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')
