def test_simple_annotate(self):
""" Annotate a simple example.
"""
base_config_location = "testdata/ensembl/saccer/"
config_parser = ConfigUtils.createConfigParser(base_config_location + "ensembl.config")
title = config_parser.get("general", "title")
version = config_parser.get("general", "version")
src_file = config_parser.get("general", "src_file")
ensembl_ds = EnsemblTranscriptDatasource(title=title, version=version, src_file=src_file)
m = MutationData()
m.chr = "22"
m.start = "22161963"
m.end = "22161963"
m.ref_allele = "C"
m.alt_allele = "A"
m2 = ensembl_ds.annotate_mutation(m)
def test_simple_annotate(self):
""" Annotate a simple example.
"""
base_config_location = "testdata/ensembl/saccer/"
config_parser = ConfigUtils.createConfigParser(base_config_location + "ensembl.config")
title = config_parser.get("general", "title")
version = config_parser.get("general", "version")
src_file = config_parser.get("general", "src_file")
ensembl_ds = EnsemblTranscriptDatasource(title=title, version=version, src_file=src_file)
m = MutationData()
m.chr = "22"
m.start = "22161963"
m.end = "22161963"
m.ref_allele = "C"
m.alt_allele = "A"
m2 = ensembl_ds.annotate_mutation(m)