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)
def __init__(self):
self.profilesDBUtils = ProfilesDatabankUtils()
self._inputFile = ""
self._outputFile = ""