Ejemplo n.º 1
0
 def _simple_annotate(self, is_skip_no_alts):
     runSpec = RunSpecification()
     runSpec.initialize(None,
                        None,
                        datasources=[],
                        is_skip_no_alts=is_skip_no_alts)
     # Initialize the annotator with the runspec
     annotator = Annotator()
     annotator.initialize(runSpec)
     m = MutationData()
     m.chr = "1"
     m.start = "12941796"
     m.end = "12941796"
     m.alt_allele = "G"
     m.ref_allele = "T"
     m.createAnnotation("alt_allele_seen", "False")
     m2 = MutationData()
     m2.chr = "1"
     m2.start = "12941796"
     m2.end = "12941796"
     m2.alt_allele = "G"
     m2.ref_allele = "T"
     muts = [m, m2]
     muts = annotator.annotate_mutations(muts)
     ctr = 0
     for m in muts:
         ctr += 1
     return ctr
Ejemplo n.º 2
0
    def testAnnotateListOfMutations(self):
        """Test that we can initialize an Annotator, without an input or output and then feed mutations,
        one at a time... using a runspec"""

        # Locate the datasource directory and create a runspec
        dbDir = self.config.get("DEFAULT", "dbDir")
        ds = DatasourceFactory.createDatasources(dbDir)
        runSpec = RunSpecification()
        runSpec.initialize(None, None, datasources=ds)

        # Initialize the annotator with the runspec
        annotator = Annotator()
        annotator.initialize(runSpec)

        m = MutationData()
        m.chr = "1"
        m.start = "12941796"
        m.end = "12941796"
        m.alt_allele = "G"
        m.ref_allele = "T"

        muts = [m]

        muts = annotator.annotate_mutations(muts)
        m2 = muts.next()
        self.assertTrue(m2.get("gene", None) is not None)
Ejemplo n.º 3
0
 def _simple_annotate(self, is_skip_no_alts):
     runSpec = RunSpecification()
     runSpec.initialize(None, None, datasources=[], is_skip_no_alts=is_skip_no_alts)
     # Initialize the annotator with the runspec
     annotator = Annotator()
     annotator.initialize(runSpec)
     m = MutationData()
     m.chr = "1"
     m.start = "12941796"
     m.end = "12941796"
     m.alt_allele = "G"
     m.ref_allele = "T"
     m.createAnnotation("alt_allele_seen", "False")
     m2 = MutationData()
     m2.chr = "1"
     m2.start = "12941796"
     m2.end = "12941796"
     m2.alt_allele = "G"
     m2.ref_allele = "T"
     muts = [m, m2]
     muts = annotator.annotate_mutations(muts)
     ctr = 0
     for m in muts:
         ctr += 1
     return ctr
Ejemplo n.º 4
0
    def testAnnotateListOfMutations(self):
        """Test that we can initialize an Annotator, without an input or output and then feed mutations,
        one at a time... using a runspec"""

        # Locate the datasource directory and create a runspec
        dbDir = self.config.get("DEFAULT", "dbDir")
        ds = DatasourceFactory.createDatasources(dbDir)
        runSpec = RunSpecification()
        runSpec.initialize(None, None, datasources=ds)

        # Initialize the annotator with the runspec
        annotator = Annotator()
        annotator.initialize(runSpec)

        m = MutationData()
        m.chr = "1"
        m.start = "12941796"
        m.end = "12941796"
        m.alt_allele = "G"
        m.ref_allele = "T"

        muts = [m]

        muts = annotator.annotate_mutations(muts)
        m2 = muts.next()
        self.assertTrue(m2.get("gene", None) is not None)
Ejemplo n.º 5
0
    def testSkippingAltsForSingleMut(self):
        """Test a simple case where a single mutation with alt_allele_seen of False is not produced."""

        runSpec = RunSpecification()
        runSpec.initialize(None, None, datasources=[], is_skip_no_alts=True)

        # Initialize the annotator with the runspec
        annotator = Annotator()
        annotator.initialize(runSpec)

        m = MutationData()
        m.chr = "1"
        m.start = "12941796"
        m.end = "12941796"
        m.alt_allele = "G"
        m.ref_allele = "T"
        m.createAnnotation("alt_allele_seen", "False")

        muts = [m]

        muts = annotator.annotate_mutations(muts)
        self.assertRaises(StopIteration, muts.next)
Ejemplo n.º 6
0
    def testSkippingAltsForSingleMut(self):
        """Test a simple case where a single mutation with alt_allele_seen of False is not produced."""

        runSpec = RunSpecification()
        runSpec.initialize(None, None, datasources=[], is_skip_no_alts=True)

        # Initialize the annotator with the runspec
        annotator = Annotator()
        annotator.initialize(runSpec)

        m = MutationData()
        m.chr = "1"
        m.start = "12941796"
        m.end = "12941796"
        m.alt_allele = "G"
        m.ref_allele = "T"
        m.createAnnotation("alt_allele_seen", "False")

        muts = [m]

        muts = annotator.annotate_mutations(muts)
        self.assertRaises(StopIteration, muts.next)