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comparison toolshed_version/saint_wrapper.py @ 0:11fe2e7c8fe3 draft

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author bornea
date Tue, 15 Mar 2016 16:06:51 -0400
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1 #######################################################################################
2 # Python-code: Dotplot Runner
3 # Author: Adam L Borne
4 # Contributers: Paul A Stewart, Brent Kuenzi
5 #######################################################################################
6 # This runs SAINTexpress found at http://saint-apms.sourceforge.net/Main.html in
7 # 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) list_file: SaintExpress output file.
20 # 2) FDR1: Primary false discovery rate. (default = 0.01)
21 # 3) FDR2: Secondary false discovery rate. (default = 0.025)
22 # 4) spec_max: Maximum spectral count. (default = 50)
23 #######################################################################################
24
25
26 import os
27 import sys
28
29
30 inter_file = sys.argv[1]
31 prey_file = sys.argv[2]
32 bait_file = sys.argv[3]
33 num_of_rep = sys.argv[4]
34 vc_bool = sys.argv[5]
35 vc_num = sys.argv[6]
36 go_bool = sys.argv[7]
37 go_file = sys.argv[8]
38 output_file = sys.argv[9]
39 ins_path = sys.argv[10]
40
41
42 def first_run_check():
43 dirs_list = []
44 for (dirpath, dirnames, filename) in os.walk(str(ins_path)):
45 dirs_list.extend(dirnames)
46 break
47 if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list:
48 pass
49 else:
50 cmd = r"unzip " + str(ins_path) + "/SAINTexpress_v3.6.1__2015-05-03.zip -d " + str(ins_path)
51 os.system(cmd)
52 os.chdir(str(ins_path) + "/SAINTexpress_v3.6.1__2015-05-03")
53 cmd1 = r"make -j"
54 os.system(cmd1)
55
56
57 def default_run(inter_file1, prey_file1, bait_file1, output_file1, num_of_rep1):
58 # Default is no virtual controls through purification and set replicates number.
59 cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc " + r"-R"
60 + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) +
61 " " + str(bait_file1))
62 os.system(cmd)
63 open('list.txt')
64 os.rename('list.txt', str(output_file1))
65
66
67 def with_L(inter_file1, prey_file1, bait_file1, output_file1, vc_num1, num_of_rep1):
68 # L is the flag for Virtual Controls through Purification.
69 cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
70 + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " +
71 str(prey_file1) + " " + str(bait_file1))
72 os.system(cmd)
73 open('list.txt')
74 os.rename('list.txt', str(output_file1))
75
76
77 def external_data_no_L(inter_file1, prey_file1, bait_file1, output_file1, go_file1, num_of_rep1):
78 # Uses external data in the GO file format and no Virtual Controls.
79 cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
80 + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " +
81 str(bait_file1) + " " + str(go_file1))
82 os.system(cmd)
83 open('list.txt')
84 os.rename('list.txt', str(output_file1))
85
86
87 def external_data_with_L(inter_file1, prey_file1, bait_file1, output_file1, go_file1, num_of_rep1, vc_num1):
88 # Uses external data in the GO file format and Virtual Controls.
89 cmd = (str(ins_path) + r"/SAINTexpress_v3.6.1__2015-05-03/bin/SAINTexpress-spc "+ r"-R"
90 + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " +
91 str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1))
92 os.system(cmd)
93 open('list.txt')
94 os.rename('list.txt', str(output_file1))
95
96
97 first_run_check()
98 if vc_bool == "true":
99 if go_bool == "false":
100 with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep)
101 elif go_bool == "true":
102 external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num)
103 elif vc_bool == "false":
104 if go_bool == "false":
105 default_run(inter_file, prey_file, bait_file, output_file, num_of_rep)
106 elif go_bool == "true":
107 external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep)