def test_parse_dna(self):
f = testdata_stream("nexus/dna.nex")
n = Nexus(f)
taxa = n.taxlabels
taxa.sort()
self.assertEquals(len(taxa), 10)
self.assertEquals(taxa[0], "Carp")
self.assertEquals(taxa[-1], "Whale")
def test_parse_f0(self):
f = testdata_stream("nexus/test_Nexus_input.nex")
n = Nexus(f)
#self.output_basics(n)
expected = [
't1', "t2 the name", "isn'that [a] strange name?",
"one should be punished, for (that)!", "t5", "t6", "t7", "t8", "t9"
]
taxa = n.taxlabels
self.assertEquals(taxa, expected)
def test_TreeTest1(self):
"""Test Tree module."""
f = testdata_stream("nexus/test_Nexus_input.nex")
n = Nexus(f)
t3 = n.trees[2]
t2 = n.trees[2]
t3.root_with_outgroup(['t1', 't5'])
# Return node_id of common ancestor if
# taxon_list is monophyletic, -1 otherwise.
self.assertEquals(t3.is_monophyletic(['t1', 't5']), 13)
t3.split(parent_id=t3.search_taxon('t9'))
def read(fin, alphabet=None):
""" Extract sequence data from a nexus file."""
n = Nexus(fin)
seqs = []
for taxon in n.taxlabels:
name = safename(taxon)
r = n.matrix[taxon]
if alphabet is None:
s = Seq(r, name=name, alphabet=r.alphabet)
else:
s = Seq(r, name=name, alphabet=alphabet)
seqs.append(s)
if len(seqs) == 0:
# Something went terrible wrong.
raise ValueError("Cannot parse file")
return SeqList(seqs)
def test_create(self):
n = Nexus()
self.assertNotEqual(n, None)
def test_parse_protein(self):
f = testdata_stream("nexus/protein.nex")
n = Nexus(f)
f.close()
