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comparison saint_wrapper.py @ 26:bb1601260366 draft

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author bornea
date Thu, 28 Jan 2016 16:31:19 -0500
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25:f6f472d55b35 26:bb1601260366
1 #######################################################################################
2 # Python-code: SAINT wrapper
3 # Author: Adam L Borne
4 # Contributers: Paul A Stewart, Brent Kuenzi
5 #######################################################################################
6 # This program takes a bait, prey and interactions file and uses SaintExpress to
7 # generate resulting matrices. This allows the software to run within galaxy.
8 #######################################################################################
9 # Copyright (C) Adam Borne.
10 # Permission is granted to copy, distribute and/or modify this document
11 # under the terms of the GNU Free Documentation License, Version 1.3
12 # or any later version published by the Free Software Foundation;
13 # with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
14 # A copy of the license is included in the section entitled "GNU
15 # Free Documentation License".
16 #######################################################################################
17 ## REQUIRED INPUT ##
18
19 # 1) inter_file: Interaction file listing experiment bait, assignement, gene name and
20 # spectrum count.
21 # 2) prey_file: Prey file listing gene name, sequence legnth, and gene id.
22 # 3) bait_file: Bait file listing bait experiment, assignment, and T or C.
23 # 4) vc_bool: Boolean used to determine if virtual controls are being used.
24 # 5) vc_num: Number of virtual controls to be used. (default = 1)
25 # 6) go_bool: Boolean used to determine used of external data set.
26 # 7) go_file: External data file if being used. (default = "None")
27 #######################################################################################
28 import os
29 import sys
30
31 inter_file = sys.argv[1]
32 prey_file = sys.argv[2]
33 bait_file = sys.argv[3]
34 num_of_rep = sys.argv[4]
35 vc_bool = sys.argv[5]
36 vc_num = sys.argv[6]
37 go_bool = sys.argv[7]
38 go_file = sys.argv[8]
39 output_file = sys.argv[9]
40 ins_path = sys.argv[10]
41
42 # Verifies the install of SaintExpress and installs if not found.
43 def first_run_check():
44 os.chdir(ins_path)
45 dirs_list = []
46 for (dirpath, dirnames, filename) in os.walk("./"):
47 dirs_list.extend(dirnames)
48 break
49 if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list:
50 pass
51 else:
52 cmd = r"unzip SAINTexpress_v3.6.1__2015-05-03.zip"
53 os.system(cmd)
54 os.chdir("./SAINTexpress_v3.6.1__2015-05-03")
55 cmd1 = r"make -j"
56 os.system(cmd1)
57
58 def default_run(inter_file1,prey_file1,bait_file1,output_file1,num_of_rep1):
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)
60 os.system(cmd)
61 open('list.txt')
62 os.rename('list.txt', str(output_file1))
63
64 def with_L(inter_file1,prey_file1,bait_file1,output_file1,vc_num1,num_of_rep1):
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)
66 os.system(cmd)
67 open('list.txt')
68 os.rename('list.txt', str(output_file1))
69
70 def external_data_no_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1):
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)
72 os.system(cmd)
73 open('list.txt')
74 os.rename('list.txt', str(output_file1))
75
76 def external_data_with_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1,vc_num1):
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)
78 os.system(cmd)
79 open('list.txt')
80 os.rename('list.txt', str(output_file1))
81
82 first_run_check()
83 if (vc_bool == "true"):
84 if (go_bool == "false"):
85 with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep)
86 elif (go_bool == "true"):
87 external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num)
88 elif (vc_bool == "false"):
89 if (go_bool == "false"):
90 default_run(inter_file, prey_file, bait_file, output_file, num_of_rep)
91 elif (go_bool == "true"):
92 external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep)