def setUp(self):
self.pd = PrimerDesigner(
folder=TEST_FOLDER,
tm="55",
min_amplength="200",
max_amplength="500",
gencode="universal",
mode="primers",
clustype="protein",
amptype="dna_GTRG",
email="*****@*****.**",
)
self.tmp_folder= os.path.join(TEST_FOLDER, '..', 'tmp_folder')
if not os.path.isdir(self.tmp_folder):
os.mkdir(self.tmp_folder)
self.maxDiff = None
class PrimerDesignerTest(unittest.TestCase):
def setUp(self):
self.pd = PrimerDesigner(
folder=TEST_FOLDER,
tm="55",
min_amplength="200",
max_amplength="500",
gencode="universal",
mode="primers",
clustype="protein",
amptype="dna_GTRG",
email="*****@*****.**",
)
self.tmp_folder= os.path.join(TEST_FOLDER, '..', 'tmp_folder')
if not os.path.isdir(self.tmp_folder):
os.mkdir(self.tmp_folder)
self.maxDiff = None
def tearDown(self):
output_html_file = '{0}.html'.format(ALIGNMENT)
if os.path.isfile(output_html_file):
os.remove(output_html_file)
if os.path.isfile(self.tmp_folder):
os.remove(self.tmp_folder)
def test_design_primers_from_empty_folder(self):
pd = copy.copy(self.pd)
pd.folder = self.tmp_folder
self.assertRaises(AttributeError, pd.design_primers)
def test_get_alignments(self):
result = self.pd.get_alignments()
self.assertTrue(len(result) > 0)
def test_get_alignments_error(self):
pd = copy.copy(self.pd)
pd.folder = "fake_folder"
self.assertRaises(AttributeError, pd.get_alignments)
@responses.activate
def test_request_primers(self):
url = "http://floresta.eead.csic.es/primers4clades/primers4clades.cgi"
with open(RESPONSE, 'r') as handle:
response_html_body = handle.read()
responses.add(responses.POST, url,
body=response_html_body,
status=200,
content_type='application/text',
)
resp = self.pd.request_primers(ALIGNMENT)
assert resp.content.decode('ascii') == response_html_body
def test_report_from_html_response(self):
expected = """\n\n\
####################################################
# Alignment Ca2.fst
# Best Amplicon 4
>F_codeh
GACCTGAAAGAAGAACTGggvaargghgc
>R_codeh
CCAGGTGTACCAGCGaadccraacca
>F_relax
GACCTGAAAGAAGAACTGggvaargghgc
>R_relax
CCAGGTGTACCAgcraadccraacca
>F_degen
gahytdaargaagaaytdggvaargghgc
>R_degen
ccnggdgtdccdgcraadccraacca
# primer pair quality = 80%
# expected PCR product length (nt) = 471
# fwd: minTm = 62.0 maxTm = 67.5
# rev: minTm = 65.5 maxTm = 68.8"""
self.pd.process_response(ALIGNMENT, open(RESPONSE).read())
self.assertEqual(expected, self.pd.report)
def test_inserting_taxon_in_fasta_seq_descriptions(self):
self.pd.taxon_for_codon_usage = 'Bombyx mori'
modified_seq = self.pd.insert_taxon_in_new_fasta_file(os.path.join(TEST_FOLDER, 'Ca3.fst'))
for seq_record in SeqIO.parse(modified_seq, 'fasta'):
print(seq_record.description)
self.assertTrue("Bombyx mori]" in seq_record.description)
if os.path.isfile(modified_seq):
os.remove(modified_seq)
