def test_primers():
'''Test primers function.'''
seq = 'ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGC' + \
'GACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAG' + \
'CTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACC' + \
'ACCTTCGGCTACGGCCTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTC' + \
'TTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGC' + \
'AACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTG' + \
'AAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAAC' + \
'AGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATC' + \
'CGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATC' + \
'GGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCGCCCTGAGCAAA' + \
'GACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACT' + \
'CTCGGCATGGACGAGCTGTACAAGTAA'
dna_seq = DNA(seq)
primers_list = design.primers(dna_seq,
tm=72,
min_len=10,
tm_undershoot=1,
tm_overshoot=3,
end_gc=False,
tm_parameters='cloning',
overhangs=None)
primers = [str(x.primer()) for x in primers_list]
assert_equals(primers,
['ATGGTGAGCAAGGGCGAGGAG', 'TTACTTGTACAGCTCGTCCATGCCG'])
def test_basic():
to_amplify = 'atgtctaaaggtgaagaattattcactggtgttgtcccaatgctgctggtattacc' + \
'catggtattgatgaattgtacaaatag'
template = DNA(to_amplify)
forward, reverse = design.primers(template)
amplicon = reaction.pcr(template, forward, reverse)
assert_equal(amplicon, template)
def test_primer_bind_error():
to_amplify = 'atgtctaaaggtgaagaattattcactggtgttgtcccaatgctgctggtattacc' + \
'catggtattgatgaattgtacaaatag'
template = DNA(to_amplify)
primer1, primer2 = design.primers(template)
# Mess up the second primer so it doesn't bind
primer2.anneal[0:10] = "AAAAAAAAAA"
assert_raises(reaction._pcr.PrimerBindError, reaction.pcr,
template, primer1, primer2)
def test_primers():
'''Test primers function.'''
seq = 'ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGC' + \
'GACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAG' + \
'CTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACC' + \
'ACCTTCGGCTACGGCCTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTC' + \
'TTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGC' + \
'AACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTG' + \
'AAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAAC' + \
'AGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATC' + \
'CGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATC' + \
'GGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCGCCCTGAGCAAA' + \
'GACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACT' + \
'CTCGGCATGGACGAGCTGTACAAGTAA'
dna_seq = DNA(seq)
primers_list = design.primers(dna_seq, tm=72, min_len=10,
tm_undershoot=1, tm_overshoot=3,
end_gc=False, tm_parameters='cloning',
overhangs=None)
primers = [str(x.primer()) for x in primers_list]
assert_equals(primers, ['ATGGTGAGCAAGGGCGAGGAG',
'TTACTTGTACAGCTCGTCCATGCCG'])
