6
+ − 1 #
+ − 2 # Copyright INRA-URGI 2009-2010
+ − 3 #
+ − 4 # This software is governed by the CeCILL license under French law and
+ − 5 # abiding by the rules of distribution of free software. You can use,
+ − 6 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 7 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 8 # "http://www.cecill.info".
+ − 9 #
+ − 10 # As a counterpart to the access to the source code and rights to copy,
+ − 11 # modify and redistribute granted by the license, users are provided only
+ − 12 # with a limited warranty and the software's author, the holder of the
+ − 13 # economic rights, and the successive licensors have only limited
+ − 14 # liability.
+ − 15 #
+ − 16 # In this respect, the user's attention is drawn to the risks associated
+ − 17 # with loading, using, modifying and/or developing or reproducing the
+ − 18 # software by the user in light of its specific status of free software,
+ − 19 # that may mean that it is complicated to manipulate, and that also
+ − 20 # therefore means that it is reserved for developers and experienced
+ − 21 # professionals having in-depth computer knowledge. Users are therefore
+ − 22 # encouraged to load and test the software's suitability as regards their
+ − 23 # requirements in conditions enabling the security of their systems and/or
+ − 24 # data to be ensured and, more generally, to use and operate it in the
+ − 25 # same conditions as regards security.
+ − 26 #
+ − 27 # The fact that you are presently reading this means that you have had
+ − 28 # knowledge of the CeCILL license and that you accept its terms.
+ − 29 #
+ − 30 from SMART.Java.Python.structure.Interval import Interval
+ − 31 from commons.core.coord.Align import Align
+ − 32
+ − 33 class SubMapping(Align):
+ − 34 """
+ − 35 A class that represents a part of a mapping, more precisely, a pair (target interval, query interval) that match together
+ − 36 @ivar targetInterval: the target interval
+ − 37 @type targetInterval: class L{Interval<Interval>}
+ − 38 @ivar queryInterval: the query interval
+ − 39 @type queryInterval: class L{Interval<Interval>}
+ − 40 @ivar size: size of this sub-mapping
+ − 41 @type size: int
+ − 42 @ivar tags: various information
+ − 43 @type tags: dict
+ − 44 """
+ − 45
+ − 46 def __init__(self, subMapping = None):
+ − 47 """
+ − 48 Constructor
+ − 49 @param subMapping: a sub-mapping to be copied
+ − 50 @type subMapping: class L{SubMapping<SubMapping>}
+ − 51 """
+ − 52 self.targetInterval = Interval()
+ − 53 self.queryInterval = Interval()
+ − 54 Align.__init__(self, self.queryInterval, self.targetInterval)
+ − 55 self.size = None
+ − 56 self.tags = {}
+ − 57 if subMapping != None:
+ − 58 self.copy(subMapping)
+ − 59
+ − 60 def __eq__(self, o):
+ − 61 if o == None:
+ − 62 return False
+ − 63 areAlignAttributesEquals = Align.__eq__(self, o)
+ − 64 return areAlignAttributesEquals and (self.targetInterval == o.targetInterval) and (self.queryInterval == o.queryInterval) and self.size == o.getSize() and self.tags == o.getTags()
+ − 65
+ − 66 def getSuperAdress(self):
+ − 67 return hex(id(super(Align, self)))
+ − 68
+ − 69 # def setRangesAlignToRangesInterval(self):
+ − 70 # self.range_query = super(Range, self.queryInterval)
+ − 71 # self.range_subject = super(Range, self.targetInterval)
+ − 72
+ − 73 def copy(self, subMapping):
+ − 74 """
+ − 75 Copy method
+ − 76 @param subMapping: a sub-mapping to be copied
+ − 77 @type subMapping: class L{SubMapping<SubMapping>}
+ − 78 """
+ − 79 self.setQueryName(subMapping.getQueryName())
+ − 80 self.setQueryStart(subMapping.getQueryStart())
+ − 81 self.setQueryEnd(subMapping.getQueryEnd())
+ − 82 self.setSubjectName(subMapping.getSubjectName())
+ − 83 self.setSubjectStart(subMapping.getSubjectStart())
+ − 84 self.setSubjectEnd(subMapping.getSubjectEnd())
+ − 85 self.e_value = subMapping.getEvalue()
+ − 86 self.score = subMapping.getScore()
+ − 87 self.identity = subMapping.getIdentity()
+ − 88
+ − 89 self.targetInterval.copy(subMapping.targetInterval)
+ − 90 self.queryInterval.copy(subMapping.queryInterval)
+ − 91 self.size = subMapping.size
+ − 92 for tag in subMapping.tags:
+ − 93 self.tags[tag] = subMapping.tags[tag]
+ − 94
+ − 95
+ − 96 def setTargetInterval(self, interval):
+ − 97 """
+ − 98 Set target interval
+ − 99 @param targetInterval: the target interval of the sub-mapping
+ − 100 @type targetInterval: class L{Interval<Interval>}
+ − 101 """
+ − 102 self.targetInterval.copy(interval)
+ − 103
+ − 104
+ − 105 def setQueryInterval(self, interval):
+ − 106 """
+ − 107 Set query interval
+ − 108 @param queryInterval: the query interval of the sub-mapping
+ − 109 @type queryInterval: class L{Interval<Interval>}
+ − 110 """
+ − 111 self.queryInterval.copy(interval)
+ − 112
+ − 113
+ − 114 def setSize(self, size):
+ − 115 """
+ − 116 Set the size of the sub-mapping
+ − 117 Possibly also target and query interval sizes, as well as number of mismatches
+ − 118 @param size: the size of the sub-mapping
+ − 119 @type size: int
+ − 120 """
+ − 121 self.size = size
+ − 122 if "identity" in self.getTagNames():
+ − 123 self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
+ − 124
+ − 125
+ − 126 def getDirection(self):
+ − 127 """
+ − 128 Get the direction of the alignment
+ − 129 """
+ − 130 return self.targetInterval.getDirection()
+ − 131
+ − 132
+ − 133 def setDirection(self, direction):
+ − 134 """
+ − 135 Set the direction of the alignment
+ − 136 @param direction: the directio of the alignment
+ − 137 type direction: int or string
+ − 138 """
+ − 139 return self.targetInterval.setDirection(direction)
+ − 140
+ − 141
+ − 142 def setTagValue(self, name, value):
+ − 143 """
+ − 144 Set the value of a tag
+ − 145 @param name: name of the tag
+ − 146 @type name: string
+ − 147 @param value: value of the tag
+ − 148 @type value: string or int
+ − 149 """
+ − 150 self.tags[name] = value
+ − 151
+ − 152
+ − 153 def getTagValue(self, name):
+ − 154 """
+ − 155 Get the value of a tag
+ − 156 @param name: name of the tag
+ − 157 @type name: string
+ − 158 @return: value of the tag
+ − 159 """
+ − 160 return self.tags[name]
+ − 161
+ − 162
+ − 163 def getTagNames(self):
+ − 164 """
+ − 165 Get all the names of the tags
+ − 166 @return: the names of the tags
+ − 167 """
+ − 168 return self.tags.keys()
+ − 169
+ − 170 def getTargetInterval(self):
+ − 171 return self.targetInterval
+ − 172
+ − 173 def getQueryInterval(self):
+ − 174 return self.queryInterval
+ − 175
+ − 176 def getSize(self):
+ − 177 return self.size
+ − 178
+ − 179 def getTags(self):
+ − 180 return self.tags
+ − 181
+ − 182 def setIdentity(self, identity):
+ − 183 """
+ − 184 Set the percentage of identity of the sub-mapping
+ − 185 Possibly also set number of mismatches
+ − 186 @param identity: the percentage of identity of the sub-mapping
+ − 187 @type identity: float
+ − 188 """
+ − 189 self.identity = identity
+ − 190 self.setTagValue("identity", identity)
+ − 191 if self.size != None and "nbMismatches" not in self.getTagNames():
+ − 192 self.setTagValue("nbMismatches", self.size - round(self.size * self.getTagValue("identity") / 100.0))
+ − 193
+ − 194
+ − 195 def setNbMismatches(self, nbMismatches):
+ − 196 """
+ − 197 Set the number of mismatches of the sub-mapping
+ − 198 Possibly also set percentage of identity
+ − 199 @param nbMismatches: the number of mismatches of the sub-mapping
+ − 200 @type nbMismatches: int
+ − 201 """
+ − 202 self.nbMismatches = nbMismatches
+ − 203 if self.size != None and "identity" not in self.getTagNames():
+ − 204 self.setTagValue("identity", (self.size - self.getTagValue("nbMismatches")) / float(self.size) * 100)
+ − 205
+ − 206
+ − 207 def setNbGaps(self, nbGaps):
+ − 208 """
+ − 209 Set the number of gaps of the sub-mapping
+ − 210 @param nbGaps: the number of gaps of the sub-mapping
+ − 211 @type nbGaps: int
+ − 212 """
+ − 213 self.setTagValue("nbGaps", nbGaps)
+ − 214
+ − 215
+ − 216 def merge(self, subMapping):
+ − 217 """
+ − 218 Merge two subMappings
+ − 219 @param subMapping: another sub-mapping
+ − 220 @type subMapping: class L{SubMapping<SubMapping>}
+ − 221 """
+ − 222 self.targetInterval.merge(subMapping.targetInterval)
+ − 223 self.queryInterval.merge(subMapping.queryInterval)
+ − 224
+ − 225
+ − 226 def printCoordinates(self):
+ − 227 """
+ − 228 Print the coordinates of the sub-mapping (considering the direction)
+ − 229 @return: a string
+ − 230 """
+ − 231 if self.getDirection() == 1:
+ − 232 return "%d-%d" % (self.targetInterval.getStart(), self.targetInterval.getEnd())
+ − 233 else:
+ − 234 return "%d-%d" % (self.targetInterval.getEnd(), self.targetInterval.getStart())
+ − 235
+ − 236
+ − 237 def __str__(self):
+ − 238 """
+ − 239 Return a representation of this object
+ − 240 @return: a string
+ − 241 """
+ − 242
+ − 243 if "match" in self.getTagNames() and not self.getTagValue("match"):
+ − 244 return "%s ---" % self.queryName
+ − 245
+ − 246 direction = "+"
+ − 247 if self.getDirection() == -1:
+ − 248 direction = "-"
+ − 249 string = "%s:%d-%d -- %s:%d-%d (%s)" % (self.targetInterval.getChromosome(), self.targetInterval.getStart(), self.targetInterval.getEnd(), self.queryInterval.name, self.queryInterval.getStart(), self.queryInterval.getEnd(), direction)
+ − 250 if "nbMismatches" in self.getTagNames():
+ − 251 string += "(%i mm)" % (self.getTagValue("nbMismatches"))
+ − 252 if "identity" in self.getTagNames():
+ − 253 string += "(id: %i%%)" % (self.getTagValue("identity"))
+ − 254 if self.targetInterval.getSize() != None and self.queryInterval.getSize() != None and self.size != None:
+ − 255 string += "(sizes: %d, %d -> %d)" % (self.targetInterval.getSize(), self.queryInterval.getSize(), self.size)
+ − 256 return string
+ − 257
+ − 258
