Python MCS_Finder 예제들

예제 #1

파일: test_MCS_Finder.py 프로젝트: sato-masayukidesu/KNApSAcK_search

 def test_make_kcfs(self):
     """
     test for make_kcfs
     """
     genus = "Citrus"
     if os.path.exists(genus):
         shutil.rmtree(genus)
     f = MCS_Finder(genus)
     f.make_kcfs2()
     kcfspath = genus + "/kcfs.kcfs"
     kcfscountpath = genus + "/kcfscount.txt"
     splitcountpath = genus + "/splitedcount.txt"
     self.assertTrue(os.path.exists(kcfspath))
     self.assertTrue(os.path.exists(kcfscountpath))
     self.assertTrue(os.path.exists(splitcountpath))
     shutil.rmtree(genus)

예제 #2

import os
import time
import pickle
import datetime
start = time.time()
with open("Brassicaceae/genuses.pickle", "rb") as fi:
    genlist = pickle.load(fi)
try:
    with open("Brassicaceae/genuses.pickle", "rb") as fi:
        genlist2 = pickle.load(fi)
    for genus in genlist:
        if not os.path.exists("Brassicaceae"):
            os.mkdir("Brassicaceae")
        if os.path.exists("Brassicaceae/" + genus):
            continue
        f = MCS_Finder(genus, "Brassicaceae")
        f.make_kcfs()
        time.sleep(15)
except:
    print(time.time() - start)
    print(datetime.datetime.now())
    raise
print(time.time() - start)
print(datetime.datetime.now())

# In[24]:

print(genlist[-21])

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예제 #3

from classes2 import MCS_Finder
import os
import time
import pickle
import datetime
start = time.time()
with open(family + "/genuses.pickle", "rb") as fi:
    genlist = pickle.load(fi)
try:
    for genus in genlist:
        if not os.path.exists(family):
            os.mkdir(family)
        if os.path.exists(family + "/" + genus):
            continue
        f = MCS_Finder(genus, family)
        f.make_kcfs()
        print(datetime.datetime.now())
        print(len(os.listdir(family)))
        time.sleep(15)
except:
    print(time.time() - start)
    print(datetime.datetime.now())
    raise
print(time.time() - start)
print(datetime.datetime.now())

# In[ ]:

# In[1]:

예제 #4

from classes2 import MCS_Finder
import os
import time
import pickle
import datetime
start = time.time()
with open(family + "/genuses.pickle", "rb")as fi:
    genlist = pickle.load(fi)
try:
    for genus in genlist:
        if not os.path.exists(family):
            os.mkdir(family)
        if os.path.exists(family + "/" + genus):
            continue
        f = MCS_Finder(genus, family)
        f.make_kcfs()
        print(datetime.datetime.now())
        print(len(os.listdir(family)))
        time.sleep(15)
except:
    print(time.time() - start)
    print(datetime.datetime.now())
    raise
print(time.time() - start)
print(datetime.datetime.now())


# ミカン科抜き終わり。

# In[20]:

예제 #5

파일: get_Fabaceae.py 프로젝트: sato-masayukidesu/KNApSAcK_search

from classes2 import MCS_Finder
import os
import time
import pickle
import datetime
start = time.time()
with open("Fabaceae/genuses.pickle", "rb") as fi:
    genlist = pickle.load(fi)
try:
    for genus in genlist:
        if not os.path.exists("Fabaceae"):
            os.mkdir("Fabaceae")
        if os.path.exists("Fabaceae/" + genus):
            continue
        f = MCS_Finder(genus, "Fabaceae")
        f.make_kcfs()
        print(datetime.datetime.now())
        print(len(os.listdir("Fabaceae")))
        time.sleep(15)
except:
    print(time.time() - start)
    print(datetime.datetime.now())
    raise
print(time.time() - start)
print(datetime.datetime.now())

# 抜き終わり

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예제 #6

from classes2 import MCS_Finder
import os
import time
import pickle
import datetime
start = time.time()
with open(family + "/genuses.pickle", "rb") as fi:
    genlist = pickle.load(fi)
try:
    for genus in genlist:
        if not os.path.exists(family):
            os.mkdir(family)
        if os.path.exists(family + "/" + genus):
            continue
        f = MCS_Finder(genus, family)
        f.make_kcfs(limit=10000)
        print(datetime.datetime.now())
        print(len(os.listdir(family)))
        time.sleep(15)
except:
    os.rmdir(family + "/" + genus)
    print(time.time() - start)
    print(datetime.datetime.now())
    raise
print(time.time() - start)
print(datetime.datetime.now())

# In[22]:

print(genlist[11])