def test_comprehensive(self):
logging.debug("\nBeginning Comprehensive Test.-----------")
(handle, filename) = tempfile.mkstemp()
handle = open(filename, "w")
handle.write("CATGTAACC\ncatgccccccccctaatct")
handle.close()
strands = helicase.load_strands_from_file(filename)
self.assertEqual(strands, ['catgtaacc', 'catgccccccccctaatct'])
framed_strands = []
for strand in strands:
framed_strands.append(helicase.frame_strand(strand))
self.assertEqual(framed_strands, [(['atg', 'taa', 'cc'], 1), (['atg', 'ccc', 'ccc', 'ccc', 'taa', 'tct'], 1)])
polypeptides = []
for strand in framed_strands:
polypeptides.append(helicase.translate_framed_strand(strand[0]))
self.assertEqual(polypeptides, [[('M', 'Met', 'Methionine')], [('M', 'Met', 'Methionine'),
('P', 'Pro', 'Proline'), ('P', 'Pro', 'Proline'),
('P', 'Pro', 'Proline')]])
polypeptide_representations = []
for polypeptide in polypeptides:
polypeptide_representations.append(helicase.represent_polypeptide(polypeptide, 1))
self.assertEqual(polypeptide_representations, ['Met', 'Met/Pro/Pro/Pro'])
logging.debug("Done Comprehensive Test.-----------\n")
transcribed_strands = []
for strand in strands:
transcribed_strands.append(helicase.transcribe(strand))
print(transcribed_strands)
print("\nRNA Transcription:")
transcribed_rna_strands = []
for strand in strands:
transcribed_rna_strands.append(helicase.transcribe_to_rna(strand))
print(transcribed_rna_strands)
print("\nTranslation:")
polypeptides = []
for strand in strands:
polypeptides.append(helicase.represent_polypeptide(helicase.translate_unframed_strand(strand),helicase.IUPAC_3))
print(polypeptides)
print("\nVerbose Translation:")
verbose_polypeptides = []
for strand in strands:
verbose_polypeptides.append(helicase.represent_polypeptide(helicase.translate_unframed_strand(strand),helicase.FULL_NAME))
print(verbose_polypeptides)
print("\nTerse Translation:")
terse_polypeptides = []
for strand in strands:
terse_polypeptides.append(helicase.represent_polypeptide(helicase.translate_unframed_strand(strand),helicase.IUPAC_1))
print(terse_polypeptides)
print("\n\nStrand -> Transcribed")
def test_represent_polypeptide(self):
print("\nBeginning Representation Test.")
polypeptide = [helicase.Met, helicase.Pro, helicase.Cys]
self.assertEqual(helicase.represent_polypeptide(polypeptide, helicase.IUPAC_1), "MPC")
self.assertEqual(helicase.represent_polypeptide(polypeptide, helicase.IUPAC_3), "Met/Pro/Cys")
self.assertEqual(helicase.represent_polypeptide(polypeptide, helicase.FULL_NAME), "Methionine, Proline, Cysteine")
def test_represent_polypeptide_raises_valueerror(self):
print("\nBeginning Invalid Verbosity Level Test.")
with self.assertRaises(ValueError):
helicase.represent_polypeptide([helicase.Met, helicase.Pro], 99)