Mercurial > repos > bornea > saint_bubblebeam

comparison Bubblebeam_For_SAINT_wrapper.py @ 1:248cd769eecb draft

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author bornea
date Tue, 17 Nov 2015 10:57:19 -0500
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children 9617d82034c6
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0:81bea7a47c68 1:248cd769eecb
1 import os
2 import sys
3 import time
4
5
6 list_file = sys.argv[1]
7 prey_file = sys.argv[2]
8 crapome = sys.argv[3]
9 color = sys.argv[4]
10 label = sys.argv[5]
11 cutoff = sys.argv[6]
12 mq_sc = sys.argv[7]
13 output_file_name = sys.argv[8]
14 bub_zoom_NSAF = sys.argv[9]
15 bub_zoom_SAINT =sys.argv[10]
16 bub_SAINT = sys.argv[11]
17 bub_NSAF = sys.argv[12]
18 ins_path =sys.argv[13]
19
20 if crapome == "None":
21 crapome = "FALSE"
22
23
24 if label == "false":
25 label = "FALSE"
26 elif label == "true":
27 label = "TRUE"
28
29 cmd = r"Rscript "+ str(ins_path) + r"/bubbles_v9_NSAF_natural_log.R " + str(list_file) + r" " + str(prey_file) + r" " + str(crapome) + r" " + str(color) + r" " + str(label) + r" " + str(cutoff) + r" " + str(mq_sc)
30 os.system(cmd)
31 time.sleep(3)
32
33 open('./output.txt')
34 os.rename('output.txt', str(output_file_name))
35
36 open('./bubble_zoom_NSAF.png')
37 os.rename('bubble_zoom_NSAF.png', str(bub_zoom_NSAF))
38
39 open('./bubble_zoom_SAINT.png')
40 os.rename('bubble_zoom_SAINT.png', str(bub_zoom_SAINT))
41
42 open('./bubble_SAINT.png')
43 os.rename('bubble_SAINT.png', str(bub_SAINT))
44
45 open('./bubble_NSAF.png')
46 os.rename('bubble_NSAF.png', str(bub_NSAF))
47