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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 : 28 Mar 2011 11:00AM
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23
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24 class Target:
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25 """
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26 Class for target regions
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27 """
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28
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29 population = 0
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30
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31 def __init__(self):
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32 self.id = 0
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33 self.gene = "unknown"
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34 self.chr = "chr1"
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35 self.start = 0
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36 self.end = 0
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37 self.numberExon = 0
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38 self.oriStart = 0
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39 self.oriEnd = 0
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40
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41 def convertTarget(target):
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42 targets = open(target)
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43
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44 targetList = []
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45
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46 count = 0
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47 for region in targets:
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48 region = region.split()
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49 chr = "chr" + region[0].strip("chr")
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50 start = region[1]
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51 end = region[2]
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52 try:
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53 gene = region[3]
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54 except:
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55 gene = "unknown"
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56 count += 1
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57
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58 aTarget = Target()
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59 aTarget.id = count
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60 aTarget.gene = gene
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61 aTarget.chr = chr
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62 aTarget.start = start
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63 aTarget.end = end
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64 aTarget.numberExon = 1
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65 aTarget.oriStart = start
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66 aTarget.oriEnd = end
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67
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68 targetList.append(aTarget)
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69
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70
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71 return targetList
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