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'))
class TestPeptide(object):
'''
Testing class for sequence.Peptide
'''
def __init__(self):
self.test_peptide = Peptide('mkgp')
def test_locate(self):
assert_equal(self.test_peptide.locate('mk'), [0])
assert_equal(self.test_peptide.locate('gp'), [2])
assert_equal(len(self.test_peptide.locate('augg')), 0)
def test_copy(self):
assert_equal(self.test_peptide, self.test_peptide.copy())
def test_getitem(self):
assert_equal(str(self.test_peptide[0]), 'M')
assert_equal(str(self.test_peptide[1]), 'K')
assert_equal(str(self.test_peptide[2]), 'G')
assert_equal(str(self.test_peptide[3]), 'P')
assert_equal(str(self.test_peptide[-1]), 'P')
def test_delitem(self):
copy0 = self.test_peptide.copy()
del copy0[0]
assert_equal(str(copy0), 'KGP')
copy1 = self.test_peptide.copy()
del copy1[1]
assert_equal(str(copy1), 'MGP')
copy2 = self.test_peptide.copy()
del copy2[2]
assert_equal(str(copy2), 'MKP')
copy3 = self.test_peptide.copy()
del copy3[3]
assert_equal(str(copy3), 'MKG')
copy_1 = self.test_peptide.copy()
del copy_1[-1]
assert_equal(str(copy_1), 'MKG')
def test_setitem(self):
copy0 = self.test_peptide.copy()
copy0[0] = 'q'
assert_equal(str(copy0), 'QKGP')
copy1 = self.test_peptide.copy()
copy1[1] = 'q'
assert_equal(str(copy1), 'MQGP')
copy2 = self.test_peptide.copy()
copy2[2] = 'q'
assert_equal(str(copy2), 'MKQP')
copy3 = self.test_peptide.copy()
copy3[3] = 'q'
assert_equal(str(copy3), 'MKGQ')
copy_1 = self.test_peptide.copy()
copy_1[-1] = 'q'
assert_equal(str(copy_1), 'MKGQ')
def test_str(self):
assert_equal(str(self.test_peptide), 'MKGP')
def test_len(self):
assert_equal(len(self.test_peptide), 4)
def test_add(self):
assert_equal(str((self.test_peptide + self.test_peptide)), 'MKGPMKGP')
def test_radd(self):
assert_equal(str(sum([self.test_peptide, self.test_peptide])),
'MKGPMKGP')
def radd_800(seq):
return 800 + seq
assert_raises(TypeError, radd_800, self.test_peptide)
def test_mul(self):
assert_equal(str(self.test_peptide * 4), 'MKGPMKGPMKGPMKGP')
def mul_float(seq):
return seq * 7.56
assert_raises(TypeError, mul_float, self.test_peptide)
def test_eq(self):
assert_true(self.test_peptide == Peptide('mkgp'))
def test_ne(self):
assert_true(self.test_peptide != Peptide('mkqp'))
def test_contains(self):
assert_true('m' in self.test_peptide)
assert_true('k' in self.test_peptide)
assert_true('g' in self.test_peptide)
assert_true('p' in self.test_peptide)
assert_false('q' in self.test_peptide)
def __init__(self):
self.test_peptide = Peptide('mkgp')
class TestPeptide(object):
'''
Testing class for sequence.Peptide
'''
def __init__(self):
self.test_peptide = Peptide('mkgp')
def test_locate(self):
assert_equal(self.test_peptide.locate('mk'), [0])
assert_equal(self.test_peptide.locate('gp'), [2])
assert_equal(len(self.test_peptide.locate('augg')), 0)
def test_copy(self):
assert_equal(self.test_peptide, self.test_peptide.copy())
def test_getitem(self):
assert_equal(str(self.test_peptide[0]), 'M')
assert_equal(str(self.test_peptide[1]), 'K')
assert_equal(str(self.test_peptide[2]), 'G')
assert_equal(str(self.test_peptide[3]), 'P')
assert_equal(str(self.test_peptide[-1]), 'P')
def test_delitem(self):
copy0 = self.test_peptide.copy()
del copy0[0]
assert_equal(str(copy0), 'KGP')
copy1 = self.test_peptide.copy()
del copy1[1]
assert_equal(str(copy1), 'MGP')
copy2 = self.test_peptide.copy()
del copy2[2]
assert_equal(str(copy2), 'MKP')
copy3 = self.test_peptide.copy()
del copy3[3]
assert_equal(str(copy3), 'MKG')
copy_1 = self.test_peptide.copy()
del copy_1[-1]
assert_equal(str(copy_1), 'MKG')
def test_setitem(self):
copy0 = self.test_peptide.copy()
copy0[0] = 'q'
assert_equal(str(copy0), 'QKGP')
copy1 = self.test_peptide.copy()
copy1[1] = 'q'
assert_equal(str(copy1), 'MQGP')
copy2 = self.test_peptide.copy()
copy2[2] = 'q'
assert_equal(str(copy2), 'MKQP')
copy3 = self.test_peptide.copy()
copy3[3] = 'q'
assert_equal(str(copy3), 'MKGQ')
copy_1 = self.test_peptide.copy()
copy_1[-1] = 'q'
assert_equal(str(copy_1), 'MKGQ')
def test_str(self):
assert_equal(str(self.test_peptide), 'MKGP')
def test_len(self):
assert_equal(len(self.test_peptide), 4)
def test_add(self):
assert_equal(str((self.test_peptide + self.test_peptide)),
'MKGPMKGP')
def test_radd(self):
assert_equal(str(sum([self.test_peptide, self.test_peptide])),
'MKGPMKGP')
def radd_800(seq):
return 800 + seq
assert_raises(TypeError, radd_800, self.test_peptide)
def test_mul(self):
assert_equal(str(self.test_peptide * 4), 'MKGPMKGPMKGPMKGP')
def mul_float(seq):
return seq * 7.56
assert_raises(TypeError, mul_float, self.test_peptide)
def test_eq(self):
assert_true(self.test_peptide == Peptide('mkgp'))
def test_ne(self):
assert_true(self.test_peptide != Peptide('mkqp'))
def test_contains(self):
assert_true('m' in self.test_peptide)
assert_true('k' in self.test_peptide)
assert_true('g' in self.test_peptide)
assert_true('p' in self.test_peptide)
assert_false('q' in self.test_peptide)
def __init__(self):
self.test_peptide = Peptide('mkgp')
