Mercurial > repos > urgi-team > teiso

comparison TEisotools-1.1.a/commons/core/seq/SequenceModifications.py @ 16:836ce3d9d47a draft default tip

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author urgi-team
date Thu, 21 Jul 2016 07:42:47 -0400
parents 255c852351c5
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15:255c852351c5 16:836ce3d9d47a
1 #!/usr/bin/env python
2
3 # Copyright INRA (Institut National de la Recherche Agronomique)
4 # http://www.inra.fr
5 # http://urgi.versailles.inra.fr
6 #
7 # This software is governed by the CeCILL license under French law and
8 # abiding by the rules of distribution of free software. You can use,
9 # modify and/ or redistribute the software under the terms of the CeCILL
10 # license as circulated by CEA, CNRS and INRIA at the following URL
11 # "http://www.cecill.info".
12 #
13 # As a counterpart to the access to the source code and rights to copy,
14 # modify and redistribute granted by the license, users are provided only
15 # with a limited warranty and the software's author, the holder of the
16 # economic rights, and the successive licensors have only limited
17 # liability.
18 #
19 # In this respect, the user's attention is drawn to the risks associated
20 # with loading, using, modifying and/or developing or reproducing the
21 # software by the user in light of its specific status of free software,
22 # that may mean that it is complicated to manipulate, and that also
23 # therefore means that it is reserved for developers and experienced
24 # professionals having in-depth computer knowledge. Users are therefore
25 # encouraged to load and test the software's suitability as regards their
26 # requirements in conditions enabling the security of their systems and/or
27 # data to be ensured and, more generally, to use and operate it in the
28 # same conditions as regards security.
29 #
30 # The fact that you are presently reading this means that you have had
31 # knowledge of the CeCILL license and that you accept its terms.
32
33 from operator import itemgetter
34 from commons.core.coord.Range import Range
35
36 class SequenceModifications(object):
37
38 def __init__(self, originalHeader = "", mutatedHeader = ""):
39 self._originalHeader = originalHeader
40 self._mutatedHeader = mutatedHeader
41 self._lMutations = []
42 self._lDeletionsRanges = []
43 self._lInsertionsRanges = []
44
45 def __str__(self):
46 result = "%s\t%s\n" % (self.getOriginalHeader(), self.getMutatedHeader())
47 result += "Insertions\n"
48 for insertion in self._lInsertionsRanges:
49 result += "%s\n" % insertion.toString()
50 result += "Deletions\n"
51 for insertion in self._lDeletionsRanges:
52 result += "%s\n" % insertion.toString()
53 result += "Mutations"
54 for mutation in self._lMutations:
55 result += "\n%i\t%s\t%s" % (mutation[0], mutation[1], mutation[2])
56 return result
57
58 def __eq__(self, o):
59 if type(o) is type(self):
60 self.sort()
61 o.sort()
62 return self._originalHeader == o._originalHeader and self._mutatedHeader == o._mutatedHeader and self._lMutations == o._lMutations \
63 and self._lDeletionsRanges == o._lDeletionsRanges and self._lInsertionsRanges == o._lInsertionsRanges
64 return False
65
66 def __ne__(self, o):
67 return not self.__eq__(o)
68
69 def getOriginalHeader(self):
70 return self._originalHeader
71
72 def getMutatedHeader(self):
73 return self._mutatedHeader
74
75 def getMutations(self):
76 self.sort()
77 return self._lMutations
78
79 def getInsertions(self):
80 self.sort()
81 return self._lInsertionsRanges
82
83 def getDeletions(self):
84 self.sort()
85 return self._lDeletionsRanges
86
87 def setOriginalHeader(self, originalHeader):
88 self._originalHeader = originalHeader
89
90 def setMutatedHeader(self, mutatedHeader):
91 self._mutatedHeader = mutatedHeader
92
93 def setMutations(self, lMutations):
94 self._lMutations = lMutations
95
96 def addMutation(self, tupleMute):
97 #tuple: (position, oldNT, newNT)
98 self._lMutations.append(tupleMute)
99
100 def addInsertion(self, start, end, insertedSeqName = "."):
101 self._lInsertionsRanges.append(Range(insertedSeqName, start, end))
102
103 def addDeletion(self, start, end):
104 self._lDeletionsRanges.append(Range(self.getOriginalHeader(), start, end))
105
106 def clear(self):
107 self._lMutations = []
108 self._lDeletionsRanges = []
109 self._lInsertionsRanges = []
110
111 def sort(self):
112 self._lMutations.sort(key = itemgetter(0), reverse = False)
113 self._lDeletionsRanges.sort(key = lambda delRange: delRange.getStart(), reverse = False)
114 self._lInsertionsRanges.sort(key = lambda insRange: insRange.getStart(), reverse = False)