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#! /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
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