comparison commons/core/writer/MySqlTranscriptWriter.py @ 18:94ab73e8a190

Uploaded

17:b0e8584489e6

        Add a list of transcripts to the transcripts to be written
        @param transcriptListParser: transcripts to be written
        @type  transcriptListParser: class L{TranscriptListParser<TranscriptListParser>}
        """
        self.transcriptListParser = transcriptListParser
        self.mySqlConnection.executeManyQueriesIterator(self)
            
            
    def getIterator(self):
        """
        Iterator to the SQL commands to insert the list

            chromosome = transcript.getChromosome()
            if chromosome not in self.tables:
                self.createTable(chromosome)
            self.nbTranscriptsByChromosome[chromosome] = self.nbTranscriptsByChromosome.get(chromosome, 0) + 1
            values = transcript.getSqlValues()
            yield "INSERT INTO '%s' (%s) VALUES (%s)" % (self.tables[chromosome].name, ", ".join(self.tables[chromosome].variables), ", ".join([MySqlTable.formatSql(values[variable], self.tables[chromosome].types[variable], self.tables[chromosome].sizes[variable]) for variable in self.tables[chromosome].variables]))
            progress.inc()
        progress.done()
            
            
    def write(self):

        Copy the content of the files into the database
        (May add transcripts to already created databases)
        """
        for chromosome in self.transcriptValues:
            if chromosome in self.transcriptValues:
                self.tables[chromosome].insertMany(self.transcriptValues[chromosome])
        self.transcriptValues = {}
        self.toBeWritten      = False
            
            
    def getTables(self):

18:94ab73e8a190

        Add a list of transcripts to the transcripts to be written
        @param transcriptListParser: transcripts to be written
        @type  transcriptListParser: class L{TranscriptListParser<TranscriptListParser>}
        """
        self.transcriptListParser = transcriptListParser
        self.mySqlConnection.executeManyFormattedQueriesIterator(self)
            
            
    def getIterator(self):
        """
        Iterator to the SQL commands to insert the list

            chromosome = transcript.getChromosome()
            if chromosome not in self.tables:
                self.createTable(chromosome)
            self.nbTranscriptsByChromosome[chromosome] = self.nbTranscriptsByChromosome.get(chromosome, 0) + 1
            values = transcript.getSqlValues()
            #yield "INSERT INTO '%s' (%s) VALUES (%s)" % (self.tables[chromosome].name, ", ".join(self.tables[chromosome].variables), ", ".join([MySqlTable.formatSql(values[variable], self.tables[chromosome].types[variable], self.tables[chromosome].sizes[variable]) for variable in self.tables[chromosome].variables]))
            yield ("INSERT INTO '%s' (%s) VALUES (%s)" % (self.tables[chromosome].name, ", ".join(self.tables[chromosome].variables), ", ".join(["?"] * len(self.tables[chromosome].variables))), [values[variable] for variable in self.tables[chromosome].variables])
            progress.inc()
        progress.done()
            
            
    def write(self):

        Copy the content of the files into the database
        (May add transcripts to already created databases)
        """
        for chromosome in self.transcriptValues:
            if chromosome in self.transcriptValues:
                self.tables[chromosome].insertManyFormatted(self.transcriptValues[chromosome])
        self.transcriptValues = {}
        self.toBeWritten      = False
            
            
    def getTables(self):