diff smart_toolShed/commons/core/coord/Set.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/coord/Set.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,125 @@
+# 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.Map import Map
+
+
+## Record a named region on a given sequence with an identifier
+#  
+class Set( Map ):
+    
+    ## Constructor
+    #
+    # @param id identifier
+    # @param name the name of the region
+    # @param seqname the name of the sequence
+    # @param start the start coordinate
+    # @param end the end coordinate
+    #
+    def __init__(self, id=-1, name="", seqname="", start=-1, end=-1):
+        Map.__init__( self, name, seqname, start, end )
+        self.id = id
+        
+    ## Equal operator
+    #    
+    def __eq__(self, o):
+        if self.id != o.id:
+            return False
+        else:
+            return Map.__eq__(self, o)
+    
+    def getId(self):
+        return self.id
+        
+    ## Reset
+    #
+    def reset(self):
+        self.setFromTuple([-1, "", "", -1, -1 ])
+            
+    ## Set attributes from tuple
+    #
+    # @param tuple: a tuple with (id, name, seqname, start, end)
+    # 
+    def setFromTuple(self, tuple):
+        self.id = int(tuple[0])
+        Map.setFromTuple(self, tuple[1:])
+        
+    ## Return the attributes as a formatted string
+    #
+    def toString(self):
+        string = "%i" % (self.id)
+        string += "\t%s" % (Map.toString(self))
+        return string
+    
+    ## Merge the instance with another Set instance
+    #
+    # @param o a Set instance
+    #
+    def merge(self, o):
+        if self.seqname == o.seqname:
+            Map.merge(self, o)
+            self.id = min(self.id, o.id)
+    
+    ## Return a Map instance with the attributes
+    #
+    def getMap(self):
+        return Map(self.name, self.seqname, self.start, self.end)
+    
+    ## Remove in the instance the region overlapping with another Set instance
+    #
+    # @param o a Set instance
+    #  
+    def diff(self, o):
+        iMap = Map.diff(self, o.getMap())
+        new = Set()
+        if not iMap.isEmpty():
+            new.id = self.id
+            new.name = self.name
+            new.seqname = self.seqname
+            new.start = iMap.start
+            new.end = iMap.end
+        return new
+    
+    ## Return a Map instance with the identifier in the name
+    #
+    def set2map(self):
+        return Map(self.name+"::"+str(self.id),self.seqname,self.start,self.end)
+    
+    
+    def getMapInstance( self ):
+        iMap = Map()
+        lAttributes = []
+        lAttributes.append( self.name )
+        lAttributes.append( self.seqname )
+        lAttributes.append( self.start )
+        lAttributes.append( self.end )
+        iMap.setFromTuple( lAttributes )
+        return iMap