def test_get_split_kcfs(self):
"""
test for get_split_kcfs
"""
path = "test"
expected = 3613
cag = control_all_genus(path)
actual = cag.get_split_kcfs()[('RING', 'C-C-C-C-C-C')]
self.assertEqual(actual, expected)
def test_get_number_of_Cnumber(self):
"""
test for make_kcfs
"""
path = "test"
expected = [('C00002198', 19), ('C00002151', 14), ('C00003672', 11),
('C00002503', 11), ('C00002499', 11)]
cag = control_all_genus(path)
Cn_dict = cag.get_number_of_Cnumber()
for Cn, exnumber in expected:
actual = Cn_dict[Cn]
self.assertEqual(actual, exnumber)
def test_get_specifics(self):
"""
test for get_specifics
"""
path = "test"
expected = [(('TRIPLET', 'C1y-C6a-O6a'), (32, 'Citrus')),
(('TRIPLET', 'O-P-O'), (24, 'Citrus')),
(('VICINITY', 'C6a(C1y+O6a+O6a)'), (16, 'Citrus')),
(('BOND', 'C1y-C6a'), (16, 'Citrus')),
(('BOND', 'O-P'), (16, 'Citrus'))]
cag = control_all_genus(path)
specific = cag.get_specifics()
for label, exnumgenus in expected:
actual = specific[label]
self.assertEqual(actual, exnumgenus)
def test_get_Cnumber_from_label(self):
"""
test for get_Cnumber_from_label
"""
path = "test"
expected = {
'Citrus': [
'C00000001', 'C00000003', 'C00000004', 'C00000008',
'C00000009', 'C00000017', 'C00000019', 'C00000020',
'C00000024', 'C00000025', 'C00000029', 'C00000044',
'C00000053', 'C00000081', 'C00001388', 'C00002074'
]
}
cag = control_all_genus(path)
actual = cag.get_Cnumber_from_label('C1y-C6a-O6a')
self.assertEqual(actual, expected)
for unit in units[:-1]:
temp = unit.split()
kosuu2[(temp[1], temp[2])] = kosuu2.get(
(temp[1], temp[2]), 0) + int(temp[3])
# In[38]:
sorted(kosuu2.items(), reverse=True, key=lambda x: x[1])
# In[1]:
from classes2 import control_all_genus
# In[2]:
cag = control_all_genus("Brassicaceae")
# In[3]:
cag.ari
# In[4]:
cag.get_number_of_Cnumber()
# In[5]:
sorted(cag.get_number_of_Cnumber().items(), reverse=True, key=lambda x: x[1])
# In[6]:
except:
print(time.time() - start)
print(datetime.datetime.now())
raise
print(time.time() - start)
print(datetime.datetime.now())
# In[ ]:
# In[1]:
from classes2 import control_all_genus
# In[2]:
cag = control_all_genus("Violaceae")
# In[3]:
cag.ari
# In[4]:
sorted(cag.get_number_of_Cnumber().items(), reverse=True, key=lambda x: x[1])
# In[5]:
sorted(cag.get_split_kcfs().items(), reverse=True, key=lambda x: x[1])
# In[6]:
print(datetime.datetime.now())
raise
print(time.time() - start)
print(datetime.datetime.now())
# ミカン科抜き終わり。
# In[20]:
from classes2 import control_all_genus
# In[21]:
cag = control_all_genus("Rutaceae")
# In[22]:
cag.ari
# 明らかにおかしいので修正する
# In[6]:
import requests
import lxml.html
print(len(os.listdir("Fabaceae")))
# In[15]:
import pickle
with open("Fabaceae/genuses.pickle", "rb") as fi:
genlist = pickle.load(fi)
print(len(genlist))
# In[1]:
from classes2 import control_all_genus
# In[2]:
cag = control_all_genus("Fabaceae")
# In[3]:
cag.ari
# In[4]:
print(len(cag.ari))
# In[5]:
glen = []
for genus in cag.ari:
with open(cag.path + "/" + genus + "/kcfs.kcfs") as f:
Cnlist = []
for i in os.listdir("Poaceae"):
if i == ".DS_Store" or i == "others" or i == "genuses.pickel":
continue
if i not in genlist:
shutil.rmtree("Poaceae/" + i)
print(i)
# イネ科抜き終わり
# In[2]:
from classes2 import control_all_genus
# In[3]:
cag = control_all_genus("Poaceae")
# In[4]:
len(cag.ari)
# In[5]:
sorted(cag.get_number_of_Cnumber().items(), reverse=True, key=lambda x: x[1])
# In[6]:
sorted(cag.get_split_kcfs().items(), reverse=True, key=lambda x: x[1])
# In[7]:
print(time.time() - start)
print(datetime.datetime.now())
# In[22]:
print(genlist[11])
# In[ ]:
# In[1]:
from classes2 import control_all_genus
# In[2]:
cag = control_all_genus("Rosaceae")
# In[4]:
cag.ari
# In[5]:
print(len(cag.ari))
# In[6]:
glen = []
for genus in cag.ari:
with open("Rosaceae/" + genus + "/kcfs.kcfs") as f:
Cnlist = []
