def test_get_max_distance_to_common_ancestor(self):
self.assertEqual(
taxonomy_util.Taxon(
name='mycoplasma').get_max_distance_to_common_ancestor(), 8)
self.assertEqual(
taxonomy_util.Taxon(name='mycoplasma genitalium').
get_max_distance_to_common_ancestor(), 9)
self.assertEqual(
taxonomy_util.Taxon(name='mycoplasma genitalium G37').
get_max_distance_to_common_ancestor(), 10)
self.assertEqual(
taxonomy_util.Taxon(name='mycoplasma genitalium XXX').
get_max_distance_to_common_ancestor(), 10)
self.assertEqual(
taxonomy_util.Taxon(name='mycoplasma genitalium XXX YYY').
get_max_distance_to_common_ancestor(), 11)
def test_Taxon_get_parent_taxa(self):
parents = taxonomy_util.Taxon(
name='mycoplasma genitalium').get_parent_taxa()
self.assertEqual(parents[-1].name, 'Mycoplasma')
self.assertEqual(parents[-2].name, 'Mycoplasmataceae')
parents = taxonomy_util.Taxon(
name='mycoplasma genitalium G37').get_parent_taxa()
self.assertEqual(parents[-1].name, 'Mycoplasma genitalium')
self.assertEqual(parents[-2].name, 'Mycoplasma')
self.assertEqual(parents[-3].name, 'Mycoplasmataceae')
parents = taxonomy_util.Taxon(
name='mycoplasma genitalium XXX').get_parent_taxa()
self.assertEqual(parents[-1].name, 'Mycoplasma genitalium')
self.assertEqual(parents[-2].name, 'Mycoplasma')
self.assertEqual(parents[-3].name, 'Mycoplasmataceae')
def test_Taxon_init_from_id(self):
taxon = taxonomy_util.Taxon(ncbi_id=2093)
self.assertEqual(taxon.name, 'Mycoplasma')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 2093)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 0)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon, '')
taxon = taxonomy_util.Taxon(ncbi_id=2097)
self.assertEqual(taxon.name, 'Mycoplasma genitalium')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 2097)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 0)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon, '')
taxon = taxonomy_util.Taxon(ncbi_id=243273)
self.assertEqual(taxon.name, 'Mycoplasma genitalium G37')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 243273)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 0)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon, '')
self.assertRaises(ValueError, taxonomy_util.Taxon, ncbi_id=-1)
def create_taxon(id_or_name):
""" Create a taxon with NCBI id=:obj:`id_or_name` or name=:obj:`id_or_name`
Args:
id_or_name (:obj:`str`): NCBI id or name
Returns:
:obj:`taxonomy_util.Taxon`: taxon
"""
ncbi_id = None
name = None
try:
ncbi_id = float(id_or_name)
except ValueError:
name = id_or_name
return taxonomy_util.Taxon(ncbi_id=ncbi_id, name=name)
def test_Taxon_init_from_name(self):
taxon = taxonomy_util.Taxon(name='mycoplasma')
self.assertEqual(taxon.name, 'Mycoplasma')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 2093)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 0)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon, '')
taxon = taxonomy_util.Taxon(name='mycoplasma genitalium')
self.assertEqual(taxon.name, 'Mycoplasma genitalium')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 2097)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 0)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon, '')
taxon = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
self.assertEqual(taxon.name, 'Mycoplasma genitalium G37')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 243273)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 0)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon, '')
taxon = taxonomy_util.Taxon(name='mycoplasma genitalium XXX')
self.assertEqual(taxon.name, 'Mycoplasma genitalium XXX')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 2097)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 1)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon,
' XXX')
taxon = taxonomy_util.Taxon(name='mycoplasma XXX')
self.assertEqual(taxon.name, 'Mycoplasma XXX')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 2093)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 1)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon,
' XXX')
taxon = taxonomy_util.Taxon(name='mycoplasma XXX YYY')
self.assertEqual(taxon.name, 'Mycoplasma XXX YYY')
self.assertEqual(taxon.id_of_nearest_ncbi_taxon, 2093)
self.assertEqual(taxon.distance_from_nearest_ncbi_taxon, 2)
self.assertEqual(taxon.additional_name_beyond_nearest_ncbi_taxon,
' XXX YYY')
def test_Taxon_get_ncbi_id(self):
taxon = taxonomy_util.Taxon(ncbi_id=2093)
self.assertEqual(taxon.get_ncbi_id(), 2093)
taxon = taxonomy_util.Taxon(name='mycoplasma XXX')
self.assertEqual(taxon.get_ncbi_id(), None)
def test_get_distance_to_common_ancestor(self):
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium')
taxon_b = taxonomy_util.Taxon(name='mycoplasma pneumoniae')
self.assertEqual(taxon_a.get_distance_to_common_ancestor(taxon_b), 1)
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
taxon_b = taxonomy_util.Taxon(name='mycoplasma genitalium XXX')
self.assertEqual(taxon_a.get_distance_to_common_ancestor(taxon_b), 1)
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
taxon_b = taxonomy_util.Taxon(name='mycoplasma pneumoniae')
self.assertEqual(taxon_a.get_distance_to_common_ancestor(taxon_b), 2)
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
taxon_b = taxonomy_util.Taxon(name='mycoplasma')
self.assertEqual(taxon_a.get_distance_to_common_ancestor(taxon_b), 2)
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium XXX')
taxon_b = taxonomy_util.Taxon(name='mycoplasma')
self.assertEqual(taxon_a.get_distance_to_common_ancestor(taxon_b), 2)
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
taxon_b = taxonomy_util.Taxon(name='escherichia coli')
self.assertEqual(taxon_a.get_distance_to_common_ancestor(taxon_b), 8)
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium XXX')
taxon_b = taxonomy_util.Taxon(name='escherichia coli')
self.assertEqual(taxon_a.get_distance_to_common_ancestor(taxon_b), 8)
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium')
taxon_b = taxonomy_util.Taxon(name='escherichia coli')
self.assertEqual(taxon_a.get_distance_to_common_ancestor(taxon_b), 7)
def test_Taxon_get_common_ancestor(self):
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium')
taxon_b = taxonomy_util.Taxon(name='mycoplasma pneumoniae')
self.assertEqual(
taxon_a.get_common_ancestor(taxon_b).name, 'Mycoplasma')
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
taxon_b = taxonomy_util.Taxon(name='mycoplasma genitalium XXX')
self.assertEqual(
taxon_a.get_common_ancestor(taxon_b).name, 'Mycoplasma genitalium')
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
taxon_b = taxonomy_util.Taxon(name='mycoplasma pneumoniae')
self.assertEqual(
taxon_a.get_common_ancestor(taxon_b).name, 'Mycoplasma')
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
taxon_b = taxonomy_util.Taxon(name='mycoplasma')
self.assertEqual(
taxon_a.get_common_ancestor(taxon_b).name, 'Mycoplasma')
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium XXX')
taxon_b = taxonomy_util.Taxon(name='mycoplasma')
self.assertEqual(
taxon_a.get_common_ancestor(taxon_b).name, 'Mycoplasma')
taxon_a = taxonomy_util.Taxon(name='mycoplasma genitalium G37')
taxon_b = taxonomy_util.Taxon(name='escherichia coli')
self.assertEqual(taxon_a.get_common_ancestor(taxon_b).name, 'Bacteria')
def test_Taxon_get_rank(self):
self.assertEqual(taxonomy_util.Taxon(ncbi_id=2093).get_rank(), 'genus')
self.assertEqual(
taxonomy_util.Taxon(ncbi_id=2097).get_rank(), 'species')
self.assertEqual(taxonomy_util.Taxon(ncbi_id=243273).get_rank(), None)