annotate smart_toolShed/SMART/Java/Python/mySql/MySqlTranscriptTable.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#
# Copyright INRA-URGI 2009-2010
# 
# This software is governed by the CeCILL license under French law and
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# modify and/ or redistribute the software under the terms of the CeCILL
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import random
import sys
from SMART.Java.Python.structure.TranscriptList import TranscriptList
from SMART.Java.Python.mySql.MySqlExonTable import MySqlExonTable
from SMART.Java.Python.mySql.MySqlTable import MySqlTable
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.misc.Progress import Progress

class MySqlTranscriptTable(MySqlTable):
    """A table of transcripts in a mySQL database"""

    def __init__(self, connection, name = None, chromosome = None, verbosity = 0):
        if chromosome == None:
            chromosome = ""
        else:
            chromosome = "_%s" % chromosome
        if name == None:
            name = "TmpTable_%d" % (random.randint(0, 100000))
        name = "%s%s" % (name, chromosome)
        super(MySqlTranscriptTable, self).__init__(connection, "%s_transcripts" % name, verbosity)


    def createTranscriptTable(self):
        self.create(Transcript.getSqlVariables(), Transcript.getSqlTypes(), Transcript.getSqlSizes())


    def rename(self, name):
        super(MySqlTranscriptTable, self).rename("%s_transcripts" % name)


    def remove(self):
        super(MySqlTranscriptTable, self).remove()
        
        
    def clear(self):
        super(MySqlTranscriptTable, self).clear()

        
    def copy(self, transcriptTable):
        self.remove()
        super(MySqlTranscriptTable, self).copy(transcriptTable)


    def add(self, transcriptTable):
        super(MySqlTranscriptTable, self).add(transcriptTable)


    def addTranscript(self, transcript):
        id = self.addLine(transcript.getSqlValues())
        transcript.id = id
            
            
    def addTranscriptList(self, transcriptList):
        progress = Progress(transcriptList.getNbTranscript(), "Storing list to %s" % (self.name), self.verbosity)
        for transcript in transcriptList.getIterator():
            self.addTranscript(transcript)
            progress.inc()
        progress.done()

            
    def removeTranscript(self, transcript):
        self.removeFromId(transcript.id)
            
            
    def retrieveTranscriptFromId(self, id):
        transcript = Transcript()
        transcript.setSqlValues(self.retrieveFromId(id))
        return transcript
    
    
    def retrieveBulkTranscriptFromId(self, ids):
        if not ids:
            return []
        transcripts = self.retrieveBulkFromId(ids)
        idsToTranscripts = {}
        for values in transcripts:
            transcript = Transcript()
            transcript.setSqlValues(values)
            idsToTranscripts[values[0]] = transcript
        return idsToTranscripts.values()
    
    
    def selectTranscripts(self, command, simple = False):
        MAXSIZE = 100000
        found   = True
        cpt     = 0
        while found:
            found = False
            if simple:
                thisCommand = command
            else:
                thisCommand = "%s LIMIT %d OFFSET %d" % (command, MAXSIZE, MAXSIZE * cpt)
            query = self.mySqlConnection.executeQuery(thisCommand)
            for line in query.getIterator():
                found      = True
                id         = int(line[0])
                transcript = Transcript()
                transcript.setSqlValues(line)
                yield (id, transcript)
            cpt += 1
            if simple:
                return

    
    def getIterator(self):
        for id, transcript in self.selectTranscripts("SELECT * FROM '%s'" % (self.name)):
            yield transcript


    def retrieveTranscriptList(self):
        transcriptList = TranscriptList()
        for transcriptLine in self.getLines():
            transcript = Transcript()
            transcript.setSqlValues(transcriptLine)
            transcriptList.addTranscript(transcript)
        return transcriptList
            

    def setDefaultTagValue(self, name, value):
        super(MySqlTranscriptTable, self).setDefaultTagValue(Transcript.getSqlVariables().index("tags")+1, name, value)