Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/profilesDB/ProfilesDB2Map.py @ 31:0ab839023fe4
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| author | m-zytnicki |
|---|---|
| date | Tue, 30 Apr 2013 14:33:21 -0400 |
| parents | 94ab73e8a190 |
| children |
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| 30:5677346472b5 | 31:0ab839023fe4 |
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| 1 from commons.pyRepetUnit.profilesDB.ProfilesDatabankUtils import ProfilesDatabankUtils | |
| 2 | |
| 3 | |
| 4 class ProfilesDB2Map ( object ): | |
| 5 """ | |
| 6 write a file in map format from a ProfilDatabank object | |
| 7 You have to set an input File and an Output File names | |
| 8 """ | |
| 9 | |
| 10 def __init__(self): | |
| 11 self.profilesDBUtils = ProfilesDatabankUtils() | |
| 12 self._inputFile = "" | |
| 13 self._outputFile = "" | |
| 14 | |
| 15 def setInputFile(self, input): | |
| 16 self._inputFile = input | |
| 17 | |
| 18 def setOutputFile(self, output): | |
| 19 self._outputFile = output | |
| 20 | |
| 21 def _readProfilesDB( self ): | |
| 22 pfamDB = self.profilesDBUtils.read( self._inputFile ) | |
| 23 return pfamDB | |
| 24 | |
| 25 def _writeMapFile( self, pfamDBList ): | |
| 26 """ | |
| 27 write a file in map format from a ProfilDatabank object | |
| 28 """ | |
| 29 if pfamDBList.getList() != []: | |
| 30 f = open( self._outputFile , "w") | |
| 31 for ProfilInstance in pfamDBList.getList(): | |
| 32 f.write(ProfilInstance.name + "\t" + ProfilInstance.desc + "\t1\t" + str(ProfilInstance.length) + "\n") | |
| 33 f.close() | |
| 34 | |
| 35 def run( self ): | |
| 36 """ | |
| 37 read a profiles DB file, parse it and, write the corresponding .map file | |
| 38 """ | |
| 39 pfamDBList = self._readProfilesDB() | |
| 40 self._writeMapFile(pfamDBList) |