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_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_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_reverse_transcription():
test_rna = RNA('AUGAUGGGCAGUGUCGAAUUAAAUCUGCGUGAGACAGAAUU' +
'GUGUUUGGGACUACCAGGCGGUGAUACAGUUGCACCAGUAA' +
'CAGGAAACAAAAGAGGAUUCUCUGAAACAGUAGAUUUGAAA' +
'CUUAAUUUGAACAAUGAGCCAGCCAACAAGGAAGGUUCCAC' +
'CACUCAUGACGUCGUCACAUUUGAUAGUAAAGAAAAGAGUG' +
'CGUGUCCAAAAGAUCCAGCUAAGCCACCUGCCAAGGCUCAA' +
'GUCGUCGGAUGGCCACCUGUGAGAUCUUAUAGAAAGAACGU' +
'AAUGGUUUCUUGUCAGAAGUCCAGUGGUGGUCCUGAAGCAG' + 'CGGCUugaaaa')
ref_dna = DNA('ATGATGGGCAGTGTCGAATTAAATCTGCGTGAGACAGAATTGTGTT' +
'TGGGACTACCAGGCGGTGATACAGTTGCACCAGTAACAGGAAACAA' +
'AAGAGGATTCTCTGAAACAGTAGATTTGAAACTTAATTTGAACAAT' +
'GAGCCAGCCAACAAGGAAGGTTCCACCACTCATGACGTCGTCACAT' +
'TTGATAGTAAAGAAAAGAGTGCGTGTCCAAAAGATCCAGCTAAGCC' +
'ACCTGCCAAGGCTCAAGTCGTCGGATGGCCACCTGTGAGATCTTAT' +
'AGAAAGAACGTAATGGTTTCTTGTCAGAAGTCCAGTGGTGGTCCTG' +
'AAGCAGCGGCTtgaaaa')
# Basic transcription should work
r_transcription = reaction.reverse_transcribe(test_rna)
assert_equal(r_transcription, ref_dna)
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)
class TestRNA(object):
'''
Testing class for sequence.RNA
'''
def __init__(self):
self.test_rna = RNA('augc')
def test_reverse_complement(self):
assert_equal(str(self.test_rna.reverse_complement()), 'GCAU')
def test_locate(self):
assert_equal(self.test_rna.locate('au'), [0])
assert_equal(self.test_rna.locate('gc'), [2])
assert_equal(len(self.test_rna.locate('augg')), 0)
def test_copy(self):
assert_equal(self.test_rna, self.test_rna.copy())
def test_getitem(self):
assert_equal(str(self.test_rna[0]), 'A')
assert_equal(str(self.test_rna[1]), 'U')
assert_equal(str(self.test_rna[2]), 'G')
assert_equal(str(self.test_rna[3]), 'C')
assert_equal(str(self.test_rna[-1]), 'C')
def test_delitem(self):
copy0 = self.test_rna.copy()
del copy0[0]
assert_equal(str(copy0), 'UGC')
copy1 = self.test_rna.copy()
del copy1[1]
assert_equal(str(copy1), 'AGC')
copy2 = self.test_rna.copy()
del copy2[2]
assert_equal(str(copy2), 'AUC')
copy3 = self.test_rna.copy()
del copy3[3]
assert_equal(str(copy3), 'AUG')
copy_1 = self.test_rna.copy()
del copy_1[-1]
assert_equal(str(copy_1), 'AUG')
def test_setitem(self):
copy0 = self.test_rna.copy()
copy0[0] = 'u'
assert_equal(str(copy0), 'UUGC')
copy1 = self.test_rna.copy()
copy1[1] = 'a'
assert_equal(str(copy1), 'AAGC')
copy2 = self.test_rna.copy()
copy2[2] = 'a'
assert_equal(str(copy2), 'AUAC')
copy3 = self.test_rna.copy()
copy3[3] = 'a'
assert_equal(str(copy3), 'AUGA')
copy_1 = self.test_rna.copy()
copy_1[-1] = 'a'
assert_equal(str(copy_1), 'AUGA')
def test_str(self):
assert_equal(str(self.test_rna), 'AUGC')
def test_len(self):
assert_equal(len(self.test_rna), 4)
def test_add(self):
assert_equal(str((self.test_rna + self.test_rna)), 'AUGCAUGC')
def test_radd(self):
assert_equal(str(sum([self.test_rna, self.test_rna])), 'AUGCAUGC')
def radd_800(seq):
return 800 + seq
assert_raises(TypeError, radd_800, self.test_rna)
def test_mul(self):
assert_equal(str((self.test_rna * 4)), 'AUGCAUGCAUGCAUGC')
def mul_float(seq):
return seq * 7.56
assert_raises(TypeError, mul_float, self.test_rna)
def test_eq(self):
assert_true(self.test_rna == RNA('augc'))
def test_ne(self):
assert_true(self.test_rna != RNA('aagc'))
def test_contains(self):
assert_true('a' in self.test_rna)
assert_true('u' in self.test_rna)
assert_true('g' in self.test_rna)
assert_true('c' in self.test_rna)
assert_false('t' in self.test_rna)
def __init__(self):
self.test_rna = RNA('augc')
def test_ne(self):
assert_true(self.test_rna != RNA('aagc'))
def test_eq(self):
assert_true(self.test_rna == RNA('augc'))
class TestRNA(object):
'''
Testing class for sequence.RNA
'''
def __init__(self):
self.test_rna = RNA('augc')
def test_reverse_complement(self):
assert_equal(str(self.test_rna.reverse_complement()), 'GCAU')
def test_locate(self):
assert_equal(self.test_rna.locate('au'), [0])
assert_equal(self.test_rna.locate('gc'), [2])
assert_equal(len(self.test_rna.locate('augg')), 0)
def test_copy(self):
assert_equal(self.test_rna, self.test_rna.copy())
def test_getitem(self):
assert_equal(str(self.test_rna[0]), 'A')
assert_equal(str(self.test_rna[1]), 'U')
assert_equal(str(self.test_rna[2]), 'G')
assert_equal(str(self.test_rna[3]), 'C')
assert_equal(str(self.test_rna[-1]), 'C')
def test_delitem(self):
copy0 = self.test_rna.copy()
del copy0[0]
assert_equal(str(copy0), 'UGC')
copy1 = self.test_rna.copy()
del copy1[1]
assert_equal(str(copy1), 'AGC')
copy2 = self.test_rna.copy()
del copy2[2]
assert_equal(str(copy2), 'AUC')
copy3 = self.test_rna.copy()
del copy3[3]
assert_equal(str(copy3), 'AUG')
copy_1 = self.test_rna.copy()
del copy_1[-1]
assert_equal(str(copy_1), 'AUG')
def test_setitem(self):
copy0 = self.test_rna.copy()
copy0[0] = 'u'
assert_equal(str(copy0), 'UUGC')
copy1 = self.test_rna.copy()
copy1[1] = 'a'
assert_equal(str(copy1), 'AAGC')
copy2 = self.test_rna.copy()
copy2[2] = 'a'
assert_equal(str(copy2), 'AUAC')
copy3 = self.test_rna.copy()
copy3[3] = 'a'
assert_equal(str(copy3), 'AUGA')
copy_1 = self.test_rna.copy()
copy_1[-1] = 'a'
assert_equal(str(copy_1), 'AUGA')
def test_str(self):
assert_equal(str(self.test_rna), 'AUGC')
def test_len(self):
assert_equal(len(self.test_rna), 4)
def test_add(self):
assert_equal(str((self.test_rna + self.test_rna)), 'AUGCAUGC')
def test_radd(self):
assert_equal(str(sum([self.test_rna, self.test_rna])), 'AUGCAUGC')
def radd_800(seq):
return 800 + seq
assert_raises(TypeError, radd_800, self.test_rna)
def test_mul(self):
assert_equal(str((self.test_rna * 4)), 'AUGCAUGCAUGCAUGC')
def mul_float(seq):
return seq * 7.56
assert_raises(TypeError, mul_float, self.test_rna)
def test_eq(self):
assert_true(self.test_rna == RNA('augc'))
def test_ne(self):
assert_true(self.test_rna != RNA('aagc'))
def test_contains(self):
assert_true(RNA('a') in self.test_rna)
assert_true(RNA('u') in self.test_rna)
assert_true(RNA('g') in self.test_rna)
assert_true(RNA('c') in self.test_rna)
assert_false(RNA('a') in RNA('ugc'))
def __init__(self):
self.test_rna = RNA('augc')
def test_contains(self):
assert_true(RNA('a') in self.test_rna)
assert_true(RNA('u') in self.test_rna)
assert_true(RNA('g') in self.test_rna)
assert_true(RNA('c') in self.test_rna)
assert_false(RNA('a') in RNA('ugc'))