def test_transcription():
test_dna = DNA('ATGATGGGCAGTGTCGAATTAAATCTGCGTGAGACAGAATTGTGTT' +
'TGGGACTACCAGGCGGTGATACAGTTGCACCAGTAACAGGAAACAA' +
'AAGAGGATTCTCTGAAACAGTAGATTTGAAACTTAATTTGAACAAT' +
'GAGCCAGCCAACAAGGAAGGTTCCACCACTCATGACGTCGTCACAT' +
'TTGATAGTAAAGAAAAGAGTGCGTGTCCAAAAGATCCAGCTAAGCC' +
'ACCTGCCAAGGCTCAAGTCGTCGGATGGCCACCTGTGAGATCTTAT' +
'AGAAAGAACGTAATGGTTTCTTGTCAGAAGTCCAGTGGTGGTCCTG' +
'AAGCAGCGGCTtgaaaa')
reference_rna = RNA('AUGAUGGGCAGUGUCGAAUUAAAUCUGCGUGAGACAGAAUU' +
'GUGUUUGGGACUACCAGGCGGUGAUACAGUUGCACCAGUAA' +
'CAGGAAACAAAAGAGGAUUCUCUGAAACAGUAGAUUUGAAA' +
'CUUAAUUUGAACAAUGAGCCAGCCAACAAGGAAGGUUCCAC' +
'CACUCAUGACGUCGUCACAUUUGAUAGUAAAGAAAAGAGUG' +
'CGUGUCCAAAAGAUCCAGCUAAGCCACCUGCCAAGGCUCAA' +
'GUCGUCGGAUGGCCACCUGUGAGAUCUUAUAGAAAGAACGU' +
'AAUGGUUUCUUGUCAGAAGUCCAGUGGUGGUCCUGAAGCAG' +
'CGGCUugaaaa')
# Basic transcription should work
transcription_output = reaction.transcribe(test_dna)
assert_equal(transcription_output, reference_rna)
# Coding RNA should exclude anything after a stop codon
coding_rna_output = reaction.coding_sequence(transcription_output)
assert_equal(coding_rna_output, reference_rna[:-3])
# Should fail is sequence lacks start codon or stop codon
assert_raises(ValueError, reaction.coding_sequence,
reaction.transcribe(DNA('aaatag')))
assert_raises(ValueError, reaction.coding_sequence,
reaction.transcribe(DNA('atgaaa')))
def test_transcription():
test_dna = DNA('ATGATGGGCAGTGTCGAATTAAATCTGCGTGAGACAGAATTGTGTT' +
'TGGGACTACCAGGCGGTGATACAGTTGCACCAGTAACAGGAAACAA' +
'AAGAGGATTCTCTGAAACAGTAGATTTGAAACTTAATTTGAACAAT' +
'GAGCCAGCCAACAAGGAAGGTTCCACCACTCATGACGTCGTCACAT' +
'TTGATAGTAAAGAAAAGAGTGCGTGTCCAAAAGATCCAGCTAAGCC' +
'ACCTGCCAAGGCTCAAGTCGTCGGATGGCCACCTGTGAGATCTTAT' +
'AGAAAGAACGTAATGGTTTCTTGTCAGAAGTCCAGTGGTGGTCCTG' +
'AAGCAGCGGCTtgaaaa')
reference_rna = RNA('AUGAUGGGCAGUGUCGAAUUAAAUCUGCGUGAGACAGAAUU' +
'GUGUUUGGGACUACCAGGCGGUGAUACAGUUGCACCAGUAA' +
'CAGGAAACAAAAGAGGAUUCUCUGAAACAGUAGAUUUGAAA' +
'CUUAAUUUGAACAAUGAGCCAGCCAACAAGGAAGGUUCCAC' +
'CACUCAUGACGUCGUCACAUUUGAUAGUAAAGAAAAGAGUG' +
'CGUGUCCAAAAGAUCCAGCUAAGCCACCUGCCAAGGCUCAA' +
'GUCGUCGGAUGGCCACCUGUGAGAUCUUAUAGAAAGAACGU' +
'AAUGGUUUCUUGUCAGAAGUCCAGUGGUGGUCCUGAAGCAG' +
'CGGCUugaaaa')
# Basic transcription should work
transcription_output = reaction.transcribe(test_dna)
assert_equal(transcription_output, reference_rna)
# Coding RNA should exclude anything after a stop codon
coding_rna_output = reaction.coding_sequence(transcription_output)
assert_equal(coding_rna_output, reference_rna[:-3])
# Should fail is sequence lacks start codon or stop codon
assert_raises(ValueError, reaction.coding_sequence,
reaction.transcribe(DNA('aaatag')))
assert_raises(ValueError, reaction.coding_sequence,
reaction.transcribe(DNA('atgaaa')))
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)
