Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/writer/MySqlTranscriptWriter.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 os |
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31 import random |
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32 from SMART.Java.Python.mySql.MySqlTable import MySqlTable |
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33 from SMART.Java.Python.mySql.MySqlTranscriptTable import MySqlTranscriptTable |
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34 from SMART.Java.Python.misc.Progress import Progress |
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35 |
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36 class MySqlTranscriptWriter(object): |
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37 """ |
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38 A class that writes a transcript list into a mySQL table |
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39 @ivar name: name of the tables |
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40 @type name: string |
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41 @ivar tables: the tables |
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42 @type tables: dict of L{MySqlTranscriptTable<MySqlTranscriptTable>} |
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43 @ivar mySqlConnection: connection to a MySQL database |
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44 @type mySqlConnection: class L{MySqlConnection<MySqlConnection>} |
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45 @ivar tmpTranscriptFileHandles: files where transcripts are temporary stored, before copy into database |
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46 @type tmpTranscriptFileHandles: dict of file handles |
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47 @ivar nbTranscriptsByChromosome: number of transcripts written |
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48 @type nbTranscriptsByChromosome: dict of int (one for each chromosome) |
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49 @ivar randomNumber: a random number, used for having a unique name for the tables |
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50 @type randomNumber: int |
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51 @ivar toBeWritten: there exists transcripts to be copied into database |
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52 @type toBeWritten: bool |
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53 @ivar verbosity: verbosity |
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54 @type verbosity: int |
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55 """ |
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56 |
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57 |
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58 def __init__(self, connection, name = None, verbosity = 0): |
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59 """ |
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60 Constructor |
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61 @param name: name of the file |
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62 @type name: string |
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63 @param verbosity: verbosity |
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64 @type verbosity: int |
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65 """ |
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66 self.name = name |
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67 self.verbosity = verbosity |
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68 self.tables = {} |
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69 self.indices = {} |
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70 self.tmpTranscriptFileHandles = {} |
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71 self.nbTranscriptsByChromosome = {} |
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72 self.toBeWritten = False |
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73 self.randomNumber = random.randint(0, 100000) |
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74 self.mySqlConnection = connection |
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75 self.nbTmpFiles = 100 |
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76 self.transcriptValues = {} |
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77 self.nbTranscriptValues = 1000 |
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78 if self.name != None: |
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79 pos = self.name.rfind(os.sep) |
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80 if pos != -1: |
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81 self.name = self.name[pos+1:] |
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82 |
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83 |
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84 def __del__(self): |
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85 """ |
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86 Destructor |
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87 Possibly write into into database the last transcripts |
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88 """ |
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89 if self.toBeWritten: |
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90 self.write() |
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91 |
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92 |
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93 def addIndex(self, name, values): |
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94 """ |
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95 Add an index to the tables |
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96 @param name: name of the index |
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97 @type name: string |
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98 @param values: values to index |
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99 @type values: list of strings |
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100 """ |
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101 self.indices[name] = values |
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102 |
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103 |
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104 def createTable(self, chromosome): |
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105 """ |
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106 Create a table for a chromosome |
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107 @param chromosome: a chromosome name |
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108 @type chromosome: string |
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109 """ |
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110 self.tables[chromosome] = MySqlTranscriptTable(self.mySqlConnection, self.name, chromosome, self.verbosity) |
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111 self.tables[chromosome].createTranscriptTable() |
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112 for name, values in self.indices.iteritems(): |
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113 self.tables[chromosome].createIndex("%s_%s_%d" % (name, chromosome, self.randomNumber), values) |
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114 |
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115 |
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116 |
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117 def addTranscript(self, transcript): |
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118 """ |
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119 Add a transcript to the list of transcripts to be written |
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120 @param transcript: transcript to be written |
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121 @type transcript: class L{Transcript<Transcript>} |
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122 """ |
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123 chromosome = transcript.getChromosome() |
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124 if chromosome not in self.tables: |
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125 self.createTable(chromosome) |
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126 self.nbTranscriptsByChromosome[chromosome] = 1 |
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127 if chromosome not in self.transcriptValues: |
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128 self.transcriptValues[chromosome] = [] |
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129 |
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130 self.transcriptValues[chromosome].append(transcript.getSqlValues()) |
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131 |
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132 self.nbTranscriptsByChromosome[chromosome] += 1 |
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133 self.toBeWritten = True |
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134 if sum([len(transcripts) for transcripts in self.transcriptValues.values()]) > self.nbTranscriptValues: |
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135 self.write() |
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136 |
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137 |
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138 def addElement(self, element): |
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139 """ |
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140 Same as "addTranscript" |
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141 @param element: transcript to be written |
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142 @type element: class L{Transcript<Transcript>} |
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143 """ |
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144 self.addTranscript(element) |
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145 |
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146 |
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147 # def addTranscriptList(self, transcriptListParser): |
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148 # """ |
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149 # Add a list of transcripts to the transcripts to be written |
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150 # @param transcriptListParser: transcripts to be written |
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151 # @type transcriptListParser: class L{TranscriptListParser<TranscriptListParser>} |
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152 # """ |
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153 # progress = Progress(transcriptListParser.getNbTranscripts(), "Storing %s into database" % (transcriptListParser.fileName), self.verbosity) |
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154 # for transcript in transcriptListParser.getIterator(): |
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155 # self.addTranscript(transcript) |
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156 # progress.inc() |
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157 # progress.done() |
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158 |
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159 |
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160 def addTranscriptList(self, transcriptListParser): |
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161 """ |
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162 Add a list of transcripts to the transcripts to be written |
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163 @param transcriptListParser: transcripts to be written |
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164 @type transcriptListParser: class L{TranscriptListParser<TranscriptListParser>} |
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165 """ |
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166 self.transcriptListParser = transcriptListParser |
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167 self.mySqlConnection.executeManyQueriesIterator(self) |
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168 |
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169 |
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170 def getIterator(self): |
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171 """ |
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172 Iterator to the SQL commands to insert the list |
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173 """ |
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174 progress = Progress(self.transcriptListParser.getNbTranscripts(), "Storing %s into database" % (self.transcriptListParser.fileName), self.verbosity) |
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175 for transcript in self.transcriptListParser.getIterator(): |
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176 chromosome = transcript.getChromosome() |
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177 if chromosome not in self.tables: |
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178 self.createTable(chromosome) |
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179 self.nbTranscriptsByChromosome[chromosome] = self.nbTranscriptsByChromosome.get(chromosome, 0) + 1 |
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180 values = transcript.getSqlValues() |
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181 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])) |
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182 progress.inc() |
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183 progress.done() |
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184 |
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185 |
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186 def write(self): |
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187 """ |
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188 Copy the content of the files into the database |
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189 (May add transcripts to already created databases) |
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190 """ |
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191 for chromosome in self.transcriptValues: |
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192 if chromosome in self.transcriptValues: |
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193 self.tables[chromosome].insertMany(self.transcriptValues[chromosome]) |
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194 self.transcriptValues = {} |
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195 self.toBeWritten = False |
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196 |
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197 |
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198 def getTables(self): |
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199 """ |
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200 Get the tables |
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201 @return: the mySQL tables |
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202 """ |
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203 if self.toBeWritten: |
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204 self.write() |
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205 return self.tables |
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206 |
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207 |
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208 |
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209 def removeTables(self): |
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210 """ |
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211 Drop the tables |
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212 """ |
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213 for chromosome in self.tables: |
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214 self.tables[chromosome].remove() |