def test_randomcodons():
'''
This test is pretty basic right now - not sure how much checking
can be done for a random DNA base generator.
'''
reference_seq = RNA('AUGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUAG')
reference_peptide = reaction.translate(reference_seq)
output = design.random_codons(reference_peptide)
output_peptide = reaction.translate(reference_seq)
assert_equal(len(output), len(reference_seq) - 3)
assert_equal(reference_peptide, output_peptide)
assert_not_equal(reference_seq, output)
# Setting too high a threshold should raise ValueError
assert_raises(ValueError,
design.random_codons,
reference_peptide,
frequency_cutoff=1.5)
# Weighted should work
w_output = design.random_codons(reference_peptide, weighted=True)
w_output_peptide = reaction.translate(reference_seq)
assert_equal(len(w_output), len(reference_seq) - 3)
assert_equal(reference_peptide, w_output_peptide)
assert_not_equal(reference_seq, w_output)
def test_randomcodons():
'''
This test is pretty basic right now - not sure how much checking
can be done for a random DNA base generator.
'''
reference_seq = RNA('AUGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUAG')
reference_peptide = reaction.translate(reference_seq)
output = design.random_codons(reference_peptide)
output_peptide = reaction.translate(reference_seq)
assert_equal(len(output), len(reference_seq) - 3)
assert_equal(reference_peptide, output_peptide)
assert_not_equal(reference_seq, output)
# Setting too high a threshold should raise ValueError
assert_raises(ValueError, design.random_codons, reference_peptide,
frequency_cutoff=1.5)
# Weighted should work
w_output = design.random_codons(reference_peptide, weighted=True)
w_output_peptide = reaction.translate(reference_seq)
assert_equal(len(w_output), len(reference_seq) - 3)
assert_equal(reference_peptide, w_output_peptide)
assert_not_equal(reference_seq, w_output)
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_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)