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1 #######################################################################################
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2 # Python-code: Dotplot Runner
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3 # Author: Adam L Borne
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4 # Contributers: Paul A Stewart, Brent Kuenzi
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5 #######################################################################################
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6 # This runs SAINTexpress found at http://saint-apms.sourceforge.net/Main.html in
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7 # galaxy.
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8 #######################################################################################
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9 # Copyright (C) Adam Borne.
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10 # Permission is granted to copy, distribute and/or modify this document
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11 # under the terms of the GNU Free Documentation License, Version 1.3
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12 # or any later version published by the Free Software Foundation;
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13 # with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
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14 # A copy of the license is included in the section entitled "GNU
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15 # Free Documentation License".
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16 #######################################################################################
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17 ## REQUIRED INPUT ##
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18
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19 # 1) list_file: SaintExpress output file.
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20 # 2) FDR1: Primary false discovery rate. (default = 0.01)
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21 # 3) FDR2: Secondary false discovery rate. (default = 0.025)
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22 # 4) spec_max: Maximum spectral count. (default = 50)
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23 #######################################################################################
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24
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25
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26 import os
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27 import sys
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29
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30 inter_file = sys.argv[1]
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31 prey_file = sys.argv[2]
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32 bait_file = sys.argv[3]
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33 num_of_rep = sys.argv[4]
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34 vc_bool = sys.argv[5]
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35 vc_num = sys.argv[6]
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36 go_bool = sys.argv[7]
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37 go_file = sys.argv[8]
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38 output_file = sys.argv[9]
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39 ins_path = sys.argv[10]
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40
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41
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42 def first_run_check():
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43 dirs_list = []
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44 for (dirpath, dirnames, filename) in os.walk("./"):
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45 dirs_list.extend(dirnames)
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46 break
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47 if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list:
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48 pass
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49 else:
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50 cmd = r"unzip SAINTexpress_v3.6.1__2015-05-03.zip"
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51 os.system(cmd)
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52 os.chdir("./SAINTexpress_v3.6.1__2015-05-03")
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53 cmd1 = r"make -j"
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54 os.system(cmd1)
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55
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56
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57 def default_run(inter_file1, prey_file1, bait_file1, output_file1, num_of_rep1):
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58 # Default is no virtual controls through purification and set replicates number.
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59 cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc " + r"-R"
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60 + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) +
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61 " " + str(bait_file1))
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62 os.system(cmd)
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63 open('list.txt')
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64 os.rename('list.txt', str(output_file1))
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65
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66
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67 def with_L(inter_file1, prey_file1, bait_file1, output_file1, vc_num1, num_of_rep1):
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68 # L is the flag for Virtual Controls through Purification.
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69 cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
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70 + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " +
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71 str(prey_file1) + " " + str(bait_file1))
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72 os.system(cmd)
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73 open('list.txt')
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74 os.rename('list.txt', str(output_file1))
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75
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76
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77 def external_data_no_L(inter_file1, prey_file1, bait_file1, output_file1, go_file1, num_of_rep1):
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78 # Uses external data in the GO file format and no Virtual Controls.
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79 cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
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80 + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " +
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81 str(bait_file1) + " " + str(go_file1))
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82 os.system(cmd)
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83 open('list.txt')
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84 os.rename('list.txt', str(output_file1))
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85
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86
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87 def external_data_with_L(inter_file1, prey_file1, bait_file1, output_file1, go_file1, num_of_rep1, vc_num1):
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88 # Uses external data in the GO file format and Virtual Controls.
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89 cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
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90 + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " +
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91 str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1))
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92 os.system(cmd)
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93 open('list.txt')
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94 os.rename('list.txt', str(output_file1))
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95
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96
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97 first_run_check()
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98 if vc_bool == "true":
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99 if go_bool == "false":
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100 with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep)
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101 elif go_bool == "true":
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102 external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num)
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103 elif vc_bool == "false":
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104 if go_bool == "false":
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105 default_run(inter_file, prey_file, bait_file, output_file, num_of_rep)
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106 elif go_bool == "true":
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107 external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep)
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