view smart_toolShed/SMART/Java/Python/mySql/MySqlExonTable.py @ 0:e0f8dcca02ed

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

#
# Copyright INRA-URGI 2009-2010
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# modify and/ or redistribute the software under the terms of the CeCILL
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import random
from SMART.Java.Python.structure.Interval import Interval
from SMART.Java.Python.mySql.MySqlTable import MySqlTable


class MySqlExonTable(MySqlTable):
    """A table of exon 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_exons" % (name, chromosome)
        super(MySqlExonTable, self).__init__(connection, name, verbosity)


    def createExonTable(self):
        variables = Interval.getSqlVariables()
        variables.append("transcriptId")
        types = Interval.getSqlTypes()
        types["transcriptId"] = "int"
        sizes = Interval.getSqlSizes()
        sizes["transcriptId"] = 11
        self.create(variables, types, sizes)


    def rename(self, name):
        super(MySqlExonTable, self).rename("%s_exons" % name)
    
        
    def addExon(self, exon, transcriptId):
        values = exon.getSqlValues()
        values["transcriptId"] = transcriptId
        id = self.addLine(values)
        exon.id = id


    def retrieveExonsFromTranscriptId(self, transcriptId):
        if not self.created:
            return []
        query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))
        exons = []
        for exonLine in query.getIterator():
            exon = Interval()
            exon.setSqlValues(exonLine)
            exons.append(exon)
        return exons
            

    def retrieveExonsFromBulkTranscriptIds(self, transcriptIds):
        if not transcriptIds:
            return {}
        if not self.created:
            return {}
        exons = dict([(transcriptId, []) for transcriptId in transcriptIds])
        query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId IN (%s)" % (self.name, ", ".join(["%s" % (transcriptId) for transcriptId in transcriptIds])))
        for exonLine in query.getIterator():
            exon = Interval()
            exon.setSqlValues(exonLine)
            exons[exonLine[-1]].append(exon)
        return exons
            

    def removeFromTranscriptId(self, transcriptId):
        self.mySqlConnection.executeQuery("DELETE FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))