def __getitem__(self, id):
"""__getitem__(self, id) -> object
Return a Prodoc entry. id is either the id or accession
for the entry. Raises a KeyError if there's an error.
"""
import time
from Bio import ExPASy
# First, check to see if enough time has passed since my
# last query.
if self.last_query_time is not None:
delay = self.last_query_time + self.delay - time.time()
if delay > 0.0:
time.sleep(delay)
self.last_query_time = time.time()
try:
handle = ExPASy.get_prodoc_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 test_prodoc_html(self):
handle = ExPASy.get_prodoc_entry('PDOC00001')
html = handle.read()
self.assertEqual(handle.url,
'http://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001')
handle.close()
self.assertTrue('{PS00001; ASN_GLYCOSYLATION}' in html)
def __getitem__(self, id):
"""__getitem__(self, id) -> object
Return a Prodoc entry. id is either the id or accession
for the entry. Raises a KeyError if there's an error.
"""
import time
from Bio import ExPASy
# First, check to see if enough time has passed since my
# last query.
if self.last_query_time is not None:
delay = self.last_query_time + self.delay - time.time()
if delay > 0.0:
time.sleep(delay)
self.last_query_time = time.time()
try:
handle = ExPASy.get_prodoc_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 test_prodoc_html(self):
with ExPASy.get_prodoc_entry("PDOC00001") as handle:
html = handle.read()
self.assertEqual(
handle.url,
"https://prosite.expasy.org/cgi-bin/prosite/get-prodoc-entry?PDOC00001"
)
self.assertIn("{PS00001; ASN_GLYCOSYLATION}", html)
def get_documentation(accession):
"""
get_documentation function gets as arg :
accesion (signature_ac example "PS00001" )
returns
html file containing full documentaion
"""
handle_1 = ExPASy.get_prosite_raw(accession)
records = Prosite.read(handle_1)
handle_2 = ExPASy.get_prodoc_entry(records.pdoc)
#record = Prodoc.read(handle_2)"
html = handle_2.read()
with open("my_prodoc_record.html", "w") as out_handle:
out_handle.write(html)
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
