Python filter_aln_by_otus 예제들

예제 #1

파일: test_filter_otus_by_sample.py 프로젝트: Ecogenomics/FrankenQIIME

    def test_filter_aln_by_otus(self):
        """filter_aln_by_otus: determines which sequences to keep and which
sequences to remove"""

        self.sample_to_extract='SampleA,SampleB'
        exp1=[]
        exp1.append(('SampleA','AAAAAAAAAAAAAAA'))
        exp2=[]
        exp2.append(('SampleB','CCCCCCC'))
        exp2.append(('SampleC','GGGGGGGGGGGGGG'))
        aln=LoadSeqs(data=self.aln,aligned=False)

        obs1,obs2=filter_aln_by_otus(aln,self.prefs)

        self.assertEqual(obs1,exp1)
        self.assertEqual(obs2,exp2)

예제 #2

    def test_filter_aln_by_otus(self):
        """filter_aln_by_otus: determines which sequences to keep and which
sequences to remove"""

        self.sample_to_extract='SampleA,SampleB'
        exp1=[]
        exp1.append(('SampleA','AAAAAAAAAAAAAAA'))
        exp2=[]
        exp2.append(('SampleB','CCCCCCC'))
        exp2.append(('SampleC','GGGGGGGGGGGGGG'))
        aln=LoadSeqs(data=self.aln,aligned=False)

        obs1,obs2=filter_aln_by_otus(aln,self.prefs)

        self.assertEqual(obs1,exp1)
        self.assertEqual(obs2,exp2)

예제 #3

파일: test_filter_otus_by_sample.py 프로젝트: rob-knight/qiime

    def test_filter_aln_by_otus(self):
        """filter_aln_by_otus: determines which sequences to keep and which
sequences to remove"""

        self.sample_to_extract = "SampleA,SampleB"
        exp1 = []
        exp1.append(("SampleA", "AAAAAAAAAAAAAAA"))
        exp2 = []
        exp2.append(("SampleB", "CCCCCCC"))
        exp2.append(("SampleC", "GGGGGGGGGGGGGG"))
        aln = LoadSeqs(data=self.aln, aligned=False)

        obs1, obs2 = filter_aln_by_otus(aln, self.prefs)

        self.assertEqual(obs1, exp1)
        self.assertEqual(obs2, exp2)

예제 #4

파일: test_filter_otus_by_sample.py 프로젝트: Springbudder/qiime

    def test_filter_aln_by_otus(self):
        """filter_aln_by_otus: determines which sequences to keep and which
sequences to remove"""

        self.sample_to_extract = 'SampleA,SampleB'
        exp1 = []
        exp1.append(('SampleA', 'AAAAAAAAAAAAAAA'))
        exp2 = []
        exp2.append(('SampleB', 'CCCCCCC'))
        exp2.append(('SampleC', 'GGGGGGGGGGGGGG'))
        aln = SequenceCollection.from_fasta_records(self.aln, DNA)

        obs1, obs2 = filter_aln_by_otus(aln, self.prefs)

        self.assertEqual(obs1, exp1)
        self.assertEqual(obs2, exp2)

예제 #5

    def test_filter_aln_by_otus(self):
        """filter_aln_by_otus: determines which sequences to keep and which
sequences to remove"""

        self.sample_to_extract = 'SampleA,SampleB'
        exp1 = []
        exp1.append(('SampleA', 'AAAAAAAAAAAAAAA'))
        exp2 = []
        exp2.append(('SampleB', 'CCCCCCC'))
        exp2.append(('SampleC', 'GGGGGGGGGGGGGG'))
        aln = SequenceCollection.from_fasta_records(self.aln, DNA)

        obs1, obs2 = filter_aln_by_otus(aln, self.prefs)

        self.assertEqual(obs1, exp1)
        self.assertEqual(obs2, exp2)