Mercurial > repos > bornea > prohits_dotplot_generator

comparison ProHits_DotPlot_Generator.py @ 14:d458f5c875f1 draft

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author bornea
date Wed, 16 Mar 2016 12:10:25 -0400
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13:e74888e94f96 14:d458f5c875f1
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
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]))