Mercurial > repos > bornea > prohits_dotplot_generator
comparison toolshed_version/ProHits_DotPlot_Generator.py @ 7:59e57834c366 draft
Uploaded
author | bornea |
---|---|
date | Tue, 15 Mar 2016 15:30:44 -0400 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
6:744905986eb9 | 7:59e57834c366 |
---|---|
1 ####################################################################################### | |
2 # Python-code: Dotplot Runner | |
3 # Author: Adam L Borne | |
4 # Contributers: Paul A Stewart, Brent Kuenzi | |
5 ####################################################################################### | |
6 # This script runs the dotplot program found at http://prohitstools.mshri.on.ca/. | |
7 ####################################################################################### | |
8 # Copyright (C) Adam Borne. | |
9 # Permission is granted to copy, distribute and/or modify this document | |
10 # under the terms of the GNU Free Documentation License, Version 1.3 | |
11 # or any later version published by the Free Software Foundation; | |
12 # with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. | |
13 # A copy of the license is included in the section entitled "GNU | |
14 # Free Documentation License". | |
15 ####################################################################################### | |
16 ## REQUIRED INPUT ## | |
17 | |
18 # 1) list_file: SaintExpress output file. | |
19 # 2) FDR1: Primary false discovery rate. (default = 0.01) | |
20 # 3) FDR2: Secondary false discovery rate. (default = 0.025) | |
21 # 4) spec_max: Maximum spectral count. (default = 50) | |
22 ####################################################################################### | |
23 import os | |
24 import os | |
25 import sys | |
26 | |
27 | |
28 FDR1 = sys.argv[2] | |
29 FDR2 = sys.argv[3] | |
30 spec_max = sys.argv[4] | |
31 os.rename(sys.argv[1], "saint_input.txt") | |
32 ins_path = sys.argv[9] | |
33 | |
34 dirs_list = [] | |
35 for (dirpath, dirnames, filename) in os.walk(str(ins_path)): | |
36 dirs_list.extend(dirnames) | |
37 break | |
38 if r"Dotplot_Release" in dirs_list: | |
39 pass | |
40 else: | |
41 cmd = r"tar -xvf /Dotplot_Release.tar.gz " + str(ins_path) + "/Dotplot_Release.tar.gz" | |
42 os.system(cmd) | |
43 | |
44 | |
45 cmd = (str(ins_path) + r"Dotplot_Release/dotplot.bash -f saint_input.txt" + r" -c b -s " + str(FDR1) + | |
46 r" -t " + str(FDR2) + " -m " + str(spec_max)) | |
47 os.system(cmd) | |
48 | |
49 cmd1 = r"cp -a ./Output_saint_input/. ." | |
50 os.system(cmd1) | |
51 | |
52 os.rename("saint_input.txt", str(sys.argv[1])) | |
53 os.rename('dotplot.pdf', str(sys.argv[5])) | |
54 os.rename('bait2bait.pdf', str(sys.argv[6])) | |
55 os.rename('estimated.pdf', str(sys.argv[7])) | |
56 os.rename('stats.pdf', str(sys.argv[8])) |