Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/writer/TranscriptWriter.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 #
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4 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 #
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30 import os
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31 import sys
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32 from commons.core.writer.WriterChooser import WriterChooser
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33 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
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34
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35 class TranscriptWriter(object):
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36 """
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37 An interface class that writes a list of transcripts, handle different formats
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 @ivar container: container of the data
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39 @type container: L{TranscriptContainer<TranscriptContainer>}
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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40 @ivar format: format of the data to be printed
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41 @type format: string
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42 @ivar file: the file where to print
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43 @type file: string
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44 @ivar type: type of the data (transcripts, mappings or mySQL)
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45 @type type: string
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46 @ivar writer: a transcript list writer
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47 @type writer: L{TranscriptListWriter<TranscriptListWriter>} or None
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48 @ivar mode: use a container or enter transcript one by one
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49 @type mode: string
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50 @ivar verbosity: verbosity
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51 @type verbosity: int
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52 """
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53
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54 def __init__(self, file, format, verbosity = 0):
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55 """
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56 Constructor
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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57 @param container: container of the data
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58 @type container: string
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59 @param format: format of the data
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60 @type format: string
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61 @param file: file where to print
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62 @type file: 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.container = None
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67 self.format = format
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68 self.file = file
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69
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70 self.verbosity = verbosity
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71 self.type = None
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72 self.writer = None
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73 self.mode = None
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74 if self.format == None:
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75 sys.exit("Error! Writer input format is empty!")
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76
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77 if self.format == "sql":
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78 self.type = "sql"
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79 pos = self.file.rfind(os.sep)
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80 if pos > -1:
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81 self.file = self.file[pos+1:]
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82 self.writer = MySqlTranscriptWriter(self.file, self.verbosity)
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83 else:
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84 writerChooser = WriterChooser(self.verbosity)
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85 writerChooser.findFormat(self.format)
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86 self.writer = writerChooser.getWriter(self.file)
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87 self.type = writerChooser.getType()
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88
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89
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90 def close(self):
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91 """
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92 Close writer
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93 """
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94 if self.writer != None:
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95 self.writer.close()
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96
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97
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98 def setContainer(self, container):
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99 """
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100 Set a container for the data
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101 @param container: container of the data
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102 @type container: class L{TranscriptContainer<TranscriptContainer>}
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103 """
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104 self.container = container
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105 if self.mode == "transcript":
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106 raise Exception("Error! TranscriptWriter '%s' on 'transcript' mode is currently used on 'container' mode." % (self.file))
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107 self.mode = "container"
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108
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109
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110 def addTranscript(self, transcript):
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111 """
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112 Add a transcript to write
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113 @param transcript: a transcript
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114 @type transcript: class L{Transcript<Transcript>}
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115 """
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116 self.writer.addTranscript(transcript)
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117 if self.mode == "container":
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118 sys.exit("Error! TranscriptWriter '%s' on 'container' mode is currently used on 'transcript' mode." % (self.file))
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119 self.mode = "transcript"
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120
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121
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122 def addElement(self, transcript):
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123 """
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124 Same as addTranscript
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125 """
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126 self.addTranscript(transcript)
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127
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128
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129 def setTitle(self, title):
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130 """
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131 Possibly write a title for the list
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132 @param title: a title for the list
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133 @type title: string
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134 """
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135 if self.writer != None:
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136 self.writer.setTitle(title)
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137
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138 def setFeature(self, feature):
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139 """
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140 Possibly Set the name of the feature
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141 @param title: the title of the feature
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142 @type feature: string
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143 """
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144 if self.writer != None:
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145 self.writer.setFeature(feature)
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146
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147 def setFeaturePart(self, featurePart):
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148 """
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149 Possibly Set the name of the feature part
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150 @param title: the title of the feature part
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151 @type featurePart: string
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152 """
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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153 if self.writer != None:
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154 self.writer.setFeaturePart(featurePart)
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155
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156 def setStrands(self, strands):
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157 """
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158 Possibly consider both strands separately
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159 @param strands: whether both strands should be considered separately
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160 @type strands: boolean
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161 """
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162 if self.writer != None:
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163 self.writer.setStrands(strands)
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164
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165
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166 def write(self):
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167 """
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168 Write the content and possibly convert data
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169 """
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170 if self.type == "transcript" or self.type == "sequence":
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171 if self.mode == "container":
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172 self.writer.addTranscriptList(self.container)
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173 return
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174
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175 if self.mode == "transcript" or self.type == "sequence":
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176 self.writer.write()
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177 return
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178
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179 if self.container.format != "sql":
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180 self.container.storeIntoDatabase()
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181 tables = self.container.getTables()
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182 for chromosome in tables:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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183 tables[chromosome].rename("%s_%s" % (self.file, chromosome))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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184 return
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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185
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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186
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187 def addSequenceFile(self, fileName):
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188 self.writer.addSequenceFile(fileName)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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189