Mercurial > repos > yufei-luo > s_mart
view commons/core/coord/test/Test_Match.py @ 14:c79b9ae3f65f
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author | m-zytnicki |
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date | Fri, 19 Apr 2013 10:13:11 -0400 |
parents | 769e306b7933 |
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# 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 )