Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/ParserChooser.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.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 |