def test_convert_trait_table_entries(self):
"""convert_trait_entries should convert labels,values using conversion fns"""
lines =[\
['organism 1','0','0.3','15','1','6'],\
['organism 2','1','1','13','-1',-1],\
['organism 3','2','0','12','0.9','5']]
val_conv_fns = []
#Handle replacement of ambiguous values
replacement_dict = {'-': 0, '-1': 0, -1: 0, 'NULL': 0, None: 0}
replace_ambig_fn = make_translate_conversion_fn(replacement_dict)
val_conv_fns.append(replace_ambig_fn)
label_conv_fns = [remove_spaces]
#Convert values to integers (in string form)
val_conv_fns.append(lambda x: str(int(float(x))))
obs = [l for l in convert_trait_table_entries(lines,\
value_conversion_fns = val_conv_fns,\
label_conversion_fns=label_conv_fns)]
exp =[\
['organism_1','0','0','15','1','6'],\
['organism_2','1','1','13','0','0'],\
['organism_3','2','0','12','0','5']]
self.assertEqual(obs, exp)
def test_convert_trait_table_entries(self):
"""convert_trait_entries should convert labels,values using conversion fns"""
lines =[\
['organism 1','0','0.3','15','1','6'],\
['organism 2','1','1','13','-1',-1],\
['organism 3','2','0','12','0.9','5']]
val_conv_fns = []
#Handle replacement of ambiguous values
replacement_dict ={'-':0,'-1':0,-1:0,'NULL':0,None:0}
replace_ambig_fn = make_translate_conversion_fn(replacement_dict)
val_conv_fns.append(replace_ambig_fn)
label_conv_fns = [remove_spaces]
#Convert values to integers (in string form)
val_conv_fns.append(lambda x: str(int(float(x))))
obs = [l for l in convert_trait_table_entries(lines,\
value_conversion_fns = val_conv_fns,\
label_conversion_fns=label_conv_fns)]
exp =[\
['organism_1','0','0','15','1','6'],\
['organism_2','1','1','13','0','0'],\
['organism_3','2','0','12','0','5']]
self.assertEqual(obs,exp)
def test_convert_trait_table_entries(self):
"""convert_trait_entries should convert labels,values using conversion fns"""
lines = [
["organism 1", "0", "0.3", "15", "1", "6"],
["organism 2", "1", "1", "13", "-1", -1],
["organism 3", "2", "0", "12", "0.9", "5"],
]
val_conv_fns = []
# Handle replacement of ambiguous values
replacement_dict = {"-": 0, "-1": 0, -1: 0, "NULL": 0, None: 0}
replace_ambig_fn = make_translate_conversion_fn(replacement_dict)
val_conv_fns.append(replace_ambig_fn)
label_conv_fns = [remove_spaces]
# Convert values to integers (in string form)
val_conv_fns.append(lambda x: str(int(float(x))))
obs = [
l
for l in convert_trait_table_entries(
lines, value_conversion_fns=val_conv_fns, label_conversion_fns=label_conv_fns
)
]
exp = [
["organism_1", "0", "0", "15", "1", "6"],
["organism_2", "1", "1", "13", "0", "0"],
["organism_3", "2", "0", "12", "0", "5"],
]
self.assertEqual(obs, exp)
def test_make_translate_conversion_fn(self):
"""make_translate_conversion_fn should make a conversion_fn given dicts """
translation_dict = {"-1": 0, -1: 0, "Unknown": 0, "?": 0}
conversion_fn = make_translate_conversion_fn(translation_dict)
values = [0, -1, 15, "10", "-1", "Unknown", "?"]
exp = ["0", "0", "15", "10", "0", "0", "0"]
obs = map(conversion_fn, values)
self.assertEqual(obs, exp)
def test_make_translate_conversion_fn(self):
"""make_translate_conversion_fn should make a conversion_fn given dicts """
translation_dict =\
{'-1':0,-1:0,'Unknown':0,'?':0}
conversion_fn =\
make_translate_conversion_fn(translation_dict)
values = [0, -1, 15, '10', '-1', 'Unknown', '?']
exp = ['0', '0', '15', '10', '0', '0', '0']
obs = map(conversion_fn, values)
self.assertEqual(obs, exp)
def test_make_translate_conversion_fn(self):
"""make_translate_conversion_fn should make a conversion_fn given dicts """
translation_dict =\
{'-1':0,-1:0,'Unknown':0,'?':0}
conversion_fn =\
make_translate_conversion_fn(translation_dict)
values = [0,-1,15,'10','-1','Unknown','?']
exp = ['0','0','15','10','0','0','0']
obs = map(conversion_fn,values)
self.assertEqual(obs,exp)
