def setUp(self):
# We are using the files of the Drosophila Gateway Vector Collection
# (<https://emb.carnegiescience.edu/drosophila-gateway-vector-collection>)
# as sample Gck files. We cannot redistribute those files along with
# Biopython, so we need to download them now for the tests to run.
if not os.path.exists("Gck/DGVC_GCK.zip"):
try:
requires_internet.check()
except MissingExternalDependencyError:
self.skipTest("Sample files missing and no Internet access")
return
try:
with urlopen(
"https://emb.carnegiescience.edu/sites/default/files/DGVC_GCK.zip"
) as src, open("Gck/DGVC_GCK.zip", "wb") as dst:
shutil.copyfileobj(src, dst)
except HTTPError:
self.skipTest("Cannot download the sample files")
return
self.zipdata = ZipFile("Gck/DGVC_GCK.zip")
scope of this file as they are already covered in test_Entrez.py.
"""
from Bio import Entrez
from Bio import Medline
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
import doctest
import os
import locale
import sys
import unittest
import requires_internet
requires_internet.check()
# This lets us set the email address to be sent to NCBI Entrez:
Entrez.email = "*****@*****.**"
Entrez.api_key = "5cfd4026f9df285d6cfc723c662d74bcbe09"
URL_HEAD = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
URL_TOOL = "tool=biopython"
URL_EMAIL = "email=biopython%40biopython.org"
URL_API_KEY = "api_key=5cfd4026f9df285d6cfc723c662d74bcbe09"
class EntrezOnlineCase(unittest.TestCase):
def test_no_api_key(self):
"""Test Entrez.read without API key."""
cached = Entrez.api_key
#!/usr/bin/env python
"""Tests HotRand.
"""
# standard library
from __future__ import print_function
import unittest
import warnings
from Bio import BiopythonDeprecationWarning
warnings.simplefilter('ignore', BiopythonDeprecationWarning)
# local stuff
import requires_internet
requires_internet.check()
from Bio.HotRand import HotRandom
# --- helper classes and functions
def are_items_in_range( a, high, low ):
for j in range( 0, len( a ) ):
if( a[ j ] > high ):
print('a[ %d ] is %d' % ( j , a[ j ] ))
return 0
if( a[ j ] < low ):
print('a[ %d ] is %d' % ( j , a[ j ] ))
return 0
return 1
