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1 # ----------------------------------------------------------------------#
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2 # Copyright (c) 2011, Richard Lupat & Jason Li.
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3 #
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4 # > Source License <
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5 # This file is part of CONTRA.
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6 #
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7 # CONTRA is free software: you can redistribute it and/or modify
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8 # it under the terms of the GNU General Public License as published by
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9 # the Free Software Foundation, either version 3 of the License, or
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10 # (at your option) any later version.
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11 #
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12 # CONTRA is distributed in the hope that it will be useful,
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13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 # GNU General Public License for more details.
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16 #
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17 # You should have received a copy of the GNU General Public License
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18 # along with CONTRA. If not, see <http://www.gnu.org/licenses/>.
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19 #
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20 #
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21 #-----------------------------------------------------------------------#
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22 # Last Updated : 03 Sep 2011 15:00PM
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23
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24
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25 import os
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26
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27 def splitByChromosome(destFolder):
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28
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29 try:
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30 os.mkdir(destFolder + "chr/")
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31 except:
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32 print "folder exist"
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33
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34 inputfile = destFolder + "sample.BEDGRAPH"
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35 outputfile = destFolder + "chr/chr1.txt"
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36 file = open(inputfile,"r")
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37 output = open(outputfile,"w")
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38 check = "1"
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39
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40 for row in file:
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41 if row[0] == '#':
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42 continue
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43
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44 cols = row.split()
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45 chr = cols[0].strip("chr")
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46 if (chr != check):
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47 output.close()
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48 check = chr
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49 output = open(destFolder+ "chr/chr"+check+".txt","w")
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50 output.write(row)
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51
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52 output.close()
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53
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54 #JLMod
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55 def splitByChromosome3(infile):
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56 destFolder = os.path.dirname(infile)+"/"
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57
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58 try:
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59 os.mkdir(destFolder + "chr/")
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60 except:
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61 print "folder exist"
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62
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63 #inputfile = destFolder + "sample.BEDGRAPH"
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64 inputfile=infile
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65 outputfile = destFolder + "chr/chr1.txt"
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66 file = open(inputfile,"r")
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67 output = open(outputfile,"w")
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68 check = "1"
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69
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70 for row in file:
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71 cols = row.split()
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72 chr = cols[0].strip("chr")
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73 if (chr != check):
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74 output.close()
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75 check = chr
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76 output = open(destFolder+ "chr/chr"+check+".txt","w")
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77 output.write(row)
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78
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79 output.close()
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80
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81 def splitByChromosome2(folder):
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82
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83 try:
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84 os.mkdir(folder + "target/")
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85 except:
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86 print "folder exist"
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87
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88 inputfile = folder + "geneRefCoverage.txt"
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89 outputfile = folder + "target/chr1.txt"
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90 file = open(inputfile,"r")
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91 output = open(outputfile,"w")
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92 check = "1"
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93
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94 for row in file:
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95 cols = row.split()
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96 chr = cols[0].strip("chr")
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97 if (chr != check):
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98 output.close()
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99 check = chr
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100 output = open(folder+ "target/chr"+check+".txt","w")
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101 output.write(row)
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102
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103 output.close()
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104
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105
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