Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/TranscriptListParser.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 import sys |
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31 from SMART.Java.Python.structure.TranscriptList import TranscriptList |
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32 from SMART.Java.Python.misc.Progress import Progress |
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33 from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress |
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34 |
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35 class TranscriptListParser(object): |
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36 """A (quite generic) class that reads a list of transcripts""" |
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37 |
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38 def __init__(self, fileName, verbosity = 0): |
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39 self.verbosity = verbosity |
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40 self.fileName = fileName |
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41 self.nbTranscripts = None |
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42 self.size = None |
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43 self.chromosomes = None |
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44 self.currentTranscript = None |
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45 self.currentLineNb = 0 |
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46 self.previousTranscriptAddress = None |
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47 try: |
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48 self.handle = open(self.fileName) |
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49 except IOError: |
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50 raise Exception("Error! Transcript file '%s' does not exist! Exiting..." % (self.fileName)) |
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51 self.skipFirstLines() |
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52 |
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53 |
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54 def __del__(self): |
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55 self.close() |
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56 |
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57 |
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58 def getFileFormats(): |
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59 pass |
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60 getFileFormats = staticmethod(getFileFormats) |
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61 |
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62 |
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63 def close(self): |
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64 if self.handle != None and not self.handle.close: |
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65 self.handle.close() |
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66 self.handle = None |
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67 |
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68 |
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69 def reset(self): |
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70 self.handle.seek(0) |
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71 self.skipFirstLines() |
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72 self.currentTranscript = None |
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73 self.currentLineNb = 0 |
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74 self.currentTranscriptAddress = self.handle.tell() |
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75 self.currentAddress = self.handle.tell() |
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76 |
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77 |
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78 def gotoAddress(self, address): |
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79 self.reset() |
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80 self.handle.seek(address) |
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81 self.currentTranscriptAddress = address |
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82 self.currentAddress = address |
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83 |
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84 |
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85 def parse(self): |
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86 transcriptList = TranscriptList() |
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87 progress = Progress(self.getNbTranscripts(), "Reading %s" % (self.fileName), self.verbosity) |
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88 for line in self.handle: |
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89 self.currentLineNb += 1 |
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90 transcript = self.parseLine(line) |
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91 transcriptList.addTranscript(transcript) |
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92 progress.inc() |
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93 progress.done() |
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94 return transcriptList |
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95 |
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96 |
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97 def getIterator(self): |
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98 self.reset() |
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99 transcript = self.getNextTranscript() |
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100 while transcript != None: |
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101 yield transcript |
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102 transcript = self.getNextTranscript() |
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103 |
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104 |
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105 def getCurrentAddress(self): |
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106 return self.currentAddress |
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107 |
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108 |
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109 def getCurrentTranscriptAddress(self): |
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110 return self.currentTranscriptAddress |
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111 |
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112 |
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113 def getNextTranscript(self): |
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114 self.currentAddress = self.handle.tell() |
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115 line = self.handle.readline() |
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116 while line != "": |
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117 line = line.strip() |
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118 self.currentLineNb += 1 |
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119 transcript = self.parseLine(line) |
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120 if transcript != None: |
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121 return transcript |
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122 self.currentAddress = self.handle.tell() |
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123 line = self.handle.readline() |
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124 transcript = self.currentTranscript |
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125 self.currentTranscriptAddress = self.previousTranscriptAddress |
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126 self.currentTranscript = None |
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127 return transcript |
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128 |
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129 |
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130 def getInfos(self): |
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131 self.chromosomes = set() |
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132 self.nbTranscripts = 0 |
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133 self.size = 0 |
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134 self.reset() |
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135 progress = UnlimitedProgress(100000, "Getting information on %s." % (self.fileName), self.verbosity-9) |
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136 transcript = self.getNextTranscript() |
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137 for transcript in self.getIterator(): |
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138 self.chromosomes.add(transcript.getChromosome()) |
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139 self.nbTranscripts += 1 |
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140 self.size += transcript.getSize() |
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141 progress.inc() |
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142 progress.done() |
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143 self.reset() |
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144 |
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145 |
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146 def getNbTranscripts(self): |
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147 if self.nbTranscripts != None: |
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148 return self.nbTranscripts |
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149 self.getInfos() |
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150 return self.nbTranscripts |
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151 |
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152 |
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153 def getNbItems(self): |
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154 return self.getNbTranscripts() |
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155 |
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156 |
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157 def getChromosomes(self): |
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158 if self.chromosomes != None: |
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159 return self.chromosomes |
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160 self.getInfos() |
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161 return self.chromosomes |
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162 |
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163 |
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164 def getSize(self): |
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165 if self.size != None: |
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166 return self.size |
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167 self.getInfos() |
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168 return self.size |
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169 |
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170 |
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171 def getNbNucleotides(self): |
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172 return self.getSize() |
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173 |
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174 |
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175 def setDefaultTagValue(self, name, value): |
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176 for transcript in self.getIterator(): |
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177 transcript.setTag(name, value) |
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178 |
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179 def __eq__(self, o): |
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180 if o == None: |
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181 return False |
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182 return self.fileName == o.fileName and self.nbTranscripts == o.nbTranscripts and self.size == o.size and self.chromosomes == o.chromosomes |