annotate TEisotools-1.1.a/commons/core/coord/CountOverlapping.py @ 15:255c852351c5 draft

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# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
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# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info". 
#
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# modify and redistribute granted by the license, users are provided only
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# economic rights,  and the successive licensors  have only  limited
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import bisect
from commons.core.checker.RepetException import RepetException
from commons.core.LoggerFactory import LoggerFactory

LOG_DEPTH = "commons.coord"
class CountOverlapping(object):
    
    ## lFeatures must be a list of objects implementing getStart, getEnd, getSeqname methods.
    # If areFeaturesOnDirectStrandsOnly is set to False, isOnReverseStrand and reverse methods must be implemented too.
    # Throws a RepetException if all the features in lFeatures don't share the same getSeqname() result
    #
    # This implementation may not be very efficient but it works
    #
    def __init__(self, lFeatures, areFeaturesOnDirectStrandsOnly = False, verbosity = 2):
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
        self._areFeaturesOnDirectStrandsOnly = areFeaturesOnDirectStrandsOnly
        self._lFeaturesToCheck = lFeatures
        self._prepareData()
        
    def _prepareData(self):
        self._nbFeatures = len(self._lFeaturesToCheck)
        sNames = set()
        for seqName in [iFeature.getSeqname() for iFeature in self._lFeaturesToCheck]:
            sNames.add(seqName)
            
        if len(sNames) not in [0, 1]:
            self._logAndRaise("ERROR: different sequence names in input features list")
        
        if not self._areFeaturesOnDirectStrandsOnly:
            for iFeature in self._lFeaturesToCheck:
                if iFeature.isOnReverseStrand():
                    iFeature.reverse()
            self._areFeaturesOnDirectStrandsOnly = True
        
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise RepetException(errorMsg)
        
    ## Count number of features overlapping with a given interval
    #
    # @param queryInterval feature to check overlaps number with (must implement getStart, getEnd, getSeqname, isOnReverseStrand and reverse methods)
    # @return int number of input features overlapping with queryInterval
    #
    def count(self, queryInterval):
        if queryInterval.isOnReverseStrand():
            queryInterval.reverse()
        if self._nbFeatures == 0:
            self._log.warning("WARNING: empty feature list. Will return 0 overlap.")
            return 0
        else:
            featuresName = self._lFeaturesToCheck[0].getSeqname()
            queryName = queryInterval.getSeqname()
            if featuresName != queryName:
                self._log.warning("WARNING: different sequence names between feature '%s' and queryInterval '%s'. Will return 0 overlap." % (featuresName, queryName))
            
            lOrderedStart = [iFeature.getStart() for iFeature in self._lFeaturesToCheck]
            lOrderedEnd = [iFeature.getEnd() for iFeature in self._lFeaturesToCheck]
            
            lOrderedStart.sort()
            lOrderedEnd.sort()
            
            first = bisect.bisect_right(lOrderedStart, queryInterval.getEnd())
            last =  bisect.bisect_right(lOrderedEnd, queryInterval.getStart())
            return self._nbFeatures - (last +(self._nbFeatures - first))