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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.parsing.TranscriptListParser import TranscriptListParser
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32 from commons.core.parsing.MapperParser import MapperParser
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33 from commons.core.parsing.SequenceListParser import SequenceListParser
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34 from commons.core.parsing.BedParser import BedParser
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35 from commons.core.parsing.GffParser import GffParser
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36 from commons.core.parsing.MapperParser import MapperParser
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37 from commons.core.parsing.CoordsParser import CoordsParser
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38 from commons.core.parsing.SeqmapParser import SeqmapParser
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39 from commons.core.parsing.SoapParser import SoapParser
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40 from commons.core.parsing.Soap2Parser import Soap2Parser
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41 from commons.core.parsing.BlastParser import BlastParser
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42 from commons.core.parsing.PslParser import PslParser
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43 from commons.core.parsing.RmapParser import RmapParser
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44 from commons.core.parsing.ShrimpParser import ShrimpParser
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45 from commons.core.parsing.AxtParser import AxtParser
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46 from commons.core.parsing.ExoParser import ExoParser
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47 from commons.core.parsing.MaqParser import MaqParser
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48 from commons.core.parsing.SamParser import SamParser
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49 from commons.core.parsing.BamParser import BamParser
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50 from commons.core.parsing.BowtieParser import BowtieParser
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51 from commons.core.parsing.ElandParser import ElandParser
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52 from commons.core.parsing.GtfParser import GtfParser
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53 from commons.core.parsing.FastaParser import FastaParser
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54 from commons.core.parsing.FastqParser import FastqParser
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55 from commons.core.parsing.MapParser import MapParser
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56 from commons.core.parsing.NCListParser import NCListParser
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57 from commons.core.parsing.PklParser import PklParser
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58
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59 #Attention!! Do not delete the imports!! They are used to know the type of file format!!!
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60
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61 class ParserChooser(object):
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62 """
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63 A class that finds the correct parser
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64 @ivar format: the format
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65 @type format: string
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66 @ivar type: transcript / mapping / sequence parser
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67 @type type: string
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68 @ivar parser: the parser
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69 @type parser: object
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70 @ivar verbosity: verbosity
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71 @type verbosity: int
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72 """
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73
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74 def __init__(self, verbosity = 0):
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75 """
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76 Constructor
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77 @param verbosity: verbosity
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78 @type verbosity: int
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79 """
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80 self.type = None
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81 self.parserClass = None
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82 self.verbosity = verbosity
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83
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84
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85 def findFormat(self, format, type = None):
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86 """
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87 Find the correct parser
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88 @ivar format: the format
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89 @type format: string
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90 @ivar type: transcript / mapping / sequence parser (None is all)
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91 @type type: string
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92 @return: a parser
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93 """
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94 classes = {}
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95 if (type == "transcript"):
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96 classes = {TranscriptListParser: "transcript"}
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97 elif (type == "mapping"):
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98 classes = {MapperParser: "mapping"}
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99 elif (type == "sequence"):
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100 classes = {SequenceListParser: "sequence"}
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101 elif (type == None):
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102 classes = {TranscriptListParser: "transcript", MapperParser: "mapping", SequenceListParser: "sequence"}
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103 else:
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104 raise Exception("Do not understand format type '%s'" % (type))
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105
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106 for classType in classes:
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107 for parserClass in classType.__subclasses__():
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108 if format in parserClass.getFileFormats():
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109 self.parserClass = parserClass
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110 self.type = classes[classType]
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111 return
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112 raise Exception("Cannot get parser for format '%s'" % (format))
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113
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114
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115 def getParser(self, fileName):
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116 """
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117 Get the parser previously found
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118 @return: the parser
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119 """
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120 return self.parserClass(fileName, self.verbosity)
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121
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122
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123 def getType(self):
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124 """
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125 Get the type of parser previously found
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126 @return: the type of parser
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127 """
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128 return self.type
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