view smart_toolShed/commons/core/coord/test/Test_Match.py @ 0:e0f8dcca02ed

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

# Copyright INRA (Institut National de la Recherche Agronomique)
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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 )