Mercurial > repos > urgi-team > teiso

comparison TEisotools-1.1.a/commons/core/coord/CountOverlapping.py @ 13:feef9a0db09d draft

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author urgi-team
date Wed, 20 Jul 2016 09:04:42 -0400
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12:22b0494ec883 13:feef9a0db09d
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 import bisect
32 from commons.core.checker.RepetException import RepetException
33 from commons.core.LoggerFactory import LoggerFactory
34
35 LOG_DEPTH = "commons.coord"
36 class CountOverlapping(object):
37
38 ## lFeatures must be a list of objects implementing getStart, getEnd, getSeqname methods.
39 # If areFeaturesOnDirectStrandsOnly is set to False, isOnReverseStrand and reverse methods must be implemented too.
40 # Throws a RepetException if all the features in lFeatures don't share the same getSeqname() result
41 #
42 # This implementation may not be very efficient but it works
43 #
44 def __init__(self, lFeatures, areFeaturesOnDirectStrandsOnly = False, verbosity = 2):
45 self._verbosity = verbosity
46 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
47
48 self._areFeaturesOnDirectStrandsOnly = areFeaturesOnDirectStrandsOnly
49 self._lFeaturesToCheck = lFeatures
50 self._prepareData()
51
52 def _prepareData(self):
53 self._nbFeatures = len(self._lFeaturesToCheck)
54 sNames = set()
55 for seqName in [iFeature.getSeqname() for iFeature in self._lFeaturesToCheck]:
56 sNames.add(seqName)
57
58 if len(sNames) not in [0, 1]:
59 self._logAndRaise("ERROR: different sequence names in input features list")
60
61 if not self._areFeaturesOnDirectStrandsOnly:
62 for iFeature in self._lFeaturesToCheck:
63 if iFeature.isOnReverseStrand():
64 iFeature.reverse()
65 self._areFeaturesOnDirectStrandsOnly = True
66
67 def _logAndRaise(self, errorMsg):
68 self._log.error(errorMsg)
69 raise RepetException(errorMsg)
70
71 ## Count number of features overlapping with a given interval
72 #
73 # @param queryInterval feature to check overlaps number with (must implement getStart, getEnd, getSeqname, isOnReverseStrand and reverse methods)
74 # @return int number of input features overlapping with queryInterval
75 #
76 def count(self, queryInterval):
77 if queryInterval.isOnReverseStrand():
78 queryInterval.reverse()
79 if self._nbFeatures == 0:
80 self._log.warning("WARNING: empty feature list. Will return 0 overlap.")
81 return 0
82 else:
83 featuresName = self._lFeaturesToCheck[0].getSeqname()
84 queryName = queryInterval.getSeqname()
85 if featuresName != queryName:
86 self._log.warning("WARNING: different sequence names between feature '%s' and queryInterval '%s'. Will return 0 overlap." % (featuresName, queryName))
87
88 lOrderedStart = [iFeature.getStart() for iFeature in self._lFeaturesToCheck]
89 lOrderedEnd = [iFeature.getEnd() for iFeature in self._lFeaturesToCheck]
90
91 lOrderedStart.sort()
92 lOrderedEnd.sort()
93
94 first = bisect.bisect_right(lOrderedStart, queryInterval.getEnd())
95 last = bisect.bisect_right(lOrderedEnd, queryInterval.getStart())
96 return self._nbFeatures - (last +(self._nbFeatures - first))