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36
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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 re
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31 import sys
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32 import os.path
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33 import struct
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34 from commons.core.parsing.TranscriptListParser import TranscriptListParser
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35 from SMART.Java.Python.structure.Transcript import Transcript
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36
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37 STRANDTOSTR = {1: "(+)", 0: "(=)", None: "(=)", -1: "(-)"}
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38
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39 nbOpenHandles = 30
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40
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41
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42 class WigParser(TranscriptListParser):
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43 """A class that parses a big WIG file, creates an index and make it possible to quickly retrieve some data"""
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44
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45 def __init__(self, fileName, verbosity = 1):
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46 self.fileName = fileName
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47 self.filler = "\xFF" * struct.calcsize('Q')
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48 self.strands = False
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49 self.indexFiles = {}
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50 self.indexBuilt = False
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51 self.defaultValue = 0.0
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52 self.currentChromosome = None
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53 self.currentStrand = 1
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54 self.verbosity = verbosity
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55 super(WigParser, self).__init__(fileName, verbosity)
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56
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57
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58 def __def__(self):
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59 for file in self.indexFiles.values():
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60 file.close()
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61
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62
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63 def setStrands(self, strands):
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64 self.strands = strands
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65
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66
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67 def setDefaultValue(self, value):
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68 self.defaultValue = value
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69
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70
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71 def getFileFormats():
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72 return ["wig"]
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73 getFileFormats = staticmethod(getFileFormats)
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74
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75
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76 def setStrands(self, strands):
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77 """
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78 Consider both strands separately
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79 """
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80 self.strands = strands
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81
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82
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83 def makeIndexName(self, chromosome, strand = None):
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84 """
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85 Create an index name for a file
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86 """
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87 directoryName = os.path.dirname(self.fileName)
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88 if strand == None:
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89 strandName = ""
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90 else:
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91 strandName = "+" if strand == 1 else "-"
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92 indexName = os.path.join(directoryName, ".%s%s.index" % (chromosome, strandName))
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93 return indexName
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94
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95
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96 def findIndexFile(self, chromosome, strand = None):
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97 """
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98 Check if the index of a file exists
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99 """
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100 indexName = self.makeIndexName(chromosome, strand)
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101 if os.path.exists(indexName):
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102 return indexName
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103 return False
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104
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105
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106 def makeIndexFile(self):
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107 """
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108 Create the index for a file
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109 """
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110 if self.indexBuilt:
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111 return
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112
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113 inputFile = open(self.fileName)
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114 outputFile = None
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115 index = 0
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116 mark = inputFile.tell()
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117 line = inputFile.readline().strip()
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118 chromosome = None
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119
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120 while line != "":
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121 m1 = re.search(r"^\s*-?\d+\.?\d*\s*$", line)
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122 m2 = re.search(r"^\s*(\d+)\s+-?\d+\.?\d*\s*$", line)
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123 m3 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=(\d+)\s+step=1\s*$", line)
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124 m4 = re.search(r"^\s*fixedStep\s+chrom=\S+\s+start=\d+\s+step=\d+\s+span=\d+\s*$", line)
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125 m5 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line)
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126 m6 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s+span=(\d+)\s*$", line)
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127
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128 if m1 != None:
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129 outputFile.write(struct.pack("Q", mark))
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130 index += 1
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131 elif m2 != None:
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132 nextIndex = int(m2.group(1))
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133 if index < nextIndex - 1:
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134 outputFile.write(self.filler * (nextIndex - index - 1))
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135 outputFile.write(struct.pack("Q", mark))
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136 index = nextIndex
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137 elif m3 != None:
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138 newChromosome = m3.group(1)
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139 if newChromosome != chromosome:
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140 if outputFile != None:
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141 outputFile.close()
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142 outputFile = open(self.makeIndexName(newChromosome), "wb")
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143 chromosome = newChromosome
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144 nextIndex = int(m3.group(2))
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145 outputFile.write(self.filler * (nextIndex - index))
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146 index = nextIndex
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147 elif m4 != None:
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148 raise Exception("Error! Cannot parse fixed step WIG files with step > 1 or span > 1")
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149 elif m5 != None:
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150 newChromosome = m5.group(1)
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151 if newChromosome != chromosome:
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152 if outputFile != None:
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153 outputFile.close()
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154 outputFile = open(self.makeIndexName(newChromosome), "wb")
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155 index = 0
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156 outputFile.write(self.filler)
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157 chromosome = newChromosome
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158 elif m6 != None:
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159 if m6.group(2) != "1":
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160 raise Exception("Error! Cannot parse variable step WIG files with step > 1 or span > 1")
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161 newChromosome = m6.group(1)
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162 if newChromosome != chromosome:
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163 if outputFile != None:
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164 outputFile.close()
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165 outputFile = open(self.makeIndexName(newChromosome), "wb")
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166 index = 0
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167 outputFile.write(self.filler)
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168 chromosome = newChromosome
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169 elif (len(line) == 0) or line[0] == "#" or line.startswith("track"):
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170 pass
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171 else:
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172 raise Exception("Error! Cannot understand line '%s' of WIG file while creating index file! Aborting." % (line))
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173
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174 mark = inputFile.tell()
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175 line = inputFile.readline().strip()
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176
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177 inputFile.close
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178 if outputFile != None:
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179 outputFile.close()
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180 self.indexBuilt = True
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181
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182
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183 def getIndexFileHandle(self, chromosome, strand = None):
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184 """
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185 Get the handle of an index file
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186 """
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187 indexFileKey = chromosome
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188 if strand != None:
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189 indexFileKey += "+" if strand == 1 else "-"
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190 if indexFileKey in self.indexFiles:
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191 return self.indexFiles[indexFileKey]
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192
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193 indexFileName = self.makeIndexName(chromosome, strand)
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194 if not self.findIndexFile(chromosome, strand):
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195 self.makeIndexFile()
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196
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197 if not os.path.exists(indexFileName):
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198 print "Warning! Index for chromosome %s, strand %s does not exist." % (chromosome, STRANDTOSTR[strand])
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199 return False
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200 indexFile = open(indexFileName, "rb")
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201
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202 if len(self.indexFiles.keys()) > nbOpenHandles:
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203 removedKey = set(self.indexFiles.keys()).pop()
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204 self.indexFiles[removedKey].close()
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205 del self.indexFiles[removedKey]
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206 self.indexFiles[indexFileKey] = indexFile
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207 return indexFile
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208
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209
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210
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211 def findIndex(self, chromosome, start, strand = None):
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212 """
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213 Find the point where to start reading file
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214 """
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215
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216 sizeOfLong = struct.calcsize("Q")
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217 empty = int(struct.unpack("Q", self.filler)[0])
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218 offset = empty
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219 indexFile = self.getIndexFileHandle(chromosome, strand)
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220
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221 if not indexFile:
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222 return (None, None)
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223
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224 while offset == empty:
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225 address = start * sizeOfLong
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226 indexFile.seek(address, os.SEEK_SET)
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227
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228 buffer = indexFile.read(sizeOfLong)
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229 if len(buffer) != sizeOfLong:
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230 if buffer == "":
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231 print "Warning! Index position %d of chromosome %s on strand %s seems out of range!" % (start, chromosome, STRANDTOSTR[strand])
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232 return (None, None)
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233 else:
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234 raise Exception("Problem fetching position %d of chromosome %s on strand %s seems out of range!" % (start, chromosome, STRANDTOSTR[strand]))
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235
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236 offset = int(struct.unpack("Q", buffer)[0])
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237 start += 1
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238
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239 start -= 1
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240 return (offset, start)
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241
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242
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243
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244 def getRange(self, chromosome, start, end):
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245 """
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246 Parse a wig file and output a range
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247 """
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248 arrays = {}
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249 strands = {1: "+", -1: "-"} if self.strands else {0: ""}
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250
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251 for strand in strands:
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252
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253 array = [self.defaultValue] * (end - start + 1)
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254 file = open(self.fileName)
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255 offset, index = self.findIndex(chromosome, start, strand if self.strands else None)
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256 if offset == None:
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257 arrays[strand] = array
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258 continue
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259 file.seek(offset, os.SEEK_SET)
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260
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261 for line in file:
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262 line = line.strip()
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263
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264 m1 = re.search(r"^\s*(-?\d+\.?\d*)\s*$", line)
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265 m2 = re.search(r"^\s*(\d+)\s+(-?\d+\.?\d*)\s*$", line)
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266 m3 = re.search(r"^\s*fixedStep\s+chrom=(\S+)\s+start=(\d+)\s+step=\d+\s*$", line)
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267 m4 = re.search(r"^\s*variableStep\s+chrom=(\S+)\s*$", line)
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268
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269 if m1 != None:
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270 if index > end:
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271 break
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272 if index >= start:
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273 array[index - start] = float(m1.group(1))
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274 index += 1
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275 elif m2 != None:
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276 index = int(m2.group(1))
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277 if index > end:
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278 break
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279 if index >= start:
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280 array[index - start] = float(m2.group(2))
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281 index += 1
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282 elif m3 != None:
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283 if m3.group(1) != "%s%s" % (chromosome, strands[strand]):
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284 break
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285 index = int(m3.group(2))
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286 elif m4 != None:
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287 if m4.group(1) != "%s%s" % (chromosome, strands[strand]):
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288 break
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289 elif (len(line) == 0) or (line[0] == "#") or line.startswith("track"):
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290 pass
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291 else:
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292 raise Exception("Error! Cannot read line '%s' of wig file" % (line))
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293
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294 file.close()
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295
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296 arrays[strand] = array
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297
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298 if self.strands:
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299 return arrays
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300 return array
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301
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302
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303 def skipFirstLines(self):
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304 return
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305
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306
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307 def parseLine(self, line):
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308 if line.startswith("track"):
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309 return None
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310 m = re.search(r"^\s*variableStep\s+chrom=(\S+)", line)
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311 if m != None:
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312 chromosome = m.group(1)
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313 if chromosome.endswith("+"):
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314 self.currentStrand = 1
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315 self.currentChromosome = chromosome[:-1]
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316 elif chromosome.endswith("-"):
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317 self.currentStrand = -1
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318 self.currentChromosome = chromosome[:-1]
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319 else:
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320 self.currentStrand = 1
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321 self.currentChromosome = chromosome
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322 return None
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323 position, value = line.split()
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324 position = int(position)
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325 value = float(value)
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326 transcript = Transcript()
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327 transcript.setChromosome(self.currentChromosome)
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328 transcript.setStart(position)
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329 transcript.setEnd(position)
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330 transcript.setDirection(self.currentStrand)
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331 transcript.setTagValue("ID", "wig_%s_%d_%d" % (self.currentChromosome, self.currentStrand, position))
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332 transcript.setTagValue("nbElements", value)
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333 return transcript
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