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#!/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))
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