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from cogent.util.unit_test import TestCase, main
from cogent.db.ensembl.species import Species
__author__ = "Gavin Huttley, Hua Ying"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley", "hua Ying"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "alpha"
class TestSpeciesNamemaps(TestCase):
def test_get_name_type(self):
"""should return the (latin|common) name given a latin, common or ensembl
db prefix names"""
self.assertEqual(Species.getSpeciesName("human"), "Homo sapiens")
self.assertEqual(Species.getSpeciesName("homo_sapiens"), "Homo sapiens")
self.assertEqual(Species.getCommonName("Mus musculus"), "Mouse")
self.assertEqual(Species.getCommonName("mus_musculus"), "Mouse")
def test_get_ensembl_format(self):
"""should take common or latin names and return the corresponding
ensembl db prefix"""
self.assertEqual(Species.getEnsemblDbPrefix("human"), "homo_sapiens")
self.assertEqual(Species.getEnsemblDbPrefix("mouse"), "mus_musculus")
self.assertEqual(Species.getEnsemblDbPrefix("Mus musculus"),
"mus_musculus")
def test_add_new_species(self):
"""should correctly add a new species/common combination and infer the
correct ensembl prefix"""
species_name, common_name = "Otolemur garnettii", "Bushbaby"
Species.amendSpecies(species_name, common_name)
self.assertEqual(Species.getSpeciesName(species_name), species_name)
self.assertEqual(Species.getSpeciesName("Bushbaby"), species_name)
self.assertEqual(Species.getSpeciesName(common_name), species_name)
self.assertEqual(Species.getCommonName(species_name), common_name)
self.assertEqual(Species.getCommonName("Bushbaby"), common_name)
self.assertEqual(Species.getEnsemblDbPrefix("Bushbaby"), "otolemur_garnettii")
self.assertEqual(Species.getEnsemblDbPrefix(species_name), "otolemur_garnettii")
self.assertEqual(Species.getEnsemblDbPrefix(common_name), "otolemur_garnettii")
def test_amend_existing(self):
"""should correctly amend an existing species"""
species_name = 'Ochotona princeps'
common_name1 = 'american pika'
common_name2 = 'pika'
ensembl_pref = 'ochotona_princeps'
Species.amendSpecies(species_name, common_name1)
self.assertEqual(Species.getCommonName(species_name),common_name1)
Species.amendSpecies(species_name, common_name2)
self.assertEqual(Species.getSpeciesName(common_name2), species_name)
self.assertEqual(Species.getSpeciesName(ensembl_pref), species_name)
self.assertEqual(Species.getCommonName(species_name), common_name2)
self.assertEqual(Species.getCommonName(ensembl_pref), common_name2)
self.assertEqual(Species.getEnsemblDbPrefix(species_name),
ensembl_pref)
self.assertEqual(Species.getEnsemblDbPrefix(common_name2),
ensembl_pref)
def test_get_compara_name(self):
"""should correctly form valid names for assignment onto objects"""
self.assertEqual(Species.getComparaName('pika'), 'Pika')
self.assertEqual(Species.getComparaName('C.elegans'), 'Celegans')
self.assertEqual(Species.getComparaName('Caenorhabditis elegans'),
'Celegans')
if __name__ == "__main__":
main()
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