Mercurial > repos > yufei-luo > s_mart
view commons/pyRepetUnit/profilesDB/ProfilesDB2Map.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils class ProfilesDB2Map ( object ): """ write a file in map format from a ProfilDatabank object You have to set an input File and an Output File names """ def __init__(self): self.profilesDBUtils = ProfilesDatabankUtils() self._inputFile = "" self._outputFile = "" def setInputFile(self, input): self._inputFile = input def setOutputFile(self, output): self._outputFile = output def _readProfilesDB( self ): pfamDB = self.profilesDBUtils.read( self._inputFile ) return pfamDB def _writeMapFile( self, pfamDBList ): """ write a file in map format from a ProfilDatabank object """ if pfamDBList.getList() != []: f = open( self._outputFile , "w") for ProfilInstance in pfamDBList.getList(): f.write(ProfilInstance.name + "\t" + ProfilInstance.desc + "\t1\t" + str(ProfilInstance.length) + "\n") f.close() def run( self ): """ read a profiles DB file, parse it and, write the corresponding .map file """ pfamDBList = self._readProfilesDB() self._writeMapFile(pfamDBList)