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1 #######################################################################################
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2 # Python-code: SAINT wrapper
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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 program takes a bait, prey and interactions file and uses SaintExpress to
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7 # generate resulting matrices. This allows the software to run within 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) inter_file: Interaction file listing experiment bait, assignement, gene name and
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20 # spectrum count.
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21 # 2) prey_file: Prey file listing gene name, sequence legnth, and gene id.
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22 # 3) bait_file: Bait file listing bait experiment, assignment, and T or C.
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23 # 4) vc_bool: Boolean used to determine if virtual controls are being used.
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24 # 5) vc_num: Number of virtual controls to be used. (default = 1)
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25 # 6) go_bool: Boolean used to determine used of external data set.
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26 # 7) go_file: External data file if being used. (default = "None")
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27 #######################################################################################
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28 import os
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29 import sys
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30
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31 inter_file = sys.argv[1]
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32 prey_file = sys.argv[2]
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33 bait_file = sys.argv[3]
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34 num_of_rep = sys.argv[4]
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35 vc_bool = sys.argv[5]
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36 vc_num = sys.argv[6]
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37 go_bool = sys.argv[7]
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38 go_file = sys.argv[8]
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39 output_file = sys.argv[9]
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40 ins_path = sys.argv[10]
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41
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42 # Verifies the install of SaintExpress and installs if not found.
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43 def first_run_check():
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44 os.chdir(ins_path)
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45 dirs_list = []
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46 for (dirpath, dirnames, filename) in os.walk("./"):
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47 dirs_list.extend(dirnames)
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48 break
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49 if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list:
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50 pass
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51 else:
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52 cmd = r"unzip SAINTexpress_v3.6.1__2015-05-03.zip"
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53 os.system(cmd)
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54 os.chdir("./SAINTexpress_v3.6.1__2015-05-03")
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55 cmd1 = r"make -j"
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56 os.system(cmd1)
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57
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58 def default_run(inter_file1,prey_file1,bait_file1,output_file1,num_of_rep1):
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59 cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc " + r"-R" + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1)
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60 os.system(cmd)
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61 open('list.txt')
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62 os.rename('list.txt', str(output_file1))
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63
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64 def with_L(inter_file1,prey_file1,bait_file1,output_file1,vc_num1,num_of_rep1):
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65 cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1)
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66 os.system(cmd)
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67 open('list.txt')
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68 os.rename('list.txt', str(output_file1))
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69
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70 def external_data_no_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1):
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71 cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + " " + str(go_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 def external_data_with_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1,vc_num1):
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77 cmd = str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1)
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78 os.system(cmd)
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79 open('list.txt')
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80 os.rename('list.txt', str(output_file1))
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81
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82 first_run_check()
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83 if (vc_bool == "true"):
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84 if (go_bool == "false"):
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85 with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep)
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86 elif (go_bool == "true"):
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87 external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num)
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88 elif (vc_bool == "false"):
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89 if (go_bool == "false"):
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90 default_run(inter_file, prey_file, bait_file, output_file, num_of_rep)
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91 elif (go_bool == "true"):
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92 external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep)
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