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"), "H**o sapiens")
self.assertEqual(Species.getSpeciesName("homo_sapiens"), "H**o sapiens")
self.assertEqual(Species.getCommonName("Mus musculus"), "Mouse")
self.assertEqual(Species.getCommonName("mus_musculus"), "Mouse")
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"), "H**o sapiens")
self.assertEqual(Species.getSpeciesName("homo_sapiens"),
"H**o sapiens")
self.assertEqual(Species.getCommonName("Mus musculus"), "Mouse")
self.assertEqual(Species.getCommonName("mus_musculus"), "Mouse")
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 __repr__(self):
my_type = self.__class__.__name__
name = _Species.getCommonName(self.Species)
coord_type = self.CoordType
c = '%s(%r,%r,%r,%d-%d,%d)'%(my_type, name, coord_type,
self.CoordName, self.Start, self.End, self.Strand)
return c.replace("'", "")
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 __repr__(self):
my_type = self.__class__.__name__
name = _Species.getCommonName(self.Species)
coord_type = self.CoordType
c = '%s(%r,%r,%r,%d-%d,%d)'%(my_type, name, coord_type,
self.CoordName, self.Start, self.End, self.Strand)
return c.replace("'", "")
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)
