def writeExpression(self, rnaQuantificationId, quantfilename):
        """
        Reads the quantification results file and adds entries to the
        specified database.
        """
        isNormalized = self._isNormalized
        units = self._units
        with open(quantfilename, "r") as quantFile:
            quantificationReader = csv.reader(quantFile, delimiter=b"\t")
            header = next(quantificationReader)
            expressionLevelColNum = self.setColNum(
                                        header, self._expressionLevelCol)
            nameColNum = self.setColNum(header, self._nameCol)
            countColNum = self.setColNum(header, self._countCol, -1)
            confColLowNum = self.setColNum(header, self._confColLow, -1)
            confColHiNum = self.setColNum(header, self._confColHi, -1)
            expressionId = 0
            for expression in quantificationReader:
                expressionLevel = expression[expressionLevelColNum]
                name = expression[nameColNum]
                rawCount = 0.0
                if countColNum != -1:
                    rawCount = expression[countColNum]
                confidenceLow = 0.0
                confidenceHi = 0.0
                score = 0.0
                if confColLowNum != -1 and confColHiNum != -1:
                    confidenceLow = float(expression[confColLowNum])
                    confidenceHi = float(expression[confColHiNum])
                    score = (confidenceLow + confidenceHi)/2

                datafields = (expressionId, rnaQuantificationId, name,
                              expressionLevel, isNormalized, rawCount, score,
                              units, confidenceLow, confidenceHi)
                self._db.addExpression(datafields)
                expressionId += 1
            self._db.batchAddExpression()
def writeExpression ( self , rnaQuantificationId , quantfilename ) : isNormalized = self . _isNormalized units = self . _units with open ( quantfilename , "r" ) as quantFile : quantificationReader = csv . reader ( quantFile , delimiter = b"\t" ) header = next ( quantificationReader ) expressionLevelColNum = self . setColNum ( header , self . _expressionLevelCol ) nameColNum = self . setColNum ( header , self . _nameCol ) countColNum = self . setColNum ( header , self . _countCol , - 1 ) confColLowNum = self . setColNum ( header , self . _confColLow , - 1 ) confColHiNum = self . setColNum ( header , self . _confColHi , - 1 ) expressionId = 0 for expression in quantificationReader : expressionLevel = expression [ expressionLevelColNum ] name = expression [ nameColNum ] rawCount = 0.0 if countColNum != - 1 : rawCount = expression [ countColNum ] confidenceLow = 0.0 confidenceHi = 0.0 score = 0.0 if confColLowNum != - 1 and confColHiNum != - 1 : confidenceLow = float ( expression [ confColLowNum ] ) confidenceHi = float ( expression [ confColHiNum ] ) score = ( confidenceLow + confidenceHi ) / 2 datafields = ( expressionId , rnaQuantificationId , name , expressionLevel , isNormalized , rawCount , score , units , confidenceLow , confidenceHi ) self . _db . addExpression ( datafields ) expressionId += 1 self . _db . batchAddExpression ( )
Reads the quantification results file and adds entries to the
        specified database.