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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 from commons.core.parsing.MapperParser import MapperParser
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33 from SMART.Java.Python.structure.Mapping import Mapping
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34 from SMART.Java.Python.structure.SubMapping import SubMapping
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35 from SMART.Java.Python.structure.Interval import Interval
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36
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37 class SamParser(MapperParser):
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38 """A class that parses SAM format (as given by BWA)"""
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39
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40 def __init__(self, fileName, verbosity = 0):
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41 super(SamParser, self).__init__(fileName, verbosity)
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42
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43
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44 def __del__(self):
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45 super(SamParser, self).__del__()
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46
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47
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48 def getFileFormats():
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49 return ["sam"]
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50 getFileFormats = staticmethod(getFileFormats)
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51
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52
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53 def skipFirstLines(self):
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54 pass
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55
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56
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57 def getInfos(self):
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58 self.chromosomes = set()
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59 self.nbMappings = 0
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60 self.size = 0
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61 self.reset()
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62 if self.verbosity >= 10:
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63 print "Getting information on SAM file"
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64 self.reset()
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65 for line in self.handle:
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66 line = line.strip()
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67 if line == "" or line[0] == "@":
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68 continue
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69 parts = line.split("\t")
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70 chromosome = parts[2]
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71 if chromosome != "*":
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72 self.chromosomes.add(chromosome)
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73 self.nbMappings += 1
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74 self.size += len(parts[8])
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75 if self.verbosity >= 10 and self.nbMappings % 100000 == 0:
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76 sys.stdout.write(" %d mappings read\r" % (self.nbMappings))
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77 sys.stdout.flush()
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78 self.reset()
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79 if self.verbosity >= 10:
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80 print " %d mappings read" % (self.nbMappings)
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81 print "Done."
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82
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83
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84 def parseLine(self, line):
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85
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86 line = line.strip()
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87 if line[0] == "@":
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88 return
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89
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90 fields = line.split("\t")
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91 if len(fields) < 11:
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92 raise Exception("Line %d '%s' does not look like a SAM line (number of fields is %d instead of 11)" % (self.currentLineNb, line, len(fields)))
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93
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94 name = fields[0]
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95 flag = int(fields[1])
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96
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97 if (flag & 0x4) == 0x4:
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98 return None
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99
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100 direction = 1 if (flag & 0x10) == 0x0 else -1
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101 chromosome = fields[2]
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102 genomeStart = int(fields[3])
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103 quality = fields[4]
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104 cigar = fields[5]
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105 mate = fields[6]
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106 mateGenomeStart = fields[7]
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107 gapSize = fields[8]
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108 sequence = fields[9]
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109 quality = fields[10]
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110 tags = fields[11:]
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111
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112 if mateGenomeStart != "*":
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113 mateGenomeStart = int(mateGenomeStart)
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114
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115 mapping = Mapping()
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116 nbOccurrences = 1
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117 nbMismatches = 0
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118 nbMatches = 0
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119 nbGaps = 0
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120 subMapping = None
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121 queryOffset = 0
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122 targetOffset = 0
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123 currentNumber = 0
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124 readStart = None
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125
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126 for tag in tags:
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127 key = tag[:2]
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128 if key == "X0":
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129 nbOccurrences = int(tag[5:])
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130 elif key == "X1":
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131 nbOccurrences += int(tag[5:])
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132 elif key == "XM":
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133 nbMismatches = int(tag[5:])
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134 mapping.setTagValue("nbOccurrences", nbOccurrences)
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135 mapping.setTagValue("quality", int(fields[4]))
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136
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137 for char in cigar:
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138 m = re.match(r"[0-9]", char)
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139 if m != None:
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140 currentNumber = currentNumber * 10 + (ord(char) - ord("0"))
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141 continue
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142 # match
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143 m = re.match(r"[M]", char)
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144 if m != None:
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145 if readStart == None:
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146 readStart = queryOffset
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147 if subMapping == None:
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148 subMapping = SubMapping()
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149 subMapping.setSize(currentNumber)
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150 subMapping.setDirection(direction)
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151 subMapping.queryInterval.setName(name)
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152 subMapping.queryInterval.setStart(queryOffset)
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153 subMapping.queryInterval.setDirection(direction)
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154 subMapping.targetInterval.setChromosome(chromosome)
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155 subMapping.targetInterval.setStart(genomeStart + targetOffset)
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156 subMapping.targetInterval.setDirection(1)
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157 nbMatches += currentNumber
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158 targetOffset += currentNumber
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159 queryOffset += currentNumber
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160 currentNumber = 0
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161 continue
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162 # insertion on the read
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163 m = re.match(r"[I]", char)
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164 if m != None:
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165 nbGaps += 1
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166 queryOffset += currentNumber
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167 currentNumber = 0
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168 continue
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169 # insertion on the genome
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170 m = re.match(r"[D]", char)
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171 if m != None:
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172 if subMapping != None:
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173 subMapping.queryInterval.setEnd(queryOffset - 1)
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174 subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
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175 mapping.addSubMapping(subMapping)
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176 subMapping = None
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177 nbGaps += 1
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178 targetOffset += currentNumber
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179 currentNumber = 0
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180 continue
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181 # intron
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182 m = re.match(r"[N]", char)
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183 if m != None:
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184 if subMapping != None:
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185 subMapping.queryInterval.setEnd(queryOffset - 1)
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186 subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
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187 mapping.addSubMapping(subMapping)
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188 subMapping = None
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189 targetOffset += currentNumber
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190 currentNumber = 0
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191 continue
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192 # soft clipping (substitution)
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193 m = re.match(r"[S]", char)
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194 if m != None:
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195 nbMismatches += currentNumber
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196 targetOffset += currentNumber
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197 queryOffset += currentNumber
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198 currentNumber = 0
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199 continue
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200 # hard clipping
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201 m = re.match(r"[H]", char)
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202 if m != None:
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203 targetOffset += currentNumber
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204 queryOffset += currentNumber
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205 currentNumber = 0
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206 continue
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207 # padding
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208 m = re.match(r"[P]", char)
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209 if m != None:
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210 continue
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211 raise Exception("Do not understand paramer '%s' in line %s" % (char, line))
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212
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213 if subMapping != None:
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214 subMapping.queryInterval.setEnd(queryOffset - 1)
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215 subMapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
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216 mapping.addSubMapping(subMapping)
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217
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218 mapping.queryInterval.setStart(readStart)
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219 mapping.queryInterval.setEnd(queryOffset - 1)
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220 mapping.targetInterval.setEnd(genomeStart + targetOffset - 1)
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221 mapping.setNbMismatches(nbMismatches)
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222 mapping.setNbGaps(nbGaps)
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223
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224 mapping.queryInterval.setName(name)
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225 mapping.queryInterval.setDirection(direction)
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226 mapping.targetInterval.setChromosome(chromosome)
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227 mapping.targetInterval.setStart(genomeStart)
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228 mapping.targetInterval.setDirection(direction)
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229 mapping.setSize(len(sequence))
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230 mapping.setDirection(direction)
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231
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232 return mapping
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233
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234
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