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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 SMART.Java.Python.structure.Mapping import Mapping
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33 from SMART.Java.Python.structure.SubMapping import SubMapping
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34 from commons.core.parsing.MapperParser import MapperParser
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35
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36
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37 def mappingToSubMapping(mapping):
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38 subMapping = SubMapping()
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39 subMapping.targetInterval.copy(mapping.targetInterval)
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40 subMapping.queryInterval.copy(mapping.queryInterval)
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41 subMapping.setDirection(mapping.getDirection())
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42 subMapping.size = mapping.size
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43 subMapping.tags = mapping.tags
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44 return subMapping
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45
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46
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47
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48 class Soap2Parser(MapperParser):
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49 """A class that parses the output of SOAP2"""
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50
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51 def __init__(self, fileName, verbosity = 0):
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52 super(Soap2Parser, self).__init__(fileName, verbosity)
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53
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54
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55 def __del__(self):
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56 super(Soap2Parser, self).__del__()
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57
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58
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59 def getFileFormats():
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60 return ["soap2"]
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61 getFileFormats = staticmethod(getFileFormats)
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62
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63
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64 def skipFirstLines(self):
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65 pass
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66
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67
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68 def getIterator(self):
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69 self.reset()
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70 currentName = None
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71 currentMappings = []
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72 for line in self.handle:
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73 mapping = self.parseLine(line)
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74 name = mapping.queryInterval.name
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75 if name == currentName:
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76 if mapping.getTagValue("end") == "a":
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77 currentMappings.append(mapping)
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78 else:
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79 otherEndMapping = currentMappings.pop(0)
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80
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81 newMapping = Mapping()
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82 subMappingA = mappingToSubMapping(otherEndMapping)
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83 subMappingB = mappingToSubMapping(mapping)
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84 subMappingB.queryInterval.setDirection(subMappingA.queryInterval.getDirection())
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85
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86 newMapping.addSubMapping(subMappingA)
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87 newMapping.addSubMapping(subMappingB)
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88
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89 newMapping.tags = otherEndMapping.tags
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90 newMapping.setSize(otherEndMapping.size + mapping.size)
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91 newMapping.setNbMismatches(otherEndMapping.getTagValue("nbMismatches") + mapping.getTagValue("nbMismatches"))
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92 print otherEndMapping.getTagValue("nbMismatches")
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93 print mapping.getTagValue("nbMismatches")
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94 print newMapping.getTagValue("nbMismatches")
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95 sys.exit()
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96 newMapping.setTagValue("qualityString", otherEndMapping.getTagValue("qualityString") + mapping.getTagValue("qualityString"))
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97 newMapping.setTagValue("occurrence", "%d" % (newMapping.getTagValue("nbOccurrences") - len(currentMappings)))
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98 newMapping.setTagValue("ID", "%s-%s" % (name, newMapping.getTagValue("occurrence")))
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99 del newMapping.tags["end"]
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100 yield newMapping
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101 else:
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102 currentName = mapping.queryInterval.name
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103 for currentMapping in currentMappings:
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104 yield currentMapping
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105 currentMappings = [mapping]
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106 self.currentLineNb += 1
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107
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108
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109 def parseLine(self, line):
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110 m = re.search(r"^\s*(\S+)\s+(\w+)\s+(\S+)\s+(\d+)\s+([ab])\s+(\d+)\s+([+-])\s+(\w+)\s+(\d+)\s+(\d+)\s+", line)
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111 if m == None:
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112 sys.exit("\nLine %d '%s' does not have a SOAP2 format" % (self.currentLineNb, line))
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113
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114 name = m.group(1)
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115 read = m.group(2)
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116 qualityString = m.group(3)
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117 nbOccurrences = int(m.group(4))
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118 end = m.group(5)
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119 size = int(m.group(6))
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120 direction = m.group(7)
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121 chromosome = m.group(8)
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122 genomeStart = int(m.group(9))
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123 nbMismatches = int(m.group(10))
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124
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125 mapping = Mapping()
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126 if name.endswith("/1") or name.endswith("/2"):
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127 name = name[:-2]
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128
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129 mapping.queryInterval.name = name
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130 mapping.queryInterval.setDirection(direction)
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131 mapping.queryInterval.setStart(1)
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132 mapping.queryInterval.setEnd(size)
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133
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134 mapping.targetInterval.setChromosome(chromosome)
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135 mapping.targetInterval.setStart(genomeStart)
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136 mapping.targetInterval.setSize(size)
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137
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138 mapping.setDirection(direction)
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139 mapping.setSize(size)
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140
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141 mapping.setNbMismatches(nbMismatches)
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142 mapping.setNbGaps(0)
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143 mapping.setTagValue("qualityString", qualityString)
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144 mapping.setTagValue("nbOccurrences", nbOccurrences)
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145 mapping.setTagValue("end", end)
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146
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147 return mapping
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148
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