def queryProsite(theSeqs):
print("Currently querying Prosite...")
prositeData = list()
for i in theSeqs:
handle = ScanProsite.scan(seq=i, skip="0")
result = ScanProsite.read(handle)
try:
handle = ExPASy.get_prosite_entry(result[0]["signature_ac"])
res = handle.read()
splitted = res.split("\n")
line = 0
for a in range(0, len(splitted)):
if splitted[a][0:2] == "DE":
line = a
prositeData.append(splitted[line][5:-1])
print(splitted[line][5:-1])
except IndexError:
prositeData.append(None)
print(None)
return prositeData
def test_prosite_html(self):
handle = ExPASy.get_prosite_entry('PS00001')
html = handle.read()
self.assertEqual(handle.url,
'http://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001')
handle.close()
self.assertTrue('<title>PROSITE: PS00001</title>' in html)
def test_prosite_html(self):
with ExPASy.get_prosite_entry("PS00001") as handle:
html = handle.read()
self.assertEqual(
handle.url,
"https://prosite.expasy.org/cgi-bin/prosite/get-prosite-entry?PS00001"
)
self.assertIn("<title>PROSITE: PS00001</title>", html)
def __getitem__(self, id):
"""__getitem__(self, id) -> object
Return a Prosite entry. id is either the id or accession
for the entry. Raises a KeyError if there's an error.
"""
from Bio import ExPASy
# First, check to see if enough time has passed since my
# last query.
self.limiter.wait()
try:
handle = ExPASy.get_prosite_entry(id)
except IOError:
raise KeyError(id)
try:
handle = File.StringHandle(_extract_record(handle))
except ValueError:
raise KeyError(id)
if self.parser is not None:
return self.parser.parse(handle)
return handle.read()
def __getitem__(self, id):
"""__getitem__(self, id) -> object
Return a Prosite entry. id is either the id or accession
for the entry. Raises a KeyError if there's an error.
"""
from Bio import ExPASy
# First, check to see if enough time has passed since my
# last query.
self.limiter.wait()
try:
handle = ExPASy.get_prosite_entry(id)
except IOError:
raise KeyError(id)
try:
handle = File.StringHandle(_extract_record(handle))
except ValueError:
raise KeyError(id)
if self.parser is not None:
return self.parser.parse(handle)
return handle.read()
def testProsite():
handle = ExPASy.get_prosite_entry('PS50943') #está como exemplo
ofile = open("test.html", "wb")
ofile.write(handle.read())
ofile.close()
from Bio import ExPASy
handle = ExPASy.get_prosite_raw("PS00001")
text = handle.read()
print(text)
# 가장 원시적인 긁는 방법 (Expasy만 있으면 됨)
"""from Bio import Prosite
handle = ExPASy.get_prosite_raw("PS51036")
record = Prosite.read(handle)
print(record)"""
# ImportError: cannot import name 'Prosite' from 'Bio' (/home/koreanraichu/PycharmProjects/pythonProject/venv/lib/python3.8/site-packages/Bio/__init__.py)가 나를 반기는디?
from Bio.ExPASy import Prodoc
handle = ExPASy.get_prosite_raw("PDOC00001")
record = Prodoc.read(handle)
print(record)
handle = ExPASy.get_prosite_entry("PS51036")
html = handle.read()
with open("myprositerecord.html", "w") as out_handle:
out_handle.write(html)
# HTML format으로 다운로드 받을 수 있다.
handle = ExPASy.get_prodoc_entry("PDOC51036")
html = handle.read()
with open("myprositerecord2.html", "w") as out_handle:
out_handle.write(html)
# 얘는 prodoc 다운로드 하는 코드
