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"""Testing code for Bio-Registries.
Goals:
Make sure that all retrieval is working as expected.
"""
import requires_internet
import os
import sys
import unittest
import StringIO
from Bio import GenBank
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests.
"""
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
tests = [GenBankRetrievalTest]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class GenBankRetrievalTest(unittest.TestCase):
"""Test convience functionality in Bio.GenBank for retrieval.
"""
def setUp(self):
self.gb_protein_ids = ["NP_058835", "8393944"]
self.gb_nuc_ids = ["NM_017139", "8393943"]
self.search_term = "Opuntia"
def t_search_for(self):
"""Search for ids using the GenBank search_for function.
"""
ids = GenBank.search_for(self.search_term, database = 'protein')
assert len(ids) >= 9 # 9 in GenBank right now
def t_download_many(self):
"""Retrieve sequences using the GenBank download_many function.
"""
nuc_results = GenBank.download_many(self.gb_nuc_ids, 'nucleotide')
iterator = GenBank.Iterator(nuc_results)
num = 0
for rec in iterator:
num += 1
assert num == 2
prot_results = GenBank.download_many(self.gb_protein_ids, 'protein')
iterator = GenBank.Iterator(prot_results)
num = 0
for rec in iterator:
num += 1
assert num == 2
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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