def test_parse_dnd(self):
"""parse_dnd returns a dict with dnd indexed by tree name"""
tree_info = get_tree_info(Nexus_tree)
header, trans_table, dnd = split_tree_info(tree_info)
dnd_dict = parse_dnd(dnd)
self.assertEqual(
dnd_dict["tree PAUP_1"],
"(1,(2,(((3,4),(5,(((((6,10),9),(11,18)),((((7,15),19),17),(8,(12,(14,16))))),13))),20)),21);",
)
def test_get_tree_info(self):
"""get_tree_info returns the Nexus file section that describes the tree"""
result = get_tree_info(Nexus_tree)
self.assertEqual(len(result), 33)
self.assertEqual(
result[0], "Begin trees; [Treefile saved Wednesday, May 5, 2004 5:02 PM]"
)
self.assertEqual(
result[31],
"tree PAUP_1 = [&R] (1,(2,(((3,4),(5,(((((6,10),9),(11,18)),((((7,15),19),17),(8,(12,(14,16))))),13))),20)),21);",
)
def test_parse_trans_table(self):
"""parse_trans_table returns a dict with the taxa names indexed by number"""
tree_info = get_tree_info(Nexus_tree)
header, trans_table, dnd = split_tree_info(tree_info)
Trans_table = parse_trans_table(trans_table)
self.assertEqual(len(Trans_table), 21)
# check that taxa are returned in the Trans_table
self.assertEqual(Trans_table["1"], "outgroup25")
self.assertEqual(Trans_table["2"], "AF078391l")
self.assertEqual(Trans_table["3"], "AF078211af")
self.assertEqual(Trans_table["4"], "AF078393l")
self.assertEqual(Trans_table["5"], "AF078187af")
self.assertEqual(Trans_table["6"], "AF078320l")
self.assertEqual(Trans_table["21"], "outgroup258")
self.assertEqual(Trans_table["20"], "AF078179af")
self.assertEqual(Trans_table["19"], "AF078251af")
def test_split_tree_info(self):
"""split_tree_info splits lines into header, Trans_table, and dnd"""
tree_info = get_tree_info(Nexus_tree)
header, trans_table, dnd = split_tree_info(tree_info)
self.assertEqual(len(header), 9)
self.assertEqual(len(trans_table), 22)
self.assertEqual(len(dnd), 2)
self.assertEqual(
header[0], "Begin trees; [Treefile saved Wednesday, May 5, 2004 5:02 PM]"
)
self.assertEqual(header[8], "\tTranslate")
self.assertEqual(trans_table[0], "\t\t1 outgroup25,")
self.assertEqual(trans_table[21], "\t\t;")
self.assertEqual(
dnd[0],
"tree PAUP_1 = [&R] (1,(2,(((3,4),(5,(((((6,10),9),(11,18)),((((7,15),19),17),(8,(12,(14,16))))),13))),20)),21);",
)
