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_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_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_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);")
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);")