Mercurial > repos > bornea > saint_bubblebeam

comparison Bubblebeam_For_SAINT_wrapper.py @ 9:9617d82034c6 draft

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Uploaded
author bornea
date Thu, 19 Nov 2015 10:48:55 -0500
parents 248cd769eecb
children e63b61738581
comparison
equal deleted inserted replaced
8:318185488e49 9:9617d82034c6
8 crapome = sys.argv[3] 8 crapome = sys.argv[3]
9 color = sys.argv[4] 9 color = sys.argv[4]
10 label = sys.argv[5] 10 label = sys.argv[5]
11 cutoff = sys.argv[6] 11 cutoff = sys.argv[6]
12 mq_sc = sys.argv[7] 12 mq_sc = sys.argv[7]
13 output_file_name = sys.argv[8] 13 inc_file = sys.argv[8]
14 bub_zoom_NSAF = sys.argv[9] 14 exc_file = sys.argv[9]
15 bub_zoom_SAINT =sys.argv[10] 15 output_file_name = sys.argv[10]
16 bub_SAINT = sys.argv[11] 16 bub_zoom_NSAF = sys.argv[11]
17 bub_NSAF = sys.argv[12] 17 bub_zoom_SAINT =sys.argv[12]
18 ins_path =sys.argv[13] 18 bub_SAINT = sys.argv[13]
19 bub_NSAF = sys.argv[14]
20 ins_path =sys.argv[15]
19 21
20 if crapome == "None": 22 if crapome == "None":
21 crapome = "FALSE" 23 crapome = "FALSE"
22 24
23 25
24 if label == "false": 26 if label == "false":
25 label = "FALSE" 27 label = "FALSE"
26 elif label == "true": 28 elif label == "true":
27 label = "TRUE" 29 label = "TRUE"
28 30
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) 31 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) + r" " + str(inc_file) + r" " + str(exc_file)
30 os.system(cmd) 32 os.system(cmd)
31 time.sleep(3) 33 time.sleep(3)
32 34
33 open('./output.txt') 35 open('./output.txt')
34 os.rename('output.txt', str(output_file_name)) 36 os.rename('output.txt', str(output_file_name))