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comparison SMART/Java/Python/structure/SubMapping.py @ 6:769e306b7933

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author yufei-luo
date Fri, 18 Jan 2013 04:54:14 -0500
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5:ea3082881bf8 6:769e306b7933
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