Rename!

1 files changed, 0 insertions, 126 deletions

diff --git a/SelectiveGenomeAmplificationUI b/SelectiveGenomeAmplificationUI
deleted file mode 100755
index 98021a9..0000000
--- a/SelectiveGenomeAmplificationUI
+++ /dev/null
@@ -1,126 +0,0 @@
-#!/usr/bin/env python
-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/foreground_background/',
-	  'variable': 'output_directory' },
-
-	{'question': "Where would you like to temporary files to be stored?",
-	 'default_str': '$output_directory/.tmp',
-	 'variable': "temp_directory" },
-
-	{'question': "Where would you like to count files to be stored?",
-	 'default_str': '$output_directory/.tmp',
-	 'variable': "counts_directory" },
-
-	{ 'question': 'maximum mer size you would like to pick?',
-	  'default_str': '12',
-	  'variable': 'max_mer_range' },
-
-	{ 'question': 'minimum mer size you would like to pick?',
-	  'default_str': '6',
-	  'variable': 'min_mer_range' },
-
-	{ 'question': 'eliminate mers that appear less frequently on average than this number ?',
-	  'default_str': '50000',
-	  'variable': 'min_foreground_binding_average' },
-
-	{ 'question': 'maximum size of mer combinations you want to search and select?',
-	  'default_str': '15',
-	  'variable': 'max_select' },
-
-	{ 'question': 'maximum number of mers you want to use as possible primers?',
-	  'default_str': '35',
-	  'variable': 'max_check' },
-
-	{'question': 'enter mers to ignore? (space seperated)',
-	 'default_str': "None",
-	 'variable': 'ignore_mers'},
-
-	{'question': 'enter files to ignore all mers from? (space seperated)',
-	 'default_str': "None",
-	 'variable': 'ignore_all_mers_from_files'},
-
-	{ 'question': 'maximum distance between mers in the final selection?',
-	  'default_str': "5000 bases",
-	  'variable': 'max_mer_distance' },
-
-	{ 'question': 'maximum melting temperature for mers?', 'default_str': '30c', 'variable': 'max_melting_temp' },
-	{ 'question': 'minimum melting temperature for mers?', 'default_str': '0c',  'variable': 'min_melting_temp' },
-	{ 'question': 'maximum number of consecutively binding mers in hetero and homodimers?', 'default_str': '4', 'variable': 'max_consecutive_binding' },
-	{ 'question': 'what extra weight do you want for highgly binding primers? (0-1)', 'default_str': '0', 'variable': 'fg_weight' },
-  { 'question': 'what extra weight do you want for sets with a higher number of primers? (0-1)', 'default_str': '0', 'variable': 'primer_weight'},
-	{ 'question': 'how many scored sets would you like in the top_scored_sets output file?', 'default_str':'10000', 'variable': 'output_top_nb'},
-	{ 'question': 'would you like to use a custom scoring function? see README.md for details', 'default_str':'', 'variable': '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['question']
-	default_str = question_dict['default_str']
-
-	ask_string = question + " (Default=" + str(default_str) + ")" + ": "
-
-	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 + " " + "SelectiveGenomeAmplification " + foreground + " " + background, shell=True)
-	except:
-		pass
-
-
-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['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))