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1 #######################################################################################
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2 # Python-code: Dotplot Runner
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3 # Author: Adam L Borne
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4 # Contributers: Paul A Stewart, Brent Kuenzi
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5 #######################################################################################
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6 # This script runs the dotplot program found at http://prohitstools.mshri.on.ca/.
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7 #######################################################################################
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8 # Copyright (C) Adam Borne.
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9 # Permission is granted to copy, distribute and/or modify this document
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10 # under the terms of the GNU Free Documentation License, Version 1.3
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11 # or any later version published by the Free Software Foundation;
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12 # with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts.
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13 # A copy of the license is included in the section entitled "GNU
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14 # Free Documentation License".
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15 #######################################################################################
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16 ## REQUIRED INPUT ##
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17
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18 # 1) list_file: SaintExpress output file.
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19 # 2) FDR1: Primary false discovery rate. (default = 0.01)
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20 # 3) FDR2: Secondary false discovery rate. (default = 0.025)
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21 # 4) spec_max: Maximum spectral count. (default = 50)
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22 #######################################################################################
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23
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24 import os
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25 import sys
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26
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27
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28 FDR1 = sys.argv[2]
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29 FDR2 = sys.argv[3]
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30 spec_max = sys.argv[4]
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19
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31 file_name = sys.argv[1]
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20
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32 cmd0 = "cp " + str(file_name) + " ./"
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33 os.system(cmd0)
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19
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34 input_file = file_name.split("/")[-1]
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35 os.rename(input_file, "saint_input.txt")
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14
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36 ins_path = sys.argv[9]
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37
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38 dirs_list = []
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39 for (dirpath, dirnames, filename) in os.walk(str(ins_path)):
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40 dirs_list.extend(dirnames)
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41 break
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42 if r"Dotplot_Release" in dirs_list:
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43 pass
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44 else:
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45 cmd = r"tar -xvf /Dotplot_Release.tar.gz " + str(ins_path) + "/Dotplot_Release.tar.gz"
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46 os.system(cmd)
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47
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48
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49 cmd = (str(ins_path) + r"Dotplot_Release/dotplot.bash -f saint_input.txt" + r" -c b -s " + str(FDR1) +
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50 r" -t " + str(FDR2) + " -m " + str(spec_max))
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51 os.system(cmd)
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52
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53 cmd1 = r"cp -a ./Output_saint_input/. ."
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54 os.system(cmd1)
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55
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56 os.rename("saint_input.txt", str(sys.argv[1]))
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57 os.rename('dotplot.pdf', str(sys.argv[5]))
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58 os.rename('bait2bait.pdf', str(sys.argv[6]))
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59 os.rename('estimated.pdf', str(sys.argv[7]))
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60 os.rename('stats.pdf', str(sys.argv[8])) |
