diff TEisotools-1.0/commons/core/seq/SequenceModifications.py @ 6:20ec0d14798e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.0/commons/core/seq/SequenceModifications.py	Wed Jul 20 05:00:24 2016 -0400
@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+
+# 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 operator import itemgetter
+from commons.core.coord.Range import Range
+            
+class SequenceModifications(object):
+    
+    def __init__(self, originalHeader = "", mutatedHeader = ""):
+        self._originalHeader = originalHeader
+        self._mutatedHeader = mutatedHeader
+        self._lMutations = []
+        self._lDeletionsRanges = []
+        self._lInsertionsRanges = []
+        
+    def __str__(self):
+        result = "%s\t%s\n" % (self.getOriginalHeader(), self.getMutatedHeader())
+        result += "Insertions\n"
+        for insertion in self._lInsertionsRanges:
+            result += "%s\n" % insertion.toString()
+        result += "Deletions\n"
+        for insertion in self._lDeletionsRanges:
+            result += "%s\n" % insertion.toString()
+        result += "Mutations"
+        for mutation in self._lMutations:
+            result += "\n%i\t%s\t%s" % (mutation[0], mutation[1], mutation[2])
+        return result
+    
+    def __eq__(self, o):
+        if type(o) is type(self):
+            self.sort()
+            o.sort()
+            return self._originalHeader == o._originalHeader and self._mutatedHeader == o._mutatedHeader and self._lMutations == o._lMutations \
+                and self._lDeletionsRanges == o._lDeletionsRanges and self._lInsertionsRanges == o._lInsertionsRanges
+        return False
+            
+    def __ne__(self, o):
+        return not self.__eq__(o)
+                
+    def getOriginalHeader(self):
+        return self._originalHeader
+                
+    def getMutatedHeader(self):
+        return self._mutatedHeader
+        
+    def getMutations(self):
+        self.sort()
+        return self._lMutations
+    
+    def getInsertions(self):
+        self.sort()
+        return self._lInsertionsRanges
+    
+    def getDeletions(self):
+        self.sort()
+        return self._lDeletionsRanges
+        
+    def setOriginalHeader(self, originalHeader):
+        self._originalHeader = originalHeader
+        
+    def setMutatedHeader(self, mutatedHeader):
+        self._mutatedHeader = mutatedHeader
+        
+    def setMutations(self, lMutations):
+        self._lMutations = lMutations
+        
+    def addMutation(self, tupleMute):
+        #tuple: (position, oldNT, newNT)
+        self._lMutations.append(tupleMute)
+        
+    def addInsertion(self, start, end, insertedSeqName = "."):
+        self._lInsertionsRanges.append(Range(insertedSeqName, start, end))
+        
+    def addDeletion(self, start, end):
+        self._lDeletionsRanges.append(Range(self.getOriginalHeader(), start, end))
+        
+    def clear(self):
+        self._lMutations = []
+        self._lDeletionsRanges = []
+        self._lInsertionsRanges = []
+        
+    def sort(self):
+        self._lMutations.sort(key = itemgetter(0), reverse = False)
+        self._lDeletionsRanges.sort(key = lambda delRange: delRange.getStart(), reverse = False)
+        self._lInsertionsRanges.sort(key = lambda insRange: insRange.getStart(), reverse = False)
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