6
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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 from SMART.Java.Python.misc.Progress import Progress
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31
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32 class TranscriptListWriter(object):
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33 """
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34 An interface that writes a transcript list into a file
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35 @ivar fileName: name of the file
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36 @type fileName: string
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37 @ivar handle: handle to the file
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38 @type handle: file handle
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39 @ivar header: first lines of the file
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40 @type header: string
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41 @ivar started: whether some transcripts have already been writted
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42 @type started: boolean
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43 @ivar lastChromosome: the chromosome on which the transcript which was inserted last
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44 @type lastChromosome: string
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45 """
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46
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47
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48 def __init__(self, fileName, verbosity = 0):
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49 """
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50 Constructor
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51 @param fileName: name of the file
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52 @type fileName: string
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53 @param verbosity: verbosity
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54 @type verbosity: int
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55 """
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56 self.fileName = fileName
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57 self.verbosity = verbosity
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58 self.handle = open(self.fileName, "w")
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59 self.started = False
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60 self.lastChromosome = None
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61 self.header = ""
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62 self.sequenceFileName = None
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63
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64
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65 def __del__(self):
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66 """
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67 Destructor
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68 """
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69 self.close()
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70
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71
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72 def close(self):
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73 """
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74 Close writer
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75 """
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76 if self.handle != None and not self.handle.closed:
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77 self.handle.close()
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78 self.handle = None
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79
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80
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81 def addTranscript(self, transcript):
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82 """
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83 Add a transcript to the list of transcripts to be written
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84 @param transcript: transcript to be written
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85 @type transcript: class L{Transcript<Transcript>}
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86 """
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87 if not self.started:
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88 self.handle.write(self.header)
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89 self.started = True
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90
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91 self.handle.write(self.printTranscript(transcript))
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92 self.lastChromosome = transcript.getChromosome()
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93
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94
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95 def addElement(self, element):
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96 """
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97 Same as "addTranscript"
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98 @param element: transcript to be written
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99 @type element: class L{Transcript<Transcript>}
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100 """
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101 self.addTranscript(element)
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102
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103
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104 def addTranscriptList(self, transcriptList):
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105 """
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106 Add a list of transcripts to the transcripts to be written
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107 @param transcriptList: transcripts to be written
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108 @type transcriptList: class L{TranscriptList<TranscriptList>}
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109 """
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110 progress = Progress(transcriptList.getNbTranscripts(), "Writing transcripts", self.verbosity)
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111 for transcript in transcriptList.getIterator():
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112 self.addTranscript(transcript)
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113 progress.inc()
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114 progress.done()
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115
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116
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117 def addTranscriptTable(self, transcriptTable):
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118 """
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119 Add a list of transcripts in a mySQL table to the transcripts to be written
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120 @param transcriptTable: transcripts to be written
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121 @type transcriptTable: class L{MySqlTranscriptTable<MySqlTranscriptTable>}
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122 """
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123 for transcript in transcriptTable.getIterator():
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124 self.addTranscript(transcript)
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125
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126
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127 def setTitle(self, title):
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128 """
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129 Possibly write a title for the list (by default, do nothing)
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130 @param title: a title for the list
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131 @type title: string
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132 """
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133 pass
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134
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135 def setFeature(self, feature):
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136 """
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137 Set the name of the feature
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138 @param title: the title of the feature
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139 @type feature: string
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140 """
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141 pass
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142
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143 def setFeaturePart(self, featurePart):
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144 """
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145 Set the name of the feature part
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146 @param title: the title of the feature part
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147 @type featurePart: string
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148 """
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149 pass
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150
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151
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152 def addSequenceFile(self, fileName):
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153 """
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154 Get the multi-fasta file of the sequences
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155 """
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156 self.sequenceFileName = fileName
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157
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158
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159 def write(self):
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160 """
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161 No-op
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162 """
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163 pass
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