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
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)
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
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)
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)
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)