|
21
|
1 import os
|
|
|
2 import sys
|
|
|
3
|
|
|
4 inter_file = sys.argv[1]
|
|
|
5 prey_file = sys.argv[2]
|
|
|
6 bait_file = sys.argv[3]
|
|
|
7 num_of_rep = sys.argv[4]
|
|
|
8 vc_bool = sys.argv[5]
|
|
|
9 vc_num = sys.argv[6]
|
|
|
10 go_bool = sys.argv[7]
|
|
|
11 go_file = sys.argv[8]
|
|
|
12 output_file = sys.argv[9]
|
|
|
13 ins_path = sys.argv[10]
|
|
|
14
|
|
|
15 def first_run_check():
|
|
|
16 os.chdir(ins_path)
|
|
|
17 dirs_list = []
|
|
|
18 for (dirpath, dirnames, filename) in os.walk("./"):
|
|
|
19 dirs_list.extend(dirnames)
|
|
|
20 break
|
|
|
21 if r"SAINTexpress_v3.6.1__2015-05-03" in dirs_list:
|
|
|
22 pass
|
|
|
23 else:
|
|
|
24 cmd = r"unzip SAINTexpress_v3.6.1__2015-05-03.zip"
|
|
|
25 os.system(cmd)
|
|
|
26 os.chdir("./SAINTexpress_v3.6.1__2015-05-03")
|
|
|
27 cmd1 = r"make -j"
|
|
|
28 os.system(cmd1)
|
|
|
29
|
|
|
30 def default_run(inter_file1,prey_file1,bait_file1,output_file1,num_of_rep1):
|
|
|
31 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)
|
|
|
32 os.system(cmd)
|
|
|
33 open('list.txt')
|
|
|
34 os.rename('list.txt', str(output_file1))
|
|
|
35
|
|
|
36 def with_L(inter_file1,prey_file1,bait_file1,output_file1,vc_num1,num_of_rep1):
|
|
|
37 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)
|
|
|
38 os.system(cmd)
|
|
|
39 open('list.txt')
|
|
|
40 os.rename('list.txt', str(output_file1))
|
|
|
41
|
|
|
42 def external_data_no_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1):
|
|
|
43 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)
|
|
|
44 os.system(cmd)
|
|
|
45 open('list.txt')
|
|
|
46 os.rename('list.txt', str(output_file1))
|
|
|
47
|
|
|
48 def external_data_with_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1,vc_num1):
|
|
|
49 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)
|
|
|
50 os.system(cmd)
|
|
|
51 open('list.txt')
|
|
|
52 os.rename('list.txt', str(output_file1))
|
|
|
53
|
|
|
54 if (vc_bool == "true"):
|
|
|
55 if (go_bool == "false"):
|
|
|
56 with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep)
|
|
|
57 elif (go_bool == "true"):
|
|
|
58 external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num)
|
|
|
59 elif (vc_bool == "false"):
|
|
|
60 if (go_bool == "false"):
|
|
|
61 default_run(inter_file, prey_file, bait_file, output_file, num_of_rep)
|
|
|
62 elif (go_bool == "true"):
|
|
|
63 external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep)
|
