[q['v']] = res 

	foreground = file_ask("Input the path to your foreground file:")
	background = file_ask("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 SelectiveWholeGenomeAmplification?", "y")):
		run(variables_to_string(variables))