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1 import os
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2 import commons.core.coord.Align
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3 import commons.pyRepetUnit.align.AlignList
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4 from commons.core.utils.FileUtils import FileUtils
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5
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6 class AlignListUtils:
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7
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8 ##read a file in align format and return a AlignList
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9 #
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10 # @param inFileName string name of file
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11 # @return listAlignInstance list list of align instance
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12 #
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13 def read( inFileName ):
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14 alignInstance = commons.core.coord.Align.Align()
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15 listAlignInstance = commons.pyRepetUnit.align.AlignList.AlignList()
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16 f = open( inFileName , "r")
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17 while alignInstance.read( f ):
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18 listAlignInstance.append(alignInstance)
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19 alignInstance = commons.core.coord.Align.Align()
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20 f.close
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21 return (listAlignInstance)
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22
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23 read = staticmethod( read )
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24
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25 ## write a file in align format from an AlignList
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26 #
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27 # @param alignListInstance list list of align instance object
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28 # @param inFileName string name of file
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29 def write( alignListInstance, inFileName ):
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30 f = open( inFileName , "w")
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31 for alignInstance in alignListInstance.getList():
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32 alignInstance.write( f )
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33 f.close
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34
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35 write = staticmethod( write )
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36
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37 ## Filter an AlignList by removing all is <= minScore
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38 #
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39 # @param listAlignInstance list list of align instance object
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40 # @param minScore integer minimum score to keep in result
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41 #
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42 def filterOnAMinimalScore( listAlignInstance, minScore ):
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43 listAlignInstanceOld = commons.pyRepetUnit.align.AlignList.AlignList()
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44 for alignInstance in listAlignInstance.getList():
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45 listAlignInstanceOld.append(alignInstance)
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46 for alignInstance in listAlignInstanceOld.getList():
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47 if alignInstance.score <= minScore:
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48 listAlignInstance.remove(alignInstance)
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49
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50 filterOnAMinimalScore = staticmethod( filterOnAMinimalScore )
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51
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52 if __name__ == "__main__":
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53 main()
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