Mercurial > repos > bornea > saint_bubblebeam

comparison Bubblebeam_For_SAINT_wrapper.py @ 21:7ce59d092bae draft

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author bornea
date Fri, 20 Nov 2015 12:04:24 -0500
parents e992232032ae
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20:964a825270ff 21:7ce59d092bae
16 bub_zoom_NSAF = sys.argv[11] 16 bub_zoom_NSAF = sys.argv[11]
17 bub_zoom_SAINT =sys.argv[12] 17 bub_zoom_SAINT =sys.argv[12]
18 bub_SAINT = sys.argv[13] 18 bub_SAINT = sys.argv[13]
19 bub_NSAF = sys.argv[14] 19 bub_NSAF = sys.argv[14]
20 ins_path =sys.argv[15] 20 ins_path =sys.argv[15]
21 #r_path = sys.argv[16]
22 #r_path = str(r_path) + r"bin/"
23 21
24 if crapome == "None": 22 if crapome == "None":
25 crapome = "FALSE" 23 crapome = "FALSE"
26 24
27 25
28 if label == "false": 26 if label == "false":
29 label = "FALSE" 27 label = "FALSE"
30 elif label == "true": 28 elif label == "true":
31 label = "TRUE" 29 label = "TRUE"
32 30
33 cmd = str(ins_path) +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) 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)
34 os.system(cmd) 32 os.system(cmd)
35 time.sleep(3) 33 time.sleep(3)
36 34
37 open('./output.txt') 35 open('./output.txt')
38 os.rename('output.txt', str(output_file_name)) 36 os.rename('output.txt', str(output_file_name))