Mercurial > repos > bornea > saint_tool
comparison saint_wrapper.py @ 0:333b4c487fc3 draft
Uploaded
| author | bornea |
|---|---|
| date | Tue, 10 Nov 2015 11:39:18 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:333b4c487fc3 |
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| 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 | |
| 14 def default_run(inter_file1,prey_file1,bait_file1,output_file1,num_of_rep1): | |
| 15 cmd = r"SAINTexpress-spc " + r"-R" + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) | |
| 16 os.system(cmd) | |
| 17 open('list.txt') | |
| 18 os.rename('list.txt', str(output_file1)) | |
| 19 | |
| 20 def with_L(inter_file1,prey_file1,bait_file1,output_file1,vc_num1,num_of_rep1): | |
| 21 cmd = r"SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + r"-L" + str(vc_num1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) | |
| 22 os.system(cmd) | |
| 23 open('list.txt') | |
| 24 os.rename('list.txt', str(output_file1)) | |
| 25 | |
| 26 def external_data_no_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1): | |
| 27 cmd = r"SAINTexpress-spc "+ r"-R" + str(num_of_rep1) + " " + str(inter_file1) + " " + str(prey_file1) + " " + str(bait_file1) + " " + str(go_file1) | |
| 28 os.system(cmd) | |
| 29 open('list.txt') | |
| 30 os.rename('list.txt', str(output_file1)) | |
| 31 | |
| 32 def external_data_with_L(inter_file1,prey_file1,bait_file1,output_file1,go_file1,num_of_rep1,vc_num1): | |
| 33 cmd = r"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) | |
| 34 os.system(cmd) | |
| 35 open('list.txt') | |
| 36 os.rename('list.txt', str(output_file1)) | |
| 37 | |
| 38 if (vc_bool == "true"): | |
| 39 if (go_bool == "false"): | |
| 40 with_L(inter_file, prey_file, bait_file, output_file, vc_num, num_of_rep) | |
| 41 elif (go_bool == "true"): | |
| 42 external_data_with_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep, vc_num) | |
| 43 elif (vc_bool == "false"): | |
| 44 if (go_bool == "false"): | |
| 45 default_run(inter_file, prey_file, bait_file, output_file, num_of_rep) | |
| 46 elif (go_bool == "true"): | |
| 47 external_data_no_L(inter_file, prey_file, bait_file, output_file, go_file, num_of_rep) |