Mercurial > repos > yufei-luo > s_mart
diff smart_toolShed/commons/core/coord/test/Test_Path.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smart_toolShed/commons/core/coord/test/Test_Path.py Thu Jan 17 10:52:14 2013 -0500 @@ -0,0 +1,146 @@ +# 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.Path import Path +from commons.core.coord.Align import Align +from commons.core.coord.Set import Set + + +class Test_Path( unittest.TestCase ): + + def setUp( self ): + self._path = Path() + + def test_setFromTuple( self ): + line = "1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2" + self._path.setFromTuple( line.split("\t") ) + self.assertEqual( self._path.id, 1 ) + self.assertEqual( self._path.range_query.seqname, "chr1" ) + self.assertEqual( self._path.range_query.start, 1 ) + self.assertEqual( self._path.range_query.end, 10 ) + self.assertEqual( self._path.range_subject.seqname, "TE2" ) + self.assertEqual( self._path.range_subject.start, 11 ) + self.assertEqual( self._path.range_subject.end, 17 ) + self.assertEqual( self._path.e_value, float("1e-20") ) + self.assertEqual( self._path.score, float("30") ) + self.assertEqual( self._path.identity, float("90.2") ) + + def test___eq__( self ): + self._path.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) + o = Path() + o.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) + self.assertEqual( self._path, o ) + o.setFromString( "2\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) + self.assertNotEqual( self._path, o ) + o.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t3000000\t90.2\n" ) + self.assertNotEqual( self._path, o ) + + def test_canMerge( self ): + tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") + self._path.setFromTuple(tuple) + tuple = ("2", "chr1","2", "9","TE2","10","13","1e-20","30","90.2") + o = Path() + o.setFromTuple(tuple) + self.assertTrue(self._path.canMerge(o)) + + def test_canMerge_on_same_id ( self ): + tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") + self._path.setFromTuple(tuple) + tuple = ("1", "chr1","2", "9","TE2","10","13","1e-20","30","90.2") + o = Path() + o.setFromTuple(tuple) + self.assertFalse(self._path.canMerge(o)) + + def test_canMerge_on_same_chr( self ): + tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") + self._path.setFromTuple(tuple) + tuple = ("2", "chr2","2", "9","TE2","10","13","1e-20","30","90.2") + o = Path() + o.setFromTuple(tuple) + self.assertFalse(self._path.canMerge(o)) + + def test_canMerge_on_diff_subj( self ): + tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") + self._path.setFromTuple(tuple) + tuple = ("2", "chr1","2", "9","TE3","10","13","1e-20","30","90.2") + o = Path() + o.setFromTuple(tuple) + self.assertFalse(self._path.canMerge(o)) + + def test_canMerge_on_queries_that_do_not_overlap( self ): + tuple = ("1", "chr1","5", "11","TE2","11","17","1e-20","30","90.2") + self._path.setFromTuple(tuple) + tuple = ("2", "chr1","1", "4","TE2","10","13","1e-20","30","90.2") + o = Path() + o.setFromTuple(tuple) + self.assertFalse(self._path.canMerge(o)) + + def test_canMerge_on_subjects_that_do_not_overlap( self ): + tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") + self._path.setFromTuple(tuple) + tuple = ("2", "chr1","2", "9","TE2","1","10","1e-20","30","90.2") + o = Path() + o.setFromTuple(tuple) + self.assertFalse(self._path.canMerge(o)) + + def test_getSubjectAsSetOfQuery( self ): + tuple = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2") + self._path.setFromTuple(tuple) + exp = Set(1,"TE2","chr1",1,10) + obs = self._path.getSubjectAsSetOfQuery() + self.assertEqual( exp, obs ) + + def test_getSubjectAsSetOfQuery_on_neg_strand( self ): + tuple = ("1","chr1","10","1","TE2","11","17","1e-20","30","90.2") + self._path.setFromTuple(tuple) + exp = Set(1,"TE2","chr1",10,1) + obs = self._path.getSubjectAsSetOfQuery() + self.assertEqual( exp, obs ) + + def test_toString( self ): + self._path.setFromString( "1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t85.2\n" ) + exp = "1\tchr1\t1\t10\tTE3\t11\t17\t%g\t30\t%f" % ( 1e-20, 85.2 ) + obs = self._path.toString() + self.assertEqual( obs, exp ) + + def test_getAlignInstance( self ): + self._path.setFromTuple( ( "2", "chr3", "250", "151", "seq5", "1", "100", "1e-32", "147", "87.9" ) ) + expAlign = Align() + expAlign.setFromTuple( ( "chr3", "151", "250", "seq5", "100", "1", "1e-32", "147", "87.9" ) ) + obsAlign = self._path.getAlignInstance() + self.assertEqual( expAlign, obsAlign ) + + +test_suite = unittest.TestSuite() +test_suite.addTest( unittest.makeSuite( Test_Path ) ) +if __name__ == "__main__": + unittest.TextTestRunner(verbosity=2).run( test_suite )