diff TEisotools-1.0/commons/core/coord/Path.py @ 6:20ec0d14798e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/commons/core/coord/Path.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,161 @@
+# 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.
+
+
+from commons.core.coord.Set import Set
+from commons.core.coord.Align import Align
+from commons.core.coord.Range import Range
+
+
+## Handle a match between two sequences, query and subject (pair of coordinates with E-value, score and identity) with an identifier
+#
+class Path( Align ):
+    
+    __slots__ = ("id")
+    
+    ## Constructor
+    #
+    # @param id identifier
+    # @param range_q: a Range instance for the query
+    # @param range_s: a Range instance for the subject
+    # @param e_value: E-value of the match 
+    # @param score: score of the match
+    # @param identity: identity percentage of the match
+    #
+    def __init__( self, id=-1, range_q=Range(), range_s=Range(), e_value=0, score=0, identity=0 ):
+        self.id = int( id )
+        Align.__init__( self, range_q, range_s, e_value, score, identity )
+        
+    ## Equal operator
+    #
+    def __eq__(self, o):
+        if type(o) is not type(self) or self.id != o.id:
+            return False
+        return Align.__eq__(self, o)
+
+    ## Not equal operator
+    #
+    def __ne__(self, o):
+        return not self.__eq__(o)
+    
+    ## repr
+    #
+    def __repr__(self):
+        return self.toString()
+    
+    ## Set attributes from tuple
+    #
+    # @param tuple a tuple with (id,queryName,queryStart,queryEnd,subjectName,subjectStar,subjectEnd,E-value,score,identity)
+    # @note data are loaded such that the query is always on the direct strand
+    #
+    def setFromTuple(self, tuple):
+        self.id = int(tuple[0])
+        Align.setFromTuple(self, tuple[1:])
+        
+    ## Reset
+    #
+    def reset(self):
+        self.id = -1
+        Align.reset(self)
+        
+    ## Return the attributes as a formatted string
+    #
+    def toString(self):
+        string = "%i" % ( self.id )
+        string += "\t%s" % (Align.toString(self))
+        return string
+    
+    
+    ## Return the identifier of the Path instance
+    #
+    def getIdentifier( self ):
+        return self.id
+    
+    ## Return a Set instance with the subject mapped on the query
+    #
+    def getSubjectAsSetOfQuery(self):
+        iSet = Set()
+        iSet.id = self.id
+        iSet.name = self.range_subject.seqname
+        iSet.seqname = self.range_query.seqname
+        if self.range_subject.isOnDirectStrand():
+            iSet.start = self.range_query.start
+            iSet.end = self.range_query.end
+        else:
+            iSet.start = self.range_query.end
+            iSet.end = self.range_query.start
+        return iSet
+    
+    #TODO: add tests !!!!
+    #WARNING: subject always in direct strand !!!
+    ## Return a Set instance with the subject mapped on the query
+    #
+    def getQuerySetOfSubject(self):
+        iSet = Set()
+        iSet.id = self.id
+        iSet.name = self.range_query.seqname
+        iSet.seqname = self.range_subject.seqname
+        if self.range_subject.isOnDirectStrand():
+            iSet.start = self.range_subject.start
+            iSet.end = self.range_subject.end
+        else:
+            iSet.start = self.range_subject.end
+            iSet.end = self.range_subject.start
+        return iSet
+    
+    ## Return True if the instance can be merged with another Path instance, False otherwise
+    #
+    # @param o a Path instance
+    #
+    def canMerge(self, o):
+        return o.id != self.id \
+            and o.range_query.seqname == self.range_query.seqname \
+            and o.range_subject.seqname == self.range_subject.seqname \
+            and o.range_query.isOnDirectStrand() == self.range_query.isOnDirectStrand() \
+            and o.range_subject.isOnDirectStrand() == self.range_subject.isOnDirectStrand() \
+            and o.range_query.isOverlapping(self.range_query) \
+            and o.range_subject.isOverlapping(self.range_subject)
+            
+    ## Return an Align instance with the same attributes, except the identifier
+    #
+    def getAlignInstance(self):
+        iAlign = Align()
+        lAttributes = []
+        lAttributes.append( self.range_query.seqname )
+        lAttributes.append( self.range_query.start )
+        lAttributes.append( self.range_query.end )
+        lAttributes.append( self.range_subject.seqname )
+        lAttributes.append( self.range_subject.start )
+        lAttributes.append( self.range_subject.end )
+        lAttributes.append( self.e_value )
+        lAttributes.append( self.score )
+        lAttributes.append( self.identity )
+        iAlign.setFromTuple( lAttributes )
+        return iAlign