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1 from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils
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2
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3
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4 class ProfilesDB2Map ( object ):
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5 """
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6 write a file in map format from a ProfilDatabank object
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7 You have to set an input File and an Output File names
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8 """
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9
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10 def __init__(self):
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11 self.profilesDBUtils = ProfilesDatabankUtils()
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12 self._inputFile = ""
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13 self._outputFile = ""
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14
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15 def setInputFile(self, input):
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16 self._inputFile = input
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17
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18 def setOutputFile(self, output):
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19 self._outputFile = output
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20
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21 def _readProfilesDB( self ):
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22 pfamDB = self.profilesDBUtils.read( self._inputFile )
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23 return pfamDB
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24
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25 def _writeMapFile( self, pfamDBList ):
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26 """
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27 write a file in map format from a ProfilDatabank object
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28 """
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29 if pfamDBList.getList() != []:
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30 f = open( self._outputFile , "w")
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31 for ProfilInstance in pfamDBList.getList():
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32 f.write(ProfilInstance.name + "\t" + ProfilInstance.desc + "\t1\t" + str(ProfilInstance.length) + "\n")
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33 f.close()
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34
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35 def run( self ):
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36 """
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37 read a profiles DB file, parse it and, write the corresponding .map file
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38 """
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39 pfamDBList = self._readProfilesDB()
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40 self._writeMapFile(pfamDBList)
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