# 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 # 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.SeqUtils.CheckSum import seguid from Bio.SwissProt import SwissProtParserError import requires_internet requires_internet.check() # This lets us set the email address to be sent to NCBI Entrez: Entrez.email = "biopython@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" handle = ExPASy.get_sprot_raw(identifier) try: record = SeqIO.read(handle, "swiss") except SwissProtParserError as e: # This is to catch an error page from our proxy if str(e) == "Failed to find ID in first line" and e.line.startswith( "