diff commons/core/coord/test/Test_Align.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/coord/test/Test_Align.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,518 @@
+# 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 unittest
+import os
+import time
+from commons.core.coord.Align import Align
+from commons.core.coord.Map import Map
+from commons.core.utils.FileUtils import FileUtils
+from commons.core.coord.Range import Range
+
+
+class Test_Align( unittest.TestCase ):
+    
+    def setUp(self):
+        self._align = Align()
+        self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() )
+        
+    def tearDown(self):
+        self._align = None
+        
+    def test_isEmpty_True(self):
+        alignInstance = Align()
+        
+        self.assertTrue(alignInstance.isEmpty())
+        
+    def test_isEmpty_True_query_is_empty(self):
+        alignInstance = Align()
+        line = "\t-1\t-1\tTE2\t3\t10\t1e-20\t30\t90.2\n"
+        alignInstance.setFromString(line)
+        
+        self.assertTrue(alignInstance.isEmpty())
+        
+    def test_isEmpty_True_subject_is_empty(self):
+        alignInstance = Align()
+        line = "chr1\t2\t20\t\t-1\t-1\t1e-20\t30\t90.2\n"
+        alignInstance.setFromString(line)
+        
+        self.assertTrue(alignInstance.isEmpty())
+        
+    def test_isEmpty_False(self):
+        alignInstance = Align()
+        line = "chr1\t2\t20\tTE2\t3\t10\t1e-20\t30\t90.2\n"
+        alignInstance.setFromString(line)
+        
+        self.assertFalse(alignInstance.isEmpty())
+        
+    def test_read(self):
+        line = "chr2\t1\t10\tTE3\t11\t17\t1e-20\t30\t90.2\n"
+        expReturn = 1
+
+        dummyMockAlignFile = "dummyMockAlignFile"
+        mockAlignFileHandle = open(dummyMockAlignFile, "w")
+        mockAlignFileHandle.write(line)
+        mockAlignFileHandle.close()
+        
+        expAlignInstance = Align()
+        expAlignInstance.setFromString(line)
+
+        mockAlignFileHandle = open(dummyMockAlignFile, "r")
+        obsAlignInstance = Align()
+        obsReturn = obsAlignInstance.read(mockAlignFileHandle)
+        
+        mockAlignFileHandle.close()
+        os.remove(dummyMockAlignFile)   
+        
+        self.assertEquals(expAlignInstance, obsAlignInstance)    
+        self.assertEquals(expReturn, obsReturn)    
+        
+    def test_read_empty_file(self):
+        expReturn = 0
+         
+        dummyMockAlignFile = "dummyMockAlignFile"
+        mockAlignFileHandle = open(dummyMockAlignFile, "w")
+        mockAlignFileHandle.close()
+       
+        mockAlignFileHandle = open(dummyMockAlignFile, "r")
+        obsAlignInstance = Align()
+        obsReturn = obsAlignInstance.read(mockAlignFileHandle)
+        os.remove(dummyMockAlignFile)   
+        
+        self.assertEquals(expReturn, obsReturn)
+        
+    def test_write (self):
+        expAlignFile = "expMockAlignFile"
+        expAlignFileHandle = open(expAlignFile, "w")
+        expLine = "chr1\t1\t10\tTE2\t3\t10\t0\t30\t90.200000\n"
+        expAlignFileHandle.write(expLine)
+        expAlignFileHandle.close()
+       
+        obsAlignFile = "obsAlignFile"
+        obsAlignFileHandle = open(obsAlignFile, "w")
+        obsAlignInstance = Align()
+        obsAlignTuple = ("chr1", 1, 10, "TE2", 3, 10, 0.0, 30, 90.2)
+        obsAlignInstance.setFromTuple(obsAlignTuple) 
+        obsAlignInstance.write(obsAlignFileHandle)
+        obsAlignFileHandle.close()   
+        
+        self.assertTrue( FileUtils.are2FilesIdentical( expAlignFile, obsAlignFile ) )
+        os.remove(expAlignFile)
+        os.remove(obsAlignFile)
+        
+    def test_merge (self):
+        alignInstanceChr1 = Align()
+        alignInstanceChr2 = Align()
+
+        line1 = "chr1\t1\t10\tTE2\t3\t10\t1e-20\t30\t90.2\n"
+        line2 = "chr2\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n"
+
+        alignInstanceChr1.setFromString(line1)
+        alignInstanceChr2.setFromString(line2)
+        
+        expResult = None
+        obsResult = alignInstanceChr1.merge(alignInstanceChr2)
+        
+        self.assertEquals(expResult, obsResult)
+        
+        line1 = "chr1\t1\t10\tTE2\t3\t10\t1e-20\t30\t90.2\n"
+        line2 = "chr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t90.2\n"
+
+        alignInstanceTE2 = Align()
+        alignInstanceTE3 = Align()
+ 
+        alignInstanceTE2.setFromString(line1)
+        alignInstanceTE3.setFromString(line2)
+        
+        expResult = None
+        obsResult = alignInstanceTE2.merge(alignInstanceTE3)
+        
+        self.assertEquals(expResult, obsResult)
+        
+    def test_merge_plus_strand1 (self):
+        alignInstance1 = Align()
+        alignInstance2 = Align()
+
+        line1 = "chr1\t2\t20\tTE2\t3\t10\t1e-20\t30\t90.2\n"
+        line2 = "chr1\t1\t10\tTE2\t1\t9\t1e-20\t30\t90.2\n"
+
+        alignInstance1.setFromString(line1)
+        alignInstance2.setFromString(line2)
+        
+        expLine = "chr1\t1\t20\tTE2\t1\t10\t1e-20\t30\t90.2\n"
+        expAlign = Align()
+        expAlign.setFromString(expLine)
+
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+
+        self.assertEquals(expAlign, obsAlign)
+        
+    def test_merge_plus_strand2 (self ):
+        alignInstance1 = Align()
+        alignInstance2 = Align()
+
+        line1 = "chr1\t2\t20\tTE2\t3\t10\t1e-20\t30\t90.2\n"
+        line2 = "chr1\t4\t30\tTE2\t4\t12\t1e-20\t30\t90.2\n"
+
+        alignInstance1.setFromString(line1)
+        alignInstance2.setFromString(line2)
+        
+        expLine = "chr1\t2\t30\tTE2\t3\t12\t1e-20\t30\t90.2\n"
+        expAlign = Align()
+        expAlign.setFromString(expLine)
+
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+
+        self.assertEquals(expAlign, obsAlign)
+        
+    def test_merge_plus_strand3 (self ):
+        alignInstance1 = Align()
+        alignInstance2 = Align()
+
+        line1 = "chr1\t2\t10\tTE2\t3\t10\t1e-20\t30\t90.2\n"
+        line2 = "chr1\t1\t20\tTE2\t1\t12\t1e-20\t30\t90.2\n"
+
+        alignInstance1.setFromString(line1)
+        alignInstance2.setFromString(line2)
+        
+        expLine = "chr1\t1\t20\tTE2\t1\t12\t1e-20\t30\t90.2\n"
+        expAlign = Align()
+        expAlign.setFromString(expLine)
+
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+
+        self.assertEquals(expAlign, obsAlign)
+        
+    def test_merge_plus_strand4 (self ):
+        alignInstance1 = Align()
+        alignInstance2 = Align()
+
+        line1 = "chr1\t1\t20\tTE2\t1\t12\t1e-20\t30\t90.2\n"
+        line2 = "chr1\t2\t10\tTE2\t2\t10\t1e-20\t30\t90.2\n"
+
+        alignInstance1.setFromString(line1)
+        alignInstance2.setFromString(line2)
+        
+        expLine = "chr1\t1\t20\tTE2\t1\t12\t1e-20\t30\t90.2\n"
+        expAlign = Align()
+        expAlign.setFromString(expLine)
+
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+
+        self.assertEquals(expAlign, obsAlign)
+        
+    def test_merge__neg_strand1 (self):
+
+        rangeQuery1 = Range("chr1", 20, 2); rangeSubject1 = Range("TE2", 10, 3)
+        rangeQuery2 = Range("chr1", 1, 10); rangeSubject2 = Range("TE2", 1, 9)
+
+        alignInstance1 = Align(rangeQuery1, rangeSubject1, 0, 30, 90.2)
+        alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.2)
+        
+        expRangeQuery = Range("chr1", 20, 1); expRangeSubject = Range("TE2", 10, 1)
+        expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.2)
+
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+        
+        self.assertEquals(expAlign, obsAlign)
+        
+    def test_merge__neg_strand2 (self):
+        rangeQuery1 = Range("chr1", 20, 2); rangeSubject1 = Range("TE2", 10, 3)
+        rangeQuery2 = Range("chr1", 4, 30); rangeSubject2 = Range("TE2", 4, 12)
+
+        alignInstance1 = Align(rangeQuery1, rangeSubject1, 0, 30, 90.2)
+        alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.2)
+        
+        expRangeQuery = Range("chr1", 30, 2); expRangeSubject = Range("TE2", 12, 3)
+        expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.2)
+
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+
+        self.assertEquals(expAlign, obsAlign)
+        
+    def test_merge_neg_strand3 (self ):
+        rangeQuery1 = Range("chr1", 10, 2); rangeSubject1 = Range("TE2", 10, 3)
+        rangeQuery2 = Range("chr1", 1, 20); rangeSubject2 = Range("TE2", 1, 12)
+
+        alignInstance1 = Align(rangeQuery1, rangeSubject1, 0, 30, 90.2)
+        alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.2)
+       
+        expRangeQuery = Range("chr1", 20, 1); expRangeSubject = Range("TE2", 12, 1)
+        expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.2)
+
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+
+        self.assertEquals(expAlign, obsAlign)
+        
+    def test_merge_neg_strand4 (self ):
+        rangeQuery1 = Range("chr1", 20, 1); rangeSubject1 = Range("TE2", 12, 1)
+        rangeQuery2 = Range("chr1", 2, 10); rangeSubject2 = Range("TE2", 2, 10)
+
+        alignInstance1 = Align(rangeQuery1, rangeSubject1, 0, 30, 90.2)
+        alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.2)
+        
+        expRangeQuery = Range("chr1", 20, 1); expRangeSubject = Range("TE2", 12, 1)
+        expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.2)
+
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+
+        self.assertEquals(expAlign, obsAlign)
+        
+    def test_merge_id_score_identity_eValue (self):
+        rangeQuery1 = Range("chr1", 20, 1); rangeSubject1 = Range("TE2", 12, 1)
+        rangeQuery2 = Range("chr1", 2, 10); rangeSubject2 = Range("TE2", 2, 10)
+
+        alignInstance1 = Align(rangeQuery1, rangeSubject1, 0.05, 20, 90.2)
+        alignInstance1.id = 1
+        alignInstance2 = Align(rangeQuery2, rangeSubject2, 0, 30, 90.3)
+        alignInstance2.id = 2
+
+        expRangeQuery = Range("chr1", 20, 1); expRangeSubject = Range("TE2", 12, 1)
+        expAlign = Align(expRangeQuery, expRangeSubject, 0, 30, 90.3)
+        expAlign.id = 1
+        
+        alignInstance1.merge(alignInstance2)
+        obsAlign = alignInstance1
+
+        self.assertEquals(expAlign, obsAlign)
+        self.assertEquals(expAlign.id, obsAlign.id)
+        
+    def test_setFromTuple_QryRev(self):
+        self._align.setFromTuple( ( "qry1", 100, 1, "sbj1", 201, 300, 0.0, 135, 97.2 ) )
+        self.assertEqual( self._align.range_query.seqname, "qry1" )
+        self.assertEqual( self._align.range_query.start, 1 )
+        self.assertEqual( self._align.range_query.end, 100 )
+        self.assertEqual( self._align.range_subject.seqname, "sbj1" )
+        self.assertEqual( self._align.range_subject.start, 300 )
+        self.assertEqual( self._align.range_subject.end, 201 )
+        self.assertEqual( self._align.e_value, 0.0 )
+        self.assertEqual( self._align.score, 135 )
+        self.assertEquals( self._align.identity, 97.2 )
+        
+    def test_setFromTuple_identityAsFloat(self):
+        self._align.setFromTuple( ( "qry1", "301", "600", "sbj1", "1", "300", "0.0", "135", 0.0) )
+        self.assertEqual( self._align.range_query.seqname, "qry1" )
+        self.assertEqual( self._align.range_query.start, 301 )
+        self.assertEqual( self._align.range_query.end, 600 )
+        self.assertEqual( self._align.range_subject.seqname, "sbj1" )
+        self.assertEqual( self._align.range_subject.start, 1 )
+        self.assertEqual( self._align.range_subject.end, 300 )
+        self.assertEqual( self._align.e_value, float("0.0") )
+        self.assertEqual( self._align.score, float("135") )
+        self.assertEquals( self._align.identity, 0.0 )
+        
+    def test_setFromString(self):
+        line = "chr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2\n"
+        self._align.setFromString( line )
+        self.assertEqual( self._align.range_query.seqname, "chr1" )
+        self.assertEqual( self._align.range_query.start, 1 )
+        self.assertEqual( self._align.range_query.end, 10 )
+        self.assertEqual( self._align.range_subject.seqname, "TE2" )
+        self.assertEqual( self._align.range_subject.start, 11 )
+        self.assertEqual( self._align.range_subject.end, 17 )
+        self.assertEqual( self._align.e_value, float("1e-20") )
+        self.assertEqual( self._align.score, float("30") )
+        self.assertEquals( float(self._align.identity), float("90.2") )
+        
+    def test__eq__(self):
+        self._align.setFromString( "chr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
+        o = Align()
+        o.setFromString( "chr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
+        self.assertEqual( self._align,  o )
+        o.setFromString( "chromosome1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
+        self.assertNotEqual( self._align, o )
+        o.setFromString( "chr1\t1\t6\ttranspElem2\t11\t16\t1e-20\t30\t90.2\n" )
+        self.assertNotEqual( self._align, o )
+        o.setFromString( "chr1\t100\t600\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
+        self.assertNotEqual( self._align, o )
+        o.setFromString( "chr1\t1\t6\tTE2\t1100\t1600\t1e-20\t30\t90.2\n" )
+        self.assertNotEqual( self._align, o )
+        o.setFromString( "chr1\t1\t6\tTE2\t11\t16\t1e-20\t30000\t90.2\n" )
+        self.assertNotEqual( self._align, o )
+        
+    def test_getSubjectAsMapOfQuery_direct(self):
+        exp = Map( name="TE2", seqname="chr1", start=1, end=6 )
+        self._align.setFromString( "chr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" )
+        obs = self._align.getSubjectAsMapOfQuery()
+        self.assertEqual( obs, exp )
+        
+    def test_getSubjectAsMapOfQuery_reverse(self):
+        exp = Map( name="TE2", seqname="chr1", start=6, end=1 )
+        self._align.setFromString( "chr1\t1\t6\tTE2\t16\t11\t1e-20\t30\t90.2\n" )
+        obs = self._align.getSubjectAsMapOfQuery()
+        self.assertEqual( obs, exp )
+        
+    def test_writeSubjectAsMapOfQuery( self ):
+        self._align.setFromTuple( ( "chr3", "250", "151", "seq5", "1", "100", "1e-32", "147", "87.9" ) )
+        expFile = "dummyExpFile_%s" % ( self._uniqId )
+        expFileHandler = open( expFile, "w" )
+        expFileHandler.write( "seq5\tchr3\t250\t151\n" )
+        expFileHandler.close()
+        obsFile = "dummyObsFile_%s" % ( self._uniqId )
+        obsFileHandler = open( obsFile, "w" )
+        self._align.writeSubjectAsMapOfQuery( obsFileHandler )
+        obsFileHandler.close()
+        self.assertTrue( FileUtils.are2FilesIdentical( expFile, obsFile ) )
+        for f in [ expFile, obsFile ]:
+            if os.path.exists( f ):
+                os.remove( f )
+                
+    def test_areQrySbjOnOppositeStrands(self):
+        self._align.setFromTuple( ( "qry1", "1", "100", "sbj1", "1", "100", "0.0", "135", "95.7" ) )
+        obs = self._align.areQrySbjOnOppositeStrands()
+        self.assertFalse( obs )
+        self._align.setFromTuple( ( "qry1", "600", "301", "sbj1", "1", "300", "0.0", "135", "95.7" ) )
+        obs = self._align.areQrySbjOnOppositeStrands()
+        self.assertTrue( obs )
+        
+    def test_reverse(self):
+        line = "chr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2"
+        expLine = "chr1\t10\t1\tTE2\t17\t11\t1e-20\t30\t90.200000"
+        
+        obsAlignInstance = Align()
+        obsAlignInstance.setFromString(line)
+        obsAlignInstance.reverse()
+        obsLine = obsAlignInstance.toString()
+
+        self.assertEquals(expLine, obsLine)
+        
+    def test_getMapsOfQueryAndSubject(self):
+        self._align.setFromTuple( ( "qry1", "1", "100", "sbj1", "1", "100", "0.0", "135", "95.7" ) )
+        
+        expMapQuery = Map()
+        expMapQuery.setFromTuple( ( "repet", "qry1", "1", "100" ) )
+        expMapSubject = Map()
+        expMapSubject.setFromTuple( ( "repet", "sbj1", "1", "100" ) )
+        
+        obsMapQuery, obsMapSubject = self._align.getMapsOfQueryAndSubject()
+        
+        self.assertEqual( expMapQuery, obsMapQuery )
+        self.assertEqual( expMapSubject, obsMapSubject )
+        
+    def test_getBin_bin_level_9(self):
+        tuple = ("chr1","190000000","390000000","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        expRes = 100000000.0
+        obsRes = self._align.getBin()
+        self.assertEquals(expRes, obsRes)
+
+    def test_getBin_bin_level_8(self):
+        tuple = ("chr1","19000000","39000000","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        expRes = 100000000.0
+        obsRes = self._align.getBin()
+        self.assertEquals(expRes, obsRes)
+        
+    def test_getBin_bin_level_7(self):
+        tuple = ("chr1","1900000","3900000","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        expRes = 10000000.0
+        obsRes = self._align.getBin()
+        self.assertEquals(expRes, obsRes)
+        
+    def test_getBin_bin_level_6(self):
+        tuple = ("chr1","190000","390000","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        obsRes = self._align.getBin()
+        expRes = 1000000.0
+        self.assertEquals(expRes, obsRes)
+        
+    def test_getBin_bin_level_5(self):
+        tuple = ("chr1","19000","39000","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        obsRes = self._align.getBin()
+        expRes = 100000.0
+        self.assertEquals(expRes, obsRes)
+        
+    def test_getBin_bin_level_4(self):
+        tuple = ("chr1","1900","3900","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        obsRes = self._align.getBin()
+        expRes = 10000.0
+        self.assertEquals(expRes, obsRes)
+        
+    def test_getBin_bin_level_3(self):
+        tuple = ("chr1","190","390","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        obsRes = self._align.getBin()
+        expRes = 1000.0
+        self.assertEquals(expRes, obsRes)
+        
+    def test_getBin_bin_level_2(self):
+        tuple = ("chr1","19","39","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        obsRes = self._align.getBin()
+        expRes = 1000.0
+        self.assertEquals(expRes, obsRes)
+        
+    def test_getBin_bin_level_1(self):
+        tuple = ("chr1","1","3","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple(tuple)
+        obsRes = self._align.getBin()
+        expRes = 1000.0
+        self.assertEquals(expRes, obsRes)
+        
+        
+    def test_switchQuerySubject_directS( self ):
+        tuple = ("chr1","1","3","TE2","11","17","1e-20","30","90.2")
+        self._align.setFromTuple( tuple )
+        exp = Align( Range("TE2","11","17"), Range("chr1","1","3"), "1e-20", "30", "90.2" )
+        self._align.switchQuerySubject()
+        self.assertEquals( exp, self._align )
+        
+        
+    def test_switchQuerySubject_reverseS( self ):
+        tuple = ("chr1","1","3","TE2","17","11","1e-20","30","90.2")
+        self._align.setFromTuple( tuple )
+        exp = Align( Range("TE2","11","17"), Range("chr1","3","1"), "1e-20", "30", "90.2" )
+        self._align.switchQuerySubject()
+        self.assertEquals( exp, self._align )
+        
+        
+    def test_toStringAsGff( self ):
+        self._align.setFromString( "chr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t85.2\n" )
+        exp = "chr1\tREPET\tmatch\t1\t10\t1e-20\t+\t.\tID=23;Target=TE3 11 17"
+        obs = self._align.toStringAsGff( ID="23" )
+        self.assertEqual( obs, exp )
+        
+        
+test_suite = unittest.TestSuite()
+test_suite.addTest( unittest.makeSuite( Test_Align ) )
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run( test_suite )