From 9f3fea70da568830012c60a74a5e9e3bea99b229 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Mon, 14 Apr 2014 23:02:52 -0400 Subject: keep asking for files if they don't exist, filter melting temperature with updated function --- SelectiveWholeGenomeAmplificationUI | 132 ++++++++++++++++++++---------------- 1 file changed, 74 insertions(+), 58 deletions(-) (limited to 'SelectiveWholeGenomeAmplificationUI') diff --git a/SelectiveWholeGenomeAmplificationUI b/SelectiveWholeGenomeAmplificationUI index decf5a1..c969d63 100755 --- a/SelectiveWholeGenomeAmplificationUI +++ b/SelectiveWholeGenomeAmplificationUI @@ -1,4 +1,6 @@ #!/usr/bin/env python +import os.path + foreground = "" background = "" @@ -7,57 +9,61 @@ 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'} + { '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': '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): @@ -74,10 +80,10 @@ def bool_ask(ask_string, default): return yes_no[ans] def ask(question_dict): - question = question_dict['question'] - default_str = question_dict['default_str'] + question = question_dict['q'] + default = question_dict['def'] - ask_string = question + " (Default=" + str(default_str) + ")" + ": " + ask_string = question + " (Default=" + str(default) + ")" + ": " ans = raw_input(ask_string) return ans @@ -100,6 +106,16 @@ def run(variables_as_a_string): 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:") @@ -110,14 +126,14 @@ if(bool_ask("would you like to input all your variables at once?", "n")): else: for q in questions: if 'bool' in q: - res = ask_bool(q['question'], q['default']) + res = ask_bool(q['q'], q['def']) else: res = ask(q) - variables[q['variable']] = res + variables[q['v']] = res - foreground = raw_input("Input the path to your foreground file:") - background = raw_input("Input the path to your background file:") + foreground = file_ask("Input the path to your foreground file:") + foreground = 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) -- cgit v1.2.1