Mercurial > repos > bornea > apostl_static_bubblegraph_generator
comparison APOSTL_Static_Bubblegraph_Generator.py @ 6:66faf09e5e8e draft
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author | bornea |
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date | Tue, 15 Mar 2016 15:19:03 -0400 |
parents | 475ef39c9eee |
children | 8f463e2a34d5 |
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5:0489ece83d7f | 6:66faf09e5e8e |
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1 ####################################################################################### | |
2 # Python-code: Bubblebeam wrapper | |
3 # Author: Adam L Borne | |
4 # Contributers: Paul A Stewart, Brent Kuenzi | |
5 ####################################################################################### | |
6 # This program runs the R script that generates a bubble plot. Python script simply | |
7 # handles arguments and interacts with 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) prey_file: Prey file listing gene name, sequence legnth, and gene id. | |
21 # 3) crapome: Crapome file can be created at http://crapome.org. (default = "None") | |
22 # 4) color: Fill color of the bubbles, if set to crapome it shades based on crapome | |
23 # potential. (default = "Red") | |
24 # 5) cutoff: Lower limit saint score for generating bubble plot. (default = 0.8) | |
25 # 6) mq_sc: MQ for MaxQuant data and SC for Scaffold data. | |
26 # 7) inc_file: List of uniprot ids to be used exclusively. (default = "None") | |
27 # 8) exc_file: List of uniprot ids to be excluded from plot. (default = "None") | |
28 ####################################################################################### | |
29 | |
30 import os | |
31 import sys | |
32 import time | |
33 | |
34 | |
35 list_file = sys.argv[1] | |
36 prey_file = sys.argv[2] | |
37 crapome = sys.argv[3] | |
38 color = sys.argv[4] | |
39 label = sys.argv[5] | |
40 cutoff = sys.argv[6] | |
41 mq_sc = sys.argv[7] | |
42 inc_file = sys.argv[8] | |
43 exc_file = sys.argv[9] | |
44 output_file_name = sys.argv[10] | |
45 bub_zoom_NSAF = sys.argv[11] | |
46 bub_zoom_SAINT =sys.argv[12] | |
47 bub_SAINT = sys.argv[13] | |
48 bub_NSAF = sys.argv[14] | |
49 ins_path = sys.argv[15] | |
50 | |
51 if crapome == "None": | |
52 crapome = "FALSE" | |
53 | |
54 | |
55 if label == "false": | |
56 label = "FALSE" | |
57 elif label == "true": | |
58 label = "TRUE" | |
59 | |
60 cmd = (r"Rscript "+ str(ins_path) + r"/bubbles_v9_NSAF_natural_log.R " + str(list_file) + r" " | |
61 + str(prey_file) + r" " + str(crapome) + r" " + str(color) + r" " + str(label) + r" " | |
62 + str(cutoff) + r" " + str(mq_sc) + r" " + str(inc_file) + r" " + str(exc_file)) | |
63 os.system(cmd) | |
64 time.sleep(3) | |
65 | |
66 open('./output.txt') | |
67 os.rename('output.txt', str(output_file_name)) | |
68 | |
69 open('./bubble_zoom_NSAF.png') | |
70 os.rename('bubble_zoom_NSAF.png', str(bub_zoom_NSAF)) | |
71 | |
72 open('./bubble_zoom_SAINT.png') | |
73 os.rename('bubble_zoom_SAINT.png', str(bub_zoom_SAINT)) | |
74 | |
75 open('./bubble_SAINT.png') | |
76 os.rename('bubble_SAINT.png', str(bub_SAINT)) | |
77 | |
78 open('./bubble_NSAF.png') | |
79 os.rename('bubble_NSAF.png', str(bub_NSAF)) | |
80 |