def make_tree(*taxa):
# We create a dict to lookup Glottolog languoids by name, ISO- or Glottocode.
langs = {}
for lang in Glottolog().languoids():
if lang.iso:
langs[lang.iso] = lang
langs[lang.name] = lang
langs[lang.id] = lang
t = TreeMaker()
for taxon in taxa:
if taxon not in langs:
print('unknown taxon: {0}'.format(taxon))
continue
t.add(taxon, ', '.join(l[1] for l in langs[taxon].lineage))
return t
def test_add(self):
t = TreeMaker()
t.add('A', 'a')
t.add('AB1', 'a, b')
t.add('AB2', 'a, b')
t.add('C', 'c')
assert str(t.tree) == "((A,(AB1,AB2)),C)"
def test_add(self):
t = TreeMaker()
t.add('A', 'a')
t.add('AB1', 'a, b')
t.add('AB2', 'a, b')
t.add('C', 'c')
assert str(t.tree) == "((A,(AB1,AB2)),C)"
def test_add_2(self):
t = TreeMaker()
t.add('A1', 'family a, subgroup 1')
t.add('A2', 'family a, subgroup 2')
t.add('B1a', 'family b, subgroup 1')
t.add('B1b', 'family b, subgroup 1')
t.add('B2', 'family b, subgroup 2')
assert str(t.tree) == "((A1,A2),((B1a,B1b),B2))"
def test_error_on_bad_taxon(self):
t = TreeMaker()
with self.assertRaises(ValueError):
t.add('A (x)', 'a')
with self.assertRaises(ValueError):
t.add('A)', 'a')
with self.assertRaises(ValueError):
t.add('A(', 'a')
def test_add_2(self):
t = TreeMaker()
t.add('A1', 'family a, subgroup 1')
t.add('A2', 'family a, subgroup 2')
t.add('B1a', 'family b, subgroup 1')
t.add('B1b', 'family b, subgroup 1')
t.add('B2', 'family b, subgroup 2')
assert str(t.tree) == "((A1,A2),((B1a,B1b),B2))"
def test_error_on_bad_taxon(self):
t = TreeMaker()
with self.assertRaises(ValueError):
t.add('A (x)', 'a')
with self.assertRaises(ValueError):
t.add('A)', 'a')
with self.assertRaises(ValueError):
t.add('A(', 'a')
def test_error_on_duplicate(self):
t = TreeMaker()
t.add('A', 'a')
with self.assertRaises(ValueError):
t.add('A', 'a')
def test_error_on_duplicate(self):
t = TreeMaker()
t.add('A', 'a')
with self.assertRaises(ValueError):
t.add('A', 'a')