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1
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1 import os
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2 import sys
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3 import time
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4
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5
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6 list_file = sys.argv[1]
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7 prey_file = sys.argv[2]
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8 crapome = sys.argv[3]
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9 color = sys.argv[4]
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10 label = sys.argv[5]
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11 cutoff = sys.argv[6]
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12 mq_sc = sys.argv[7]
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9
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13 inc_file = sys.argv[8]
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14 exc_file = sys.argv[9]
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15 output_file_name = sys.argv[10]
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16 bub_zoom_NSAF = sys.argv[11]
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17 bub_zoom_SAINT =sys.argv[12]
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18 bub_SAINT = sys.argv[13]
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19 bub_NSAF = sys.argv[14]
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20 ins_path =sys.argv[15]
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13
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21 r_path = sys.argv[16]
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22 r_path = str(r_path) + r"bin/"
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1
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23
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24 if crapome == "None":
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25 crapome = "FALSE"
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26
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27
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28 if label == "false":
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29 label = "FALSE"
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30 elif label == "true":
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31 label = "TRUE"
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32
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13
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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)
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1
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34 os.system(cmd)
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35 time.sleep(3)
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36
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37 open('./output.txt')
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38 os.rename('output.txt', str(output_file_name))
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39
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40 open('./bubble_zoom_NSAF.png')
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41 os.rename('bubble_zoom_NSAF.png', str(bub_zoom_NSAF))
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42
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43 open('./bubble_zoom_SAINT.png')
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44 os.rename('bubble_zoom_SAINT.png', str(bub_zoom_SAINT))
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45
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46 open('./bubble_SAINT.png')
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47 os.rename('bubble_SAINT.png', str(bub_SAINT))
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48
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49 open('./bubble_NSAF.png')
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50 os.rename('bubble_NSAF.png', str(bub_NSAF))
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51
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