Mercurial > repos > bornea > saint_bubblebeam

comparison Bubblebeam_For_SAINT_wrapper.py @ 17:b11a6884496e draft

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Uploaded
author bornea
date Fri, 20 Nov 2015 11:10:22 -0500
parents e63b61738581
children e992232032ae
comparison
equal deleted inserted replaced
16:54102aee991e 17:b11a6884496e
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] 21 #r_path = sys.argv[16]
22 r_path = str(r_path) + r"bin/" 22 #r_path = str(r_path) + r"bin/"
23 23
24 if crapome == "None": 24 if crapome == "None":
25 crapome = "FALSE" 25 crapome = "FALSE"
26 26
27 27
28 if label == "false": 28 if label == "false":
29 label = "FALSE" 29 label = "FALSE"
30 elif label == "true": 30 elif label == "true":
31 label = "TRUE" 31 label = "TRUE"
32 32
33 cmd = str(r_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) 33 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) 34 os.system(cmd)
35 time.sleep(3) 35 time.sleep(3)
36 36
37 open('./output.txt') 37 open('./output.txt')
38 os.rename('output.txt', str(output_file_name)) 38 os.rename('output.txt', str(output_file_name))