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

def run_generic(cmd):
	'''
		get the length of a fasta file by piping it through several unix 
		programs.

		1) remove headers by grepping for any ">" at the start of a line
		2) delete all occurances of a new line, to join sequences together
		3) sum the number of characters.
	'''
	from subprocess import Popen
	from subprocess import PIPE

	fh = Popen(cmd, stdout=PIPE, shell=True, executable='/bin/bash')

	return fh.stdout.readlines()

foreground = ""
background = ""

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

variables = {}

questions = [
	{ 'q' : "what is your foreground fasta file?", 
	  'def': '',
		'tab': 'file',
	  'v': 'foreground',
		't': 'file'},

	{ 'q' : "what is your background fasta file?", 
	  'def': '',
	  'v': 'background',
		'tab': 'file',
		't': 'file'},

	{ 'q' : "Where would you like your output directory to be?", 
	  'def': 'current directory/foreground_background/',
	  'v': 'output_directory',
		'tab': 'file',
		't': 'dir'},

	{'q': "Where would you like to temporary files to be stored?",
	 'def': '$output_directory/.tmp',
	 'v': "temp_directory",
		'tab': 'file',
	 't': 'dir'},

	{'q': "Where would you like to count files to be stored?",
	 'def': '$output_directory/.tmp',
	 'v': "counts_directory", 
   'tab': 'file',
	 't': 'dir' },

	{ 'q': 'maximum mer size you would like to pick?',
	  'def': '12',
	  'v': 'max_mer_range',
   'tab': 'filter',
		't': 'int'},

	{ 'q': 'minimum mer size you would like to pick?',
	  'def': '6',
	  'v': 'min_mer_range',
   'tab': 'filter',
		't': 'int'},

	{ 'q': 'eliminate mers that appear on average less than this ?',
	  'def': '50000',
	  'v': 'min_foreground_binding_average', 
   'tab': 'filter',
		't': 'int'},

	{ 'q': 'maximum size of mer combinations you want to search and select?',
	  'def': '15',
	  'v': 'max_select',
   'tab': 'filter',
		't': 'int'},

	{ 'q': 'maximum number of mers you want to use as possible primers?',
	  'def': '35',
	  'v': 'max_check',
   'tab': 'filter',
		't': 'int'},

	{'q': 'enter mers to ignore? (space seperated)',
	 'def': "None",
	 'v': 'ignore_mers',
   'tab': 'filter',
		't': 'str'},

	{'q': 'enter files to ignore all mers from? (space seperated)',
	 'def': "None",
	 'v': 'ignore_all_mers_from_files',
   'tab': 'filter',
	 't': 'file',
	 'opt': 'multiple'},

	{ 'q': 'maximum distance between mers in the final selection?',
	  'def': "5000",
	  'v': 'max_mer_distance',
   'tab': 'filter',
		't': 'int'},

	{ 'q': 'minimum background ratio?',
	  'def': "None",
	  'v': 'min_bg_ratio',
   'tab': 'filter',
		't': 'int'},

	{ 'q': 'maximum melting temperature for mers?', 'def': '30c', 'v': 'max_melting_temp', 't': 'float', 'tab':'melting'},
	{ 'q': 'minimum melting temperature for mers?', 'def': '0c',  'v': 'min_melting_temp', 't': 'float' , 'tab':'melting'},
	{ 'q': 'DNA Concentration (nM)?', 'def': '5000nM',  'v': 'dna_con', 't':'float', 'tab':'melting' },
	{ 'q': 'Salt Concentration (mM) ?', 'def': '10mM',  'v': 'na_con', 't':'float', 'tab':'melting' },
	{ 'q': 'Magnesium Concentration (mM)?', 'def': '20mM',  'v': 'mg_con', 't':'float', 'tab':'melting'},
	{ 'q': 'dNTPs Concentration (mM) ?', 'def': '10mM',  'v': 'dntps_con', 't':'float', 'tab':'melting'},
	{ 'q': 'maximum number of consecutively binding mers in hetero and homodimers?', 'def': '4', 'v': 'max_consecutive_binding', 't':'int', 'tab':'filter' },
	{ 'q': 'what extra weight do you want for highgly binding primers? (0-1)', 'def': '0', 'v': 'fg_weight', 't':'float', 'tab':'scoring'},
  { 'q': 'what extra weight do you want for sets with a higher number of primers? (0-1)', 'def': '0', 'v': 'primer_weight', 't':'float', 'tab':'scoring'},
	{ 'q': 'how many scored sets would you like in the top_scored_sets output file?', 'def':'10000', 'v': 'output_top_nb', 't':'int', 'tab':'scoring'},
	{ 'q': 'custom scoring function (see README.md for details) ', 'def':'', 'v': 'score_func', 't':'str', 'tab':'scoring'}
]

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 yad_ask_all_questions(questions):
	import random

	key = random.randint(0,100000)

	cmd_d = { 
		'file': "yad --form --plug=" + str(key) + " --tabnum=1 ", 
		'filter': "yad --form --plug=" + str(key) + " --tabnum=2 ", 
		'melting': "yad --form --plug=" + str(key) + " --tabnum=3 ", 
		'scoring': "yad --form --plug=" + str(key) + " --tabnum=4 "
	}
	container = 'yad --notebook --key=' + str(key) + ' --tab="Files" --tab="filter" --tab="Melting Temperature" --tab="Scoring" --title="Selective Genome Amplification Options" '
	shmcleanup = "ipcrm -M `printf 0x%0.8x "+ str(key) + "` 2> /dev/null"

	for q in questions:
		qstr = '--field="' + q['q'] + " (" + q['v'] + ')":LBL '

		# if it's a directory
		if q['t'] is 'dir':
			qstr += "--field=" + q['v'] + ":DIR"

		# if it's a file
		elif q['t'] is 'file':
			if 'opt' in q:
				if q['opt'] is 'multiple':
					qstr += "--field" + q['v'] + ":TXT"
			else:
				qstr += "--field=" + q['v'] + ":FL"

		elif q['t'] is 'bool':
			qstr += "--field" + q['v'] + ":CHK"

		elif q['t'] is 'int':
			qstr += "--field=" + q['v'] + ":NUM"
		
		elif q['t'] is 'float':
			qstr += "--field=" + q['v'] + ":NUM"
		elif q['t'] is 'txt':
			qstr += "--field=" + q['v'] + ":TXT"

		elif q['t'] is 'str':
			qstr += "--field=" + q['v'] + ""

		cmd_d[q['tab']] += qstr + " "
	
	cmd = "cat <( %s ) <( %s ) <( %s ) <( %s ) & %s; %s" % (cmd_d['file'], cmd_d['filter'], cmd_d['melting'], cmd_d['scoring'], container, shmcleanup)

	print cmd
	res = run_generic(cmd)
	return res


variable = yad_ask_all_questions(questions)
print variable

print variables_to_string(variables)
run(variables_to_string(variables))
raw_input("Press Enter to exit...")