Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/writer/TranscriptListWriter.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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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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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 |