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36
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1 #
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2 # Copyright INRA-URGI 2009-2010
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3 #
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4 # This software is governed by the CeCILL license under French law and
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5 # abiding by the rules of distribution of free software. You can use,
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6 # modify and/ or redistribute the software under the terms of the CeCILL
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
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8 # "http://www.cecill.info".
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9 #
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10 # As a counterpart to the access to the source code and rights to copy,
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11 # modify and redistribute granted by the license, users are provided only
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12 # with a limited warranty and the software's author, the holder of the
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13 # economic rights, and the successive licensors have only limited
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14 # liability.
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15 #
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16 # In this respect, the user's attention is drawn to the risks associated
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17 # with loading, using, modifying and/or developing or reproducing the
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18 # software by the user in light of its specific status of free software,
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19 # that may mean that it is complicated to manipulate, and that also
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20 # therefore means that it is reserved for developers and experienced
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21 # professionals having in-depth computer knowledge. Users are therefore
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22 # encouraged to load and test the software's suitability as regards their
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23 # requirements in conditions enabling the security of their systems and/or
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24 # data to be ensured and, more generally, to use and operate it in the
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25 # same conditions as regards security.
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26 #
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27 # The fact that you are presently reading this means that you have had
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28 # knowledge of the CeCILL license and that you accept its terms.
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29 #
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30 import random
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31 import sys
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32 from SMART.Java.Python.structure.TranscriptList import TranscriptList
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33 from SMART.Java.Python.mySql.MySqlExonTable import MySqlExonTable
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34 from SMART.Java.Python.mySql.MySqlTable import MySqlTable
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36 from SMART.Java.Python.misc.Progress import Progress
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37
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38 class MySqlTranscriptTable(MySqlTable):
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39 """A table of transcripts in a mySQL database"""
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40
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41 def __init__(self, connection, name = None, chromosome = None, verbosity = 0):
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42 if chromosome == None:
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43 chromosome = ""
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44 else:
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45 chromosome = "_%s" % chromosome
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46 if name == None:
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47 name = "TmpTable_%d" % (random.randint(0, 100000))
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48 name = "%s%s" % (name, chromosome)
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49 super(MySqlTranscriptTable, self).__init__(connection, "%s_transcripts" % name, verbosity)
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50
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51
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52 def createTranscriptTable(self):
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53 self.create(Transcript.getSqlVariables(), Transcript.getSqlTypes(), Transcript.getSqlSizes())
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54
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55
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56 def rename(self, name):
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57 super(MySqlTranscriptTable, self).rename("%s_transcripts" % name)
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58
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59
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60 def remove(self):
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61 super(MySqlTranscriptTable, self).remove()
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62
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63
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64 def clear(self):
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65 super(MySqlTranscriptTable, self).clear()
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66
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67
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68 def copy(self, transcriptTable):
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69 self.remove()
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70 super(MySqlTranscriptTable, self).copy(transcriptTable)
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71
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72
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73 def add(self, transcriptTable):
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74 super(MySqlTranscriptTable, self).add(transcriptTable)
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75
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76
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77 def addTranscript(self, transcript):
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78 id = self.addLine(transcript.getSqlValues())
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79 transcript.id = id
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80
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81
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82 def addTranscriptList(self, transcriptList):
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83 progress = Progress(transcriptList.getNbTranscript(), "Storing list to %s" % (self.name), self.verbosity)
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84 for transcript in transcriptList.getIterator():
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85 self.addTranscript(transcript)
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86 progress.inc()
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87 progress.done()
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88
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89
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90 def removeTranscript(self, transcript):
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91 self.removeFromId(transcript.id)
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92
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93
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94 def retrieveTranscriptFromId(self, id):
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95 transcript = Transcript()
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96 transcript.setSqlValues(self.retrieveFromId(id))
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97 return transcript
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98
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99
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100 def retrieveBulkTranscriptFromId(self, ids):
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101 if not ids:
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102 return []
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103 transcripts = self.retrieveBulkFromId(ids)
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104 idsToTranscripts = {}
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105 for values in transcripts:
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106 transcript = Transcript()
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107 transcript.setSqlValues(values)
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108 idsToTranscripts[values[0]] = transcript
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109 return idsToTranscripts.values()
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110
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111
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112 def selectTranscripts(self, command, simple = False):
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113 MAXSIZE = 100000
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114 found = True
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115 cpt = 0
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116 while found:
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117 found = False
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118 if simple:
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119 thisCommand = command
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120 else:
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121 thisCommand = "%s LIMIT %d OFFSET %d" % (command, MAXSIZE, MAXSIZE * cpt)
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122 query = self.mySqlConnection.executeQuery(thisCommand)
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123 for line in query.getIterator():
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124 found = True
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125 id = int(line[0])
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126 transcript = Transcript()
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127 transcript.setSqlValues(line)
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128 yield (id, transcript)
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129 cpt += 1
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130 if simple:
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131 return
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132
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133
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134 def getIterator(self):
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135 for id, transcript in self.selectTranscripts("SELECT * FROM '%s'" % (self.name)):
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136 yield transcript
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137
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138
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139 def retrieveTranscriptList(self):
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140 transcriptList = TranscriptList()
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141 for transcriptLine in self.getLines():
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142 transcript = Transcript()
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143 transcript.setSqlValues(transcriptLine)
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144 transcriptList.addTranscript(transcript)
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145 return transcriptList
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146
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147
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148 def setDefaultTagValue(self, name, value):
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46
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149 super(MySqlTranscriptTable, self).setDefaultTagValue(Transcript.getSqlVariables().index("tags")+1, name, value)
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