diff smart_toolShed/commons/core/coord/test/Test_Match.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/test/Test_Match.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,363 @@
+# 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
+from commons.core.coord.Match import Match
+from commons.core.coord.Path import Path
+
+
+class Test_Match( unittest.TestCase ):
+    
+    def test_eq_match_equals( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_query_name( self ):
+        tuple1 = ("Name", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_query_start( self ):
+        tuple1 = ("QName", 2, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_query_end( self ):
+        tuple1 = ("QName", 1, 6, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_query_length( self ):
+        tuple1 = ("QName", 1, 5, 6, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_query_length_perc( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.15, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_match_length_perc( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.25, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_name( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "Name", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_start( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 6, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_end( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 26, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_length( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 21, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_length_perc( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.16, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_e_value( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-21, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_score( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 16, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_identity( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 85.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_eq_match_not_equals_subject_id( self ):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 2)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertNotEquals( match1, match2 )
+        
+    def test_setFromTuple_direct_strand( self ):
+        tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        obsMatch = Match()
+        obsMatch.setFromTuple(tuple)
+        expMatch = Match()
+        expMatch.range_query.seqname = "QName"
+        expMatch.range_query.start = 1
+        expMatch.range_query.end = 5
+        expMatch.query_length = 5
+        expMatch.query_length_perc = 0.1
+        expMatch.match_length_perc = 0.2
+        expMatch.range_subject.seqname = "SName"
+        expMatch.range_subject.start = 5
+        expMatch.range_subject.end = 25
+        expMatch.subject_length = 20
+        expMatch.subject_length_perc = 0.15
+        expMatch.e_value = 1e-20
+        expMatch.score = 15
+        expMatch.identity = 87.2
+        expMatch.id = 1
+        expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
+        expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
+        self.assertEquals( expMatch, obsMatch )
+   
+    def test_setFromTuple_reverse_strand_on_subject( self ):
+        tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 25, 5, 20, 0.15, 1e-20, 15, 87.2, 1)
+        obsMatch = Match()
+        obsMatch.setFromTuple(tuple)
+        expMatch = Match()
+        expMatch.range_query.seqname = "QName"
+        expMatch.range_query.start = 1
+        expMatch.range_query.end = 5
+        expMatch.query_length = 5
+        expMatch.query_length_perc = 0.1
+        expMatch.match_length_perc = 0.2
+        expMatch.range_subject.seqname = "SName"
+        expMatch.range_subject.start = 25
+        expMatch.range_subject.end = 5
+        expMatch.subject_length = 20
+        expMatch.subject_length_perc = 0.15
+        expMatch.e_value = 1e-20
+        expMatch.score = 15
+        expMatch.identity = 87.2
+        expMatch.id = 1
+        expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
+        expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
+        self.assertEquals( expMatch, obsMatch )
+        
+    def test_setFromTuple_reverse_strand_on_query( self ):
+        tuple = ("QName", 5, 1, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        obsMatch = Match()
+        obsMatch.setFromTuple(tuple)
+        expMatch = Match()
+        expMatch.range_query.seqname = "QName"
+        expMatch.range_query.start = 1
+        expMatch.range_query.end = 5
+        expMatch.query_length = 5
+        expMatch.query_length_perc = 0.1
+        expMatch.match_length_perc = 0.2
+        expMatch.range_subject.seqname = "SName"
+        expMatch.range_subject.start = 25
+        expMatch.range_subject.end = 5
+        expMatch.subject_length = 20
+        expMatch.subject_length_perc = 0.15
+        expMatch.e_value = 1e-20
+        expMatch.score = 15
+        expMatch.identity = 87.2
+        expMatch.id = 1
+        expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
+        expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
+        self.assertEquals( expMatch, obsMatch )
+        
+    def test_setFromTuple_reverse_strand_on_query_and_subject( self ):
+        tuple = ("QName", 5, 1, 5, 0.1, 0.2, "SName", 25, 5, 20, 0.15, 1e-20, 15, 87.2, 1)
+        obsMatch = Match()
+        obsMatch.setFromTuple(tuple)
+        expMatch = Match()
+        expMatch.range_query.seqname = "QName"
+        expMatch.range_query.start = 1
+        expMatch.range_query.end = 5
+        expMatch.query_length = 5
+        expMatch.query_length_perc = 0.1
+        expMatch.match_length_perc = 0.2
+        expMatch.range_subject.seqname = "SName"
+        expMatch.range_subject.start = 5
+        expMatch.range_subject.end = 25
+        expMatch.subject_length = 20
+        expMatch.subject_length_perc = 0.15
+        expMatch.e_value = 1e-20
+        expMatch.score = 15
+        expMatch.identity = 87.2
+        expMatch.id = 1
+        expMatch.subject_seqlength = int( expMatch.subject_length / expMatch.subject_length_perc )
+        expMatch.query_seqlength = int( expMatch.query_length / expMatch.query_length_perc )
+        self.assertEquals( expMatch, obsMatch )
+        
+    def test_toString( self ):        
+        tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match = Match()
+        match.setFromTuple(tuple)
+        expString = "QName\t1\t5\t5\t%f\t%f\tSName\t5\t25\t20\t%f\t%g\t15\t%f\t1" % (0.1,0.2,0.15,1e-20, 87.2)
+        obsString = match.toString()
+        self.assertEquals(expString, obsString)
+        
+    def test_getPathInstance( self ):
+        tuple = ( "QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1 )
+        match = Match()
+        match.setFromTuple( tuple )
+        tuple = ( 1, "QName", 1, 5, "SName", 5, 25, 1e-20, 15, 87.2 )
+        exp = Path()
+        exp.setFromTuple( tuple )
+        obs = match.getPathInstance()
+        self.assertEqual( exp, obs )
+        
+    def test_getQryIsIncluded(self):
+        tuple = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match = Match()
+        match.setFromTuple(tuple)
+        expString = "query QName (50 bp: 1-5) is contained in subject SName (133 bp: 5-25): id=87.20 - 0.100 - 0.200 - 0.150"
+        obsString = match.getQryIsIncluded()
+        self.assertEquals(expString, obsString)
+        
+    def test_isDoublonWith_Matchs_equals(self):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertTrue(match1.isDoublonWith(match2))
+        
+    def test_isDoublonWith_Matchs_unequals_on_MatchNumbers(self):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 86.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertFalse(match1.isDoublonWith(match2))
+        
+    def test_isDoublonWith_Matchs_unequals_on_SeqNames(self):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 5, 5, 0.1, 0.2, "Name", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertFalse(match1.isDoublonWith(match2))
+        
+    def test_isDoublonWith_Matchs_unequals_on_Coordinates(self):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("QName", 1, 6, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertFalse(match1.isDoublonWith(match2))
+        
+    def test_isDoublonWith_Reversed_Matchs_equals(self):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("SName", 5, 25, 20, 0.15, 0.2, "QName", 1, 5, 5, 0.1, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertTrue(match1.isDoublonWith(match2))
+        
+    def test_isDoublonWith_Reversed_Matchs_unequals(self):
+        tuple1 = ("QName", 1, 5, 5, 0.1, 0.2, "SName", 5, 25, 20, 0.15, 1e-20, 15, 87.2, 1)
+        match1 = Match()
+        match1.setFromTuple(tuple1)
+        tuple2 = ("SName", 5, 25, 20, 0.15, 0.2, "QName", 1, 6, 5, 0.1, 1e-20, 15, 87.2, 1)
+        match2 = Match()
+        match2.setFromTuple(tuple2)
+        self.assertFalse(match1.isDoublonWith(match2))
+        
+        
+test_suite = unittest.TestSuite()
+test_suite.addTest( unittest.makeSuite( Test_Match ) )
+if __name__ == "__main__":
+    unittest.TextTestRunner(verbosity=2).run( test_suite )