def test_parse_phylip_test_4(self):
f = data_stream("phylip_test_4.phy")
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 25)
self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG")
self.assertEqual(seqs[2].name, "ddrasa")
f.close()
def test_read(self):
f = data_stream("phylip_test_1.phy")
seqs = phylip_io.read(f)
# print seqs
self.assertEqual(len(seqs), 10)
self.assertEqual(seqs[0].name, "Cow")
self.assertEqual(len(seqs[1]), 234)
f.close()
def test_parse_phylip_test_3(self):
f = data_stream("phylip_test_3.phy")
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 20)
self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
self.assertEqual(seqs[1].name, "Hesperorni")
f.close()
def test_parse_phylip_dna(self):
f = data_stream("dna.phy")
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 10)
self.assertEqual(len(seqs[0]), 705)
self.assertEqual(str(seqs[1][0:10]), "ATGGCACACC")
self.assertEqual(seqs[2].name, "Chicken")
f.close()