diff commons/core/tree/test/Test_Tree.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/tree/test/Test_Tree.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,90 @@
+import unittest
+import os
+import time
+from commons.core.tree.Tree import Tree
+from commons.core.utils.FileUtils import FileUtils
+
+
+class Test_Tree( unittest.TestCase ):
+    
+    def setUp( self ):
+        self._tree = Tree()
+        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
+        
+        
+    def test_parseTree_oneLeaf( self ):
+        inString = "seq1:0.0023"
+        obs = self._tree.parseTree( inString )
+        exp = { "left":None, "right":None, "name":"seq1", "length":0.0023 }
+        self.assertEqual( obs, exp )
+        
+        
+    def test_parseTree_twoLeaves( self ):
+        inString = "(seq1:0.0023,seq2:0.0017)"
+        obs = self._tree.parseTree( inString )
+        exp = {'length':0, 'right':{'length':0.0016999999999999999, 'right':None, 'name':'seq2', 'left':None}, 'name':'internal', 'left':{'length':0.0023, 'right':None, 'name':'seq1', 'left':None}}
+        self.assertEqual( obs, exp )
+        
+##     def test_parseTree_threeLeaves( self ):
+##         inString = "(seq1:0.0023,(seq2:0.0017,seq3:0.0009))"
+##         obs = self._tree.parseTree( inString )
+##         print obs
+##         exp = {'length':0, 'right':{'length':0.0016999999999999999, 'right':None, 'name':'seq2', 'left':None}, 'name':'internal', 'left':{'length':0.0023, 'right':None, 'name':'seq1', 'left':None}}
+##         self.assertEqual( obs, exp )
+        
+        
+    def test_parseSubTree( self ):
+        inString = "(seq1:0.0023,seq2:0.0017)"
+        lExp = [ "seq1:0.0023", "seq2:0.0017" ]
+        lObs = self._tree.parseSubTree( inString )
+        self.assertEqual( lObs, lExp )
+        
+        
+    def test_saveTree( self ):
+        inFileName = "dummyInFile_%s" % ( self._uniqId )
+        inF = open( inFileName, "w" )
+        inF.write( "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))" )
+        inF.close()
+        self._tree = Tree( inFileName )
+        obsFileName = "dummyObsFile_%s" % ( self._uniqId )
+        self._tree.saveTree( obsFileName )
+        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, inFileName ) )
+        for f in [ inFileName, obsFileName ]:
+            os.remove( f )
+            
+            
+    def test_retrieveInitialSequenceHeaders( self ):
+        inString = "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))"
+        self._tree.tree = self._tree.parseTree( inString )
+        dNew2Init = { "seq2":"consensus524::215 dmel_chr4 142..765", "seq3":"DmelChr4-B-G387-MAP16", "seq4":"1360|1cl-3gr" }
+        expFileName = "dummyExpFile_%s"  % ( self._uniqId )
+        expF = open( expFileName, "w" )
+        expF.write( "(1360|1cl-3gr:0.012511,(DmelChr4-B-G387-MAP16:0.005340,consensus524-215_dmel_chr4_142..765:0.002201))" )
+        expF.close()
+        obsFileName = "dummyObsFile_%s"  % ( self._uniqId )
+        self._tree.retrieveInitialSequenceHeaders( dNew2Init, obsFileName )
+        self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
+        for f in [ expFileName, obsFileName ]:
+            os.remove( f )
+            
+            
+    def test_getNbOfLeaves( self ):
+        inString = "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))"
+        self._tree.tree = self._tree.parseTree( inString )
+        exp = 3
+        obs = self._tree.getNbOfLeaves()
+        self.assertEqual( obs, exp )
+        
+        
+    def test_getNbOfNodes( self ):
+        inString = "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))"
+        self._tree.tree = self._tree.parseTree( inString )
+        exp = 4
+        obs = self._tree.getNbOfNodes()
+        self.assertEqual( obs, exp )
+        
+        
+test_suite = unittest.TestSuite()
+test_suite.addTest( unittest.makeSuite( Test_Tree ) )
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run( test_suite )