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+ − 1 #
+ − 2 # Copyright INRA-URGI 2009-2010
+ − 3 #
+ − 4 # This software is governed by the CeCILL license under French law and
+ − 5 # abiding by the rules of distribution of free software. You can use,
+ − 6 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 7 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 8 # "http://www.cecill.info".
+ − 9 #
+ − 10 # As a counterpart to the access to the source code and rights to copy,
+ − 11 # modify and redistribute granted by the license, users are provided only
+ − 12 # with a limited warranty and the software's author, the holder of the
+ − 13 # economic rights, and the successive licensors have only limited
+ − 14 # liability.
+ − 15 #
+ − 16 # In this respect, the user's attention is drawn to the risks associated
+ − 17 # with loading, using, modifying and/or developing or reproducing the
+ − 18 # software by the user in light of its specific status of free software,
+ − 19 # that may mean that it is complicated to manipulate, and that also
+ − 20 # therefore means that it is reserved for developers and experienced
+ − 21 # professionals having in-depth computer knowledge. Users are therefore
+ − 22 # encouraged to load and test the software's suitability as regards their
+ − 23 # requirements in conditions enabling the security of their systems and/or
+ − 24 # data to be ensured and, more generally, to use and operate it in the
+ − 25 # same conditions as regards security.
+ − 26 #
+ − 27 # The fact that you are presently reading this means that you have had
+ − 28 # knowledge of the CeCILL license and that you accept its terms.
+ − 29 #
+ − 30 import random
+ − 31 from SMART.Java.Python.structure.Interval import Interval
+ − 32 from SMART.Java.Python.mySql.MySqlTable import MySqlTable
+ − 33
+ − 34
+ − 35 class MySqlExonTable(MySqlTable):
+ − 36 """A table of exon in a mySQL database"""
+ − 37
+ − 38 def __init__(self, connection, name = None, chromosome = None, verbosity = 0):
+ − 39 if chromosome == None:
+ − 40 chromosome = ""
+ − 41 else:
+ − 42 chromosome = "_%s" % chromosome
+ − 43 if name == None:
+ − 44 name = "TmpTable_%d" % (random.randint(0, 100000))
+ − 45 name = "%s%s_exons" % (name, chromosome)
+ − 46 super(MySqlExonTable, self).__init__(connection, name, verbosity)
+ − 47
+ − 48
+ − 49 def createExonTable(self):
+ − 50 variables = Interval.getSqlVariables()
+ − 51 variables.append("transcriptId")
+ − 52 types = Interval.getSqlTypes()
+ − 53 types["transcriptId"] = "int"
+ − 54 sizes = Interval.getSqlSizes()
+ − 55 sizes["transcriptId"] = 11
+ − 56 self.create(variables, types, sizes)
+ − 57
+ − 58
+ − 59 def rename(self, name):
+ − 60 super(MySqlExonTable, self).rename("%s_exons" % name)
+ − 61
+ − 62
+ − 63 def addExon(self, exon, transcriptId):
+ − 64 values = exon.getSqlValues()
+ − 65 values["transcriptId"] = transcriptId
+ − 66 id = self.addLine(values)
+ − 67 exon.id = id
+ − 68
+ − 69
+ − 70 def retrieveExonsFromTranscriptId(self, transcriptId):
+ − 71 if not self.created:
+ − 72 return []
+ − 73 query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))
+ − 74 exons = []
+ − 75 for exonLine in query.getIterator():
+ − 76 exon = Interval()
+ − 77 exon.setSqlValues(exonLine)
+ − 78 exons.append(exon)
+ − 79 return exons
+ − 80
+ − 81
+ − 82 def retrieveExonsFromBulkTranscriptIds(self, transcriptIds):
+ − 83 if not transcriptIds:
+ − 84 return {}
+ − 85 if not self.created:
+ − 86 return {}
+ − 87 exons = dict([(transcriptId, []) for transcriptId in transcriptIds])
+ − 88 query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId IN (%s)" % (self.name, ", ".join(["%s" % (transcriptId) for transcriptId in transcriptIds])))
+ − 89 for exonLine in query.getIterator():
+ − 90 exon = Interval()
+ − 91 exon.setSqlValues(exonLine)
+ − 92 exons[exonLine[-1]].append(exon)
+ − 93 return exons
+ − 94
+ − 95
+ − 96 def removeFromTranscriptId(self, transcriptId):
+ − 97 self.mySqlConnection.executeQuery("DELETE FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))