Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Fetching contributors…

Cannot retrieve contributors at this time

91 lines (74 sloc) 3.252 kb
# Copyright 2007-2010 by Peter Cock. All rights reserved.
# Revisions copyright 2007-2008 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Testing online code for fetching sequences, and parsing them
Uses Bio.SeqIO to parse files downloaded with Bio.GenBank, Bio.WWW.NCBI,
Bio.ExPASy etc.
Goals:
Make sure that all retrieval is working as expected.
May catch some format changes early too.
"""
import unittest
import requires_internet
requires_internet.check()
# We want to test these:
from Bio import Entrez
from Bio import ExPASy
# In order to check any sequences returned
from Bio import SeqIO
from Bio._py3k import StringIO
from Bio.SeqUtils.CheckSum import seguid
from Bio.File import UndoHandle
from Bio._py3k import _as_string
# This lets us set the email address to be sent to NCBI Entrez:
Entrez.email = "biopython-dev@biopython.org"
class ExPASyTests(unittest.TestCase):
"""Tests for Bio.ExPASy module."""
def test_get_sprot_raw(self):
"""Bio.ExPASy.get_sprot_raw("O23729")"""
identifier = "O23729"
# This is to catch an error page from our proxy:
handle = UndoHandle(ExPASy.get_sprot_raw(identifier))
if _as_string(handle.peekline()).startswith("<!DOCTYPE HTML"):
raise IOError
record = SeqIO.read(handle, "swiss")
handle.close()
self.assertEqual(record.id, identifier)
self.assertEqual(len(record), 394)
self.assertEqual(seguid(record.seq), "5Y08l+HJRDIlhLKzFEfkcKd1dkM")
class EntrezTests(unittest.TestCase):
def simple(self, database, formats, entry, length, checksum):
for f in formats:
handle = Entrez.efetch(db=database, id=entry, rettype=f, retmode="text")
if f == "gbwithparts":
f = "gb"
record = SeqIO.read(handle, f)
handle.close()
self.assertTrue((entry in record.name) or
(entry in record.id) or
("gi" in record.annotations
and record.annotations["gi"] == entry),
"%s got %s, %s" % (entry, record.name, record.id))
self.assertEqual(len(record), length)
self.assertEqual(seguid(record.seq), checksum)
for database, formats, entry, length, checksum in [
("nuccore", ["fasta", "gb"], "X52960", 248,
"Ktxz0HgMlhQmrKTuZpOxPZJ6zGU"),
("nucleotide", ["fasta", "gb"], "6273291", 902,
"bLhlq4mEFJOoS9PieOx4nhGnjAQ"),
("protein", ["fasta", "gbwithparts"], "16130152", 367,
"fCjcjMFeGIrilHAn6h+yju267lg"),
]:
def funct(d, f, e, l, c):
method = lambda x: x.simple(d, f, e, l, c)
method.__doc__ = "Bio.Entrez.efetch(%r, id=%r, ...)" % (d, e)
return method
setattr(EntrezTests, "test_%s_%s" % (database, entry),
funct(database, formats, entry, length, checksum))
del funct
del database, formats, entry, length, checksum
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
Jump to Line
Something went wrong with that request. Please try again.