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#!/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...")
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