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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 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
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