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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.SequenceList import SequenceList
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32 from SMART.Java.Python.misc.Progress import Progress
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33
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34 class SequenceListParser(object):
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35 """
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36 A virtual class that reads a list of sequences
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37 @ivar verbosity: verbosity
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38 @type verbosity: int
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39 @ivar fileName: name of the file to parse
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40 @type fileName: string
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41 @ivar handle: file to parse
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42 @type handle: file
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43 @ivar nbSequences: number of sequences in the file
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44 @type nbSequences: int
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45 @ivar nbReadSequences: number of sequences read
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46 @type nbReadSequences: int
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47 @ivar currentLine: line currently read
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48 @type currentLine: string
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49 @ivar size: total number of nucleotides in the sequences
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50 @type size: int
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51 @ivar sizes: number of nucleotides per sequences
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52 @type sizes: dict of string to int
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53 """
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54
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55 def __init__(self, fileName, verbosity = 0):
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56 """
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57 Constructor
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58 @param verbosity: verbosity
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59 @type verbosity: int
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60 @param fileName: name of the file to parse
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61 @type fileName: string
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62 """
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63 self.verbosity = verbosity
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64 self.fileName = fileName
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65 self.nbSequences = None
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66 self.nbReadSequences = 0
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67 self.currentLine = None
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68 self.size = None
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69 self.sizes = None
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70 try:
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71 self.handle = open(self.fileName, "rb")
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72 except IOError:
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73 raise Exception("Error! Sequence file '%s' does not exist! Exiting..." % (self.fileName))
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74
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75
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76 def __del__(self):
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77 """
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78 Destructor
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79 """
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80 if not self.handle.closed:
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81 self.handle.close()
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82
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83
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84 def close(self):
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85 """
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86 Close file handle
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87 """
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88 self.handle.close()
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89
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90
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91 def reset(self):
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92 """
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93 Prepare the file to be read again from start
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94 """
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95 self.handle.seek(0)
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96 self.currentLine = None
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97 self.nbReadSequences = 0
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98
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99
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100 def getFileFormats(self):
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101 pass
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102 getFileFormats = staticmethod(getFileFormats)
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103
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104
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105 def parse(self):
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106 """
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107 Parse the whole file in one shot
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108 @return: a list of sequence
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109 """
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110 sequenceList = SequenceList()
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111 progress = Progress(self.getNbSequences(), "Reading %s" % (self.fileName), self.verbosity)
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112 for sequence in self.getIterator():
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113 sequenceList.addSequence(sequence)
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114 progress.inc()
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115 progress.done()
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116 return sequenceList
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117
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118
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119 def getIterator(self):
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120 """
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121 Iterate on the file, sequence by sequence
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122 @return: an iterator to sequences
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123 """
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124 self.reset()
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125 sequence = self.parseOne()
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126 while sequence != None:
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127 self.nbReadSequences += 1
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128 yield sequence
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129 sequence = self.parseOne()
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130
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131
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132 def getInfos(self):
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133 """
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134 Get some generic information about the sequences
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135 """
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136 self.nbSequences = 0
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137 self.size = 0
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138 self.reset()
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139 if self.verbosity >= 10:
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140 print "Getting information on %s." % (self.fileName)
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141 for sequence in self.getIterator():
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142 self.nbSequences += 1
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143 self.size += sequence.getSize()
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144 if self.verbosity >= 10 and self.nbSequences % 100000 == 0:
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145 sys.stdout.write(" %d sequences read\r" % (self.nbSequences))
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146 sys.stdout.flush()
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147 self.reset()
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148 if self.verbosity >= 10:
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149 print " %d sequences read" % (self.nbSequences)
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150 print "Done."
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151
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152
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153 def getNbSequences(self):
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154 """
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155 Get the number of sequences in the file
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156 @return: the number of sequences
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157 """
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158 if self.nbSequences != None:
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159 return self.nbSequences
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160 self.getInfos()
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161 return self.nbSequences
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162
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163
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164 def getNbItems(self):
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165 """
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166 Get the number of sequences in the file
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167 @return: the number of sequences
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168 """
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169 return self.getNbSequences()
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170
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171
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172 def getSize(self):
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173 """
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174 Get the size of all the sequences
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175 @return: the size
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176 """
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177 if self.size != None:
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178 return self.size
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179 self.getInfos()
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180 return self.size
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181
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182
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183 def getRegions(self):
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184 """
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185 Get the names of the sequences
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186 @return: the names
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187 """
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188 if self.sizes != None:
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189 return self.sizes.keys()
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190
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191 self.sizes = {}
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192 self.reset()
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193 if self.verbosity >= 10:
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194 print "Getting information on %s." % (self.fileName)
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195 self.nbSequences = 0
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196 for sequence in self.getIterator():
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197 self.sizes[sequence.name] = sequence.getSize()
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198 self.nbSequences += 1
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199 if self.verbosity >= 10 and self.nbSequences % 100000 == 0:
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200 sys.stdout.write(" %d sequences read\r" % (self.nbSequences))
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201 sys.stdout.flush()
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202 self.reset()
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203 if self.verbosity >= 10:
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204 print " %d sequences read" % (self.nbSequences)
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205 print "Done."
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206 return self.sizes.keys()
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207
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208
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209 def getSizeOfRegion(self, region):
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210 """
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211 Get the size of a sequence
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212 @param region: the name of the sequence
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213 @type region: string
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214 @return: the size of the sequence
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215 """
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216 if self.sizes != None:
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217 if region not in self.sizes:
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218 raise Exception("Region %s is not found" % region)
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219 return self.sizes[region]
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220
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221 self.getRegions()
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222 if region not in self.sizes:
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223 raise Exception("Region %s is not found" % region)
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224
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225 def __eq__(self, o):
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226 if o == None:
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227 return False
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228 return self.fileName == o.fileName and self.nbSequences == o.nbSequences
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