Mercurial > repos > yufei-luo > s_mart
comparison commons/core/coord/Path.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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1 # Copyright INRA (Institut National de la Recherche Agronomique) | |
2 # http://www.inra.fr | |
3 # http://urgi.versailles.inra.fr | |
4 # | |
5 # This software is governed by the CeCILL license under French law and | |
6 # abiding by the rules of distribution of free software. You can use, | |
7 # modify and/ or redistribute the software under the terms of the CeCILL | |
8 # license as circulated by CEA, CNRS and INRIA at the following URL | |
9 # "http://www.cecill.info". | |
10 # | |
11 # As a counterpart to the access to the source code and rights to copy, | |
12 # modify and redistribute granted by the license, users are provided only | |
13 # with a limited warranty and the software's author, the holder of the | |
14 # economic rights, and the successive licensors have only limited | |
15 # liability. | |
16 # | |
17 # In this respect, the user's attention is drawn to the risks associated | |
18 # with loading, using, modifying and/or developing or reproducing the | |
19 # software by the user in light of its specific status of free software, | |
20 # that may mean that it is complicated to manipulate, and that also | |
21 # therefore means that it is reserved for developers and experienced | |
22 # professionals having in-depth computer knowledge. Users are therefore | |
23 # encouraged to load and test the software's suitability as regards their | |
24 # requirements in conditions enabling the security of their systems and/or | |
25 # data to be ensured and, more generally, to use and operate it in the | |
26 # same conditions as regards security. | |
27 # | |
28 # The fact that you are presently reading this means that you have had | |
29 # knowledge of the CeCILL license and that you accept its terms. | |
30 | |
31 | |
32 from commons.core.coord.Align import Align | |
33 from commons.core.coord.Set import Set | |
34 from commons.core.coord.Range import Range | |
35 | |
36 | |
37 ## Handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity) with an identifier | |
38 # | |
39 class Path( Align ): | |
40 | |
41 ## Constructor | |
42 # | |
43 # @param id identifier | |
44 # @param range_q: a Range instance for the query | |
45 # @param range_s: a Range instance for the subject | |
46 # @param e_value: E-value of the match | |
47 # @param score: score of the match | |
48 # @param identity: identity percentage of the match | |
49 # | |
50 def __init__( self, id=-1, range_q=Range(), range_s=Range(), e_value=0, score=0, identity=0 ): | |
51 self.id = int( id ) | |
52 Align.__init__( self, range_q, range_s, e_value, score, identity ) | |
53 | |
54 ## Equal operator | |
55 # | |
56 def __eq__(self, o): | |
57 if o == None or self.id != o.id: | |
58 return False | |
59 return Align.__eq__(self, o) | |
60 | |
61 ## Set attributes from tuple | |
62 # | |
63 # @param tuple a tuple with (id,queryName,queryStart,queryEnd,subjectName,subjectStar,subjectEnd,E-value,score,identity) | |
64 # @note data are loaded such that the query is always on the direct strand | |
65 # | |
66 def setFromTuple(self, tuple): | |
67 self.id = int(tuple[0]) | |
68 Align.setFromTuple(self, tuple[1:]) | |
69 | |
70 ## Reset | |
71 # | |
72 def reset(self): | |
73 self.id = -1 | |
74 Align.reset(self) | |
75 | |
76 ## Return the attributes as a formatted string | |
77 # | |
78 def toString(self): | |
79 string = "%i" % ( self.id ) | |
80 string += "\t%s" % (Align.toString(self)) | |
81 return string | |
82 | |
83 | |
84 ## Return the identifier of the Path instance | |
85 # | |
86 def getIdentifier( self ): | |
87 return self.id | |
88 | |
89 ## Return a Set instance with the subject mapped on the query | |
90 # | |
91 def getSubjectAsSetOfQuery(self): | |
92 iSet = Set() | |
93 iSet.id = self.id | |
94 iSet.name = self.range_subject.seqname | |
95 iSet.seqname = self.range_query.seqname | |
96 if self.range_subject.isOnDirectStrand(): | |
97 iSet.start = self.range_query.start | |
98 iSet.end = self.range_query.end | |
99 else: | |
100 iSet.start = self.range_query.end | |
101 iSet.end = self.range_query.start | |
102 return iSet | |
103 | |
104 #TODO: add tests !!!! | |
105 #WARNING: subject always in direct strand !!! | |
106 ## Return a Set instance with the subject mapped on the query | |
107 # | |
108 def getQuerySetOfSubject(self): | |
109 iSet = Set() | |
110 iSet.id = self.id | |
111 iSet.name = self.range_query.seqname | |
112 iSet.seqname = self.range_subject.seqname | |
113 if self.range_subject.isOnDirectStrand(): | |
114 iSet.start = self.range_subject.start | |
115 iSet.end = self.range_subject.end | |
116 else: | |
117 iSet.start = self.range_subject.end | |
118 iSet.end = self.range_subject.start | |
119 return iSet | |
120 | |
121 ## Return True if the instance can be merged with another Path instance, False otherwise | |
122 # | |
123 # @param o a Path instance | |
124 # | |
125 def canMerge(self, o): | |
126 return o.id != self.id \ | |
127 and o.range_query.seqname == self.range_query.seqname \ | |
128 and o.range_subject.seqname == self.range_subject.seqname \ | |
129 and o.range_query.isOnDirectStrand() == self.range_query.isOnDirectStrand() \ | |
130 and o.range_subject.isOnDirectStrand() == self.range_subject.isOnDirectStrand() \ | |
131 and o.range_query.isOverlapping(self.range_query) \ | |
132 and o.range_subject.isOverlapping(self.range_subject) | |
133 | |
134 ## Return an Align instance with the same attributes, except the identifier | |
135 # | |
136 def getAlignInstance(self): | |
137 iAlign = Align() | |
138 lAttributes = [] | |
139 lAttributes.append( self.range_query.seqname ) | |
140 lAttributes.append( self.range_query.start ) | |
141 lAttributes.append( self.range_query.end ) | |
142 lAttributes.append( self.range_subject.seqname ) | |
143 lAttributes.append( self.range_subject.start ) | |
144 lAttributes.append( self.range_subject.end ) | |
145 lAttributes.append( self.e_value ) | |
146 lAttributes.append( self.score ) | |
147 lAttributes.append( self.identity ) | |
148 iAlign.setFromTuple( lAttributes ) | |
149 return iAlign |