diff TEisotools-1.1.a/commons/core/coord/CountOverlapping.py @ 16:836ce3d9d47a draft default tip

Uploaded

--- a/TEisotools-1.1.a/commons/core/coord/CountOverlapping.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,96 +0,0 @@
-# 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
-# abiding by the rules of distribution of free software.  You can  use, 
-# 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". 
-#
-# As a counterpart to the access to the source code and  rights to copy,
-# modify and redistribute granted by the license, users are provided only
-# with a limited warranty  and the software's author,  the holder of the
-# economic rights,  and the successive licensors  have only  limited
-# liability. 
-#
-# In this respect, the user's attention is drawn to the risks associated
-# with loading,  using,  modifying and/or developing or reproducing the
-# software by the user in light of its specific status of free software,
-# that may mean  that it is complicated to manipulate,  and  that  also
-# therefore means  that it is reserved for developers  and  experienced
-# professionals having in-depth computer knowledge. Users are therefore
-# encouraged to load and test the software's suitability as regards their
-# requirements in conditions enabling the security of their systems and/or 
-# data to be ensured and,  more generally, to use and operate it in the 
-# same conditions as regards security. 
-#
-# The fact that you are presently reading this means that you have had
-# knowledge of the CeCILL license and that you accept its terms.
-
-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))