Mercurial > repos > yufei-luo > s_mart

comparison commons/core/coord/Path.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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37:d22fadc825e3 38:2c0c0a89fad7
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