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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
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