def test_utils(): test_DNA = DNA('ATAGCGATACGAT') test_RNA = RNA('AUGCGAUAGCGAU') test_peptide = Peptide('msvkkkpvqg') test_str = 'msvkkkpvgq' assert_equal(analysis.utils.sequence_type(test_DNA), 'dna') assert_equal(analysis.utils.sequence_type(test_RNA), 'rna') assert_equal(analysis.utils.sequence_type(test_peptide), 'peptide') assert_raises(Exception, analysis.utils.sequence_type, test_str)
def test_translation(): test_rna = RNA('AUGAUGGGCAGUGUCGAAUUAAAUCUGCGUGAGACAGAAUU' + 'GUGUUUGGGACUACCAGGCGGUGAUACAGUUGCACCAGUAA' + 'CAGGAAACAAAAGAGGAUUCUCUGAAACAGUAGAUUUGAAA' + 'CUUAAUUUGAACAAUGAGCCAGCCAACAAGGAAGGUUCCAC' + 'CACUCAUGACGUCGUCACAUUUGAUAGUAAAGAAAAGAGUG' + 'CGUGUCCAAAAGAUCCAGCUAAGCCACCUGCCAAGGCUCAA' + 'GUCGUCGGAUGGCCACCUGUGAGAUCUUAUAGAAAGAACGU' + 'AAUGGUUUCUUGUCAGAAGUCCAGUGGUGGUCCUGAAGCAG' + 'CGGCUugaaaa') reference_peptide = Peptide('MMGSVELNLRETELCLGLPGGDTVAPVTGNK' + 'RGFSETVDLKLNLNNEPANKEGSTTHDVVTF' + 'DSKEKSACPKDPAKPPAKAQVVGWPPVRSYR' + 'KNVMVSCQKSSGGPEAAA') # Basic transcription should work translation_output = reaction.translate(test_rna) assert_equal(translation_output, reference_peptide) # Coding peptide should exclude anything after a stop codon coding_rna = reaction.coding_sequence(test_rna) coding_peptide = reaction.translate(coding_rna) assert_equal(coding_peptide, reference_peptide)
def test_ne(self): assert_true(self.test_peptide != Peptide('mkqp'))
def test_eq(self): assert_true(self.test_peptide == Peptide('mkgp'))
def __init__(self): self.test_peptide = Peptide('mkgp')