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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 from SMART.Java.Python.structure.SubMapping import SubMapping
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31 from SMART.Java.Python.structure.Transcript import Transcript
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32 from SMART.Java.Python.structure.Interval import Interval
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33
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34 class Mapping(object):
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35 """A class that represents a mapping"""
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36
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37 def __init__(self):
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38 self.targetInterval = None
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39 self.queryInterval = None
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40 self.subMappings = []
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41 self.size = None
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42 self.transcript = None
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43 self.tags = {}
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44
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45
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46 def copy(self, mapping):
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47 for subMapping in mapping.subMappings:
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48 newSubMapping = SubMapping(subMapping)
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49 self.addSubMapping(newSubMapping)
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50 self.targetInterval = Interval(mapping.targetInterval)
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51 self.queryInterval = Interval(mapping.queryInterval)
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52 self.size = mapping.size
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53 self.tags = {}
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54 for tag in mapping.tags:
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55 self.tags[tag] = mapping[tag]
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56 self.transcript.copy(mapping.transcript)
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57
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58
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59 def setTargetInterval(self, interval):
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60 self.targetInterval = Interval(interval)
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61 if self.queryInterval != None:
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62 self.setDirection(self.targetInterval.getDirection() * self.queryInterval.getDirection())
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63
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64
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65 def setQueryInterval(self, interval):
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66 self.queryInterval = Interval(interval)
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67 if self.targetInterval != None:
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68 self.setDirection(self.targetInterval.getDirection() * self.queryInterval.getDirection())
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69
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70
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71 def getQueryInterval(self):
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72 return self.queryInterval
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73
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74
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75 def addSubMapping(self, subMapping):
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76 subMappingCopy = SubMapping(subMapping)
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77 self.subMappings.append(subMappingCopy)
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78
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79 if self.targetInterval:
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80 self.targetInterval.setStart(min(self.targetInterval.getStart(), subMapping.targetInterval.getStart()))
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81 self.targetInterval.setEnd(max(self.targetInterval.getEnd(), subMapping.targetInterval.getEnd()))
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82 else:
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83 self.setTargetInterval(subMapping.targetInterval)
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84 if self.queryInterval:
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85 self.queryInterval.setStart(min(self.queryInterval.getStart(), subMapping.queryInterval.getStart()))
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86 self.queryInterval.setEnd(max(self.queryInterval.getEnd(), subMapping.queryInterval.getEnd()))
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87 else:
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88 self.setQueryInterval(subMapping.queryInterval)
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89
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90 if self.getDirection() != 0:
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91 subMapping.setDirection(self.getDirection())
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92 if self.size == None:
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93 self.size = 0
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94 if "identity" in subMapping.getTagNames() and "identity" not in self.getTagNames():
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95 self.setTagValue("identity", subMapping.getTagValue("identity"))
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96 elif "identity" in subMapping.getTagNames() and subMapping.size != None:
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97 self.setTagValue("identity", (self.getTagValue("identity") * self.size + subMapping.getTagValue("identity") * subMapping.size) / (self.size + subMapping.size))
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98 if subMapping.size != None:
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99 self.size += subMapping.size
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100 if "nbMismatches" in subMapping.getTagNames() and "nbMismatches" not in self.getTagNames():
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101 self.setTagValue("nbMismatches", subMapping.getTagValue("nbMismatches"))
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102 elif "nbMismatches" in subMapping.getTagNames():
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103 self.setTagValue("nbMismatches", self.getTagValue("nbMismatches") + subMapping.getTagValue("nbMismatches"))
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104 if "nbGaps" in subMapping.getTagNames() and "nbGaps" not in self.getTagNames():
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105 self.setTagValue("nbGaps", subMapping.getTagValue("nbGaps"))
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106 elif "nbGaps" in subMapping.getTagNames():
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107 self.setTagValue("nbGaps", self.getTagValue("nbGaps") + subMapping.getTagValue("nbGaps"))
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108
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109
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110 def setDirection(self, direction):
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111 for subMapping in self.subMappings:
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112 subMapping.setDirection(direction)
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113
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114
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115 def getDirection(self):
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116 if not self.subMappings:
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117 raise Exception("Error! Mapping '%s' has no submapping" % (self))
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118 return self.subMappings[0].getDirection()
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119
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120
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121 def setSize(self, size):
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122 self.size = size
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123 if "identity" in self.getTagNames():
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124 self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
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125
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126
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127 def setTagValue(self, name, value):
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128 self.tags[name] = value
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129 self.transcript = None
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130
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131
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132 def getTagValue(self, name):
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133 return self.tags[name]
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134
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135
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136 def getTagNames(self):
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137 return self.tags.keys()
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138
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139
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140 def setIdentity(self, identity):
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141 self.setTagValue("identity", identity)
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142 if self.size != None and "nbMismatches" not in self.getTagNames():
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143 nbMismatches = 0 if self.size == 0 else self.size - round(self.size * self.getTagValue("identity") / 100.0)
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144 self.setTagValue("nbMismatches", nbMismatches)
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145
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146
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147 def setNbOccurrences(self, nbOccurrences):
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148 self.setTagValue("nbOccurrences", nbOccurrences)
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149
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150
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151 def setNbMismatches(self, nbMismatches):
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152 self.setTagValue("nbMismatches", nbMismatches)
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153 if self.size != None and "identity" not in self.getTagNames():
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154 identity = 100 if self.size == 0 else (self.size - self.getTagValue("nbMismatches")) / float(self.size) * 100
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155 self.setTagValue("identity", identity)
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156
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157
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158 def setNbGaps(self, nbGaps):
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159 self.setTagValue("nbGaps", nbGaps)
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160
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161
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162 def setRank(self, rank):
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163 self.setTagValue("rank", rank)
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164
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165
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166 def setEvalue(self, evalue):
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167 self.setTagValue("evalue", evalue)
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168
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169
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170 def setOccurrence(self, occurrence):
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171 self.setTagValue("occurrence", occurrence)
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172
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173
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174 def setBestRegion(self, bestRegion):
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175 self.setTagValue("bestRegion", bestRegion)
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176
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177
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178 def mergeExons(self, distance):
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179 previousSubMapping = None
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180 subMappings = []
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181 for subMapping in self.subMappings:
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182 if previousSubMapping == None:
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183 subMappings.append(subMapping)
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184 previousSubMapping = subMapping
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185 else:
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186 targetDistance = subMapping.targetInterval.getDistance(previousSubMapping.targetInterval)
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187 queryDistance = subMapping.queryInterval.getDistance(previousSubMapping.queryInterval)
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188 if targetDistance <= distance:
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189 self.setTagValue("nbGaps", self.getTagValue("nbGaps") + queryDistance)
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190 previousSubMapping.merge(subMapping)
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191 else:
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192 subMappings.append(subMapping)
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193 previousSubMapping = subMapping
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194 self.subMappings = subMappings
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195
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196
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197 def getTranscript(self):
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198 """
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199 Extract a transcript from this mapping
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200 @return: a transcript
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201 """
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202 if self.transcript != None:
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203 return self.transcript
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204 self.transcript = Transcript()
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205 self.transcript.copy(self.targetInterval)
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206 self.transcript.setDirection(self.getDirection())
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207 self.transcript.setName(self.queryInterval.getName())
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208 self.transcript.removeExons()
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209 if len(self.subMappings) > 1:
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210 for subMapping in self.subMappings:
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211 self.transcript.addExon(subMapping.targetInterval)
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212 cpt = 1
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213 for exon in self.transcript.exons:
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214 exon.setDirection(self.transcript.getDirection())
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215 exon.setName("%s-exon%d" % (self.transcript.getName(), cpt))
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216 exon.setChromosome(self.transcript.getChromosome())
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217 cpt += 1
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218 self.transcript.setDirection(self.getDirection())
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219 self.transcript.sortExons()
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220 for tag in self.tags:
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221 if "bestRegion" not in self.getTagNames():
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222 self.transcript.setTagValue("bestRegion", "(self)")
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223 self.transcript.setTagValue(tag, self.getTagValue(tag))
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224 return self.transcript
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225
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226
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227 def getChromosome(self):
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228 if not self.subMappings:
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229 raise Exception("Error! Mapping '%s' has no submapping" % (self))
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230 return self.subMappings[0].targetInterval.getChromosome()
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231
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232
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233
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234 def getErrorScore(self):
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235 return self.getTagValue("nbGaps") * 3 + self.getTagValue("nbMismatches") + (len(self.subMappings) - 1) * 0.1
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236
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237
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238 def printGBrowseReference(self):
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239 return self.getTranscript().printGBrowseReference()
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240
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241
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242 def printGBrowseLine(self):
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243 return self.getTranscript().printGBrowseLine()
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244
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245
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246 def printGBrowse(self):
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247 return self.getTranscript().printGBrowse()
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248
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249
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250 def printBed(self):
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251 return self.getTranscript().printBed()
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252
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253
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254 def __str__(self):
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255 return "%s ---- %s" % (str(self.getTranscript()), ", ". join([str(submapping) for submapping in self.subMappings]))
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