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# 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 sys
import unittest
import requires_internet
requires_internet.check()
from Bio import MissingExternalDependencyError
#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 StringIO import StringIO
from Bio.SeqUtils.CheckSum import seguid
from Bio.File import UndoHandle
#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"
try:
#This is to catch an error page from our proxy:
handle = UndoHandle(ExPASy.get_sprot_raw(identifier))
if handle.peekline().startswith("<!DOCTYPE HTML"):
raise IOError
record = SeqIO.read(handle, "swiss")
handle.close()
except IOError:
raise MissingExternalDependencyError(
"internet (or maybe just ExPASy) not available")
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:
try:
handle = Entrez.efetch(db=database, id=entry, rettype=f)
record = SeqIO.read(handle, f)
handle.close()
except IOError:
raise MissingExternalDependencyError(
"internet (or maybe just NCBI) not available")
self.assert_((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 [
("genome", ["fasta", "gb"], "X52960", 248,
"Ktxz0HgMlhQmrKTuZpOxPZJ6zGU"),
("nucleotide", ["fasta", "gb"], "6273291", 902,
"bLhlq4mEFJOoS9PieOx4nhGnjAQ"),
("protein", ["fasta", "gb"], "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(%s, %s, ...)" % (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)
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