Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/writer/WriterChooser.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 sys |
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31 from commons.core.writer.TranscriptListWriter import TranscriptListWriter |
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32 from commons.core.writer.SequenceListWriter import SequenceListWriter |
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33 from commons.core.writer.BedWriter import BedWriter |
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34 from commons.core.writer.CsvWriter import CsvWriter |
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35 from commons.core.writer.EmblWriter import EmblWriter |
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36 from commons.core.writer.FastaWriter import FastaWriter |
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37 from commons.core.writer.FastqWriter import FastqWriter |
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38 from commons.core.writer.GbWriter import GbWriter |
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39 from commons.core.writer.Gff2Writer import Gff2Writer |
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40 from commons.core.writer.SamWriter import SamWriter |
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41 from commons.core.writer.UcscWriter import UcscWriter |
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42 from commons.core.writer.WigWriter import WigWriter |
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43 from commons.core.writer.Gff3Writer import Gff3Writer |
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44 from commons.core.writer.GtfWriter import GtfWriter |
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45 from commons.core.writer.MapWriter import MapWriter |
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46 |
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47 |
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48 class WriterChooser(object): |
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49 """ |
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50 A class that finds the correct writer |
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51 @ivar type: transcript / sequence writer |
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52 @type type: string |
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53 @ivar format: the format of the writer |
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54 @type format: string |
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55 @ivar writerClass: the class of the writer |
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56 @type writerClass: string |
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57 @ivar extension: default extension of the file |
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58 @type extension: string |
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59 @ivar verbosity: verbosity |
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60 @type verbosity: int |
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61 """ |
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62 |
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63 def __init__(self, verbosity = 0): |
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64 """ |
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65 Constructor |
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66 @param verbosity: verbosity |
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67 @type verbosity: int |
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68 """ |
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69 self.type = None |
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70 self.format = None |
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71 self.writerClass = None |
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72 self.extension = None |
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73 self.verbosity = verbosity |
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74 |
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75 |
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76 def findFormat(self, format, type = None): |
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77 """ |
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78 Find the correct parser |
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79 @ivar format: the format |
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80 @type format: string |
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81 @ivar type: transcript sequence parser (None is all) |
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82 @type type: string |
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83 @return: a parser |
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84 """ |
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85 classes = {} |
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86 if (type == "transcript"): |
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87 classes = {TranscriptListWriter: "transcript"} |
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88 elif (type == "sequence"): |
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89 classes = {SequenceListWriter: "sequence"} |
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90 elif (type == None): |
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91 classes = {TranscriptListWriter: "transcript", SequenceListWriter: "sequence"} |
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92 else: |
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93 sys.exit("Do not understand format type '%s'" % (type)) |
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94 |
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95 for classType in classes: |
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96 for writerClass in classType.__subclasses__(): |
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97 if format in writerClass.getFileFormats(): |
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98 self.writerClass = writerClass |
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99 self.extension = writerClass.getExtension() |
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100 self.type = classes[classType] |
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101 return |
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102 sys.exit("Cannot get writer for format '%s'" % (format)) |
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103 |
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104 |
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105 def getWriter(self, fileName): |
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106 """ |
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107 Get the writer previously found |
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108 @return: the writer |
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109 """ |
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110 return self.writerClass(fileName, self.verbosity) |
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111 |
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112 |
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113 def getType(self): |
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114 """ |
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115 Get the type of writer previously found |
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116 @return: the type of writer |
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117 """ |
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118 return self.type |
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119 |
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120 |
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121 def getExtension(self): |
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122 """ |
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123 Get the default extension of writer previously found |
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124 @return: the extension |
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125 """ |
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126 return self.extension |
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127 |