def test_over_origin():
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
assert_true(template.topology == "circular")
primer1 = design.primer(template[-200:])
primer2 = design.primer(template.reverse_complement()[-200:])
over_origin = reaction.pcr(template, primer1, primer2)
expected = template[-200:] + template[0:200]
assert_equal(str(over_origin), str(expected))
def test_primer():
'''Test primer function.'''
seq = 'ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGC' + \
'GACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAG' + \
'CTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACC' + \
'ACCTTCGGCTACGGCCTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTC' + \
'TTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGC' + \
'AACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTG' + \
'AAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAAC' + \
'AGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATC' + \
'CGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATC' + \
'GGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCGCCCTGAGCAAA' + \
'GACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACT' + \
'CTCGGCATGGACGAGCTGTACAAGTAA'
dna_seq = DNA(seq)
primer = design.primer(dna_seq, tm=72, min_len=10, tm_undershoot=1,
tm_overshoot=3, end_gc=False,
tm_parameters='cloning', overhang=None)
assert_equals(str(primer), 'ATGGTGAGCAAGGGCGAGGAG')
# Ensure that overhang is appropriately applied
overhang_primer = design.primer(dna_seq, tm=72, min_len=10,
tm_undershoot=1, tm_overshoot=3,
end_gc=False,
tm_parameters='cloning',
overhang=DNA('GATCGATAT'))
assert_equals(str(overhang_primer), 'GATCGATATATGGTGAGCAAGGGCGAGGAG')
# If sequence is too short (too low of Tm), raise ValueError
too_short = DNA('at')
assert_raises(ValueError, design.primer, too_short, tm=72)
# Should design different primers (sometimes) if ending on GC is preferred
diff_template = DNA('GATCGATCGATACGATCGATATGCGATATGATCGATAT')
nogc = design.primer(diff_template, tm=72, min_len=10,
tm_undershoot=1, tm_overshoot=3, end_gc=False,
tm_parameters='cloning', overhang=None)
withgc = design.primer(diff_template, tm=72, min_len=10,
tm_undershoot=1, tm_overshoot=3,
end_gc=True, tm_parameters='cloning', overhang=None)
assert_not_equal(nogc, withgc)
# Should raise ValueError if it's impossible to create an end_gc primer
end_at_template = DNA('ATGCGATACGATACGCGATATGATATATatatatat' +
'ATAAaaaaaaaaaattttttttTTTTTTTTTTTTTT' +
'TTTTTTTTTT')
assert_raises(ValueError, design.primer, end_at_template,
end_gc=True, tm=72)
def test_primer():
'''Test primer function.'''
seq = 'ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGC' + \
'GACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAG' + \
'CTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACC' + \
'ACCTTCGGCTACGGCCTGCAGTGCTTCGCCCGCTACCCCGACCACATGAAGCAGCACGACTTC' + \
'TTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGC' + \
'AACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTG' + \
'AAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAAC' + \
'AGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATC' + \
'CGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATC' + \
'GGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCGCCCTGAGCAAA' + \
'GACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACT' + \
'CTCGGCATGGACGAGCTGTACAAGTAA'
dna_seq = DNA(seq)
primer = design.primer(dna_seq,
tm=72,
min_len=10,
tm_undershoot=1,
tm_overshoot=3,
end_gc=False,
tm_parameters='cloning',
overhang=None)
assert_equals(str(primer), 'ATGGTGAGCAAGGGCGAGGAG')
# Ensure that overhang is appropriately applied
overhang_primer = design.primer(dna_seq,
tm=72,
min_len=10,
tm_undershoot=1,
tm_overshoot=3,
end_gc=False,
tm_parameters='cloning',
overhang=DNA('GATCGATAT'))
assert_equals(str(overhang_primer), 'GATCGATATATGGTGAGCAAGGGCGAGGAG')
# If sequence is too short (too low of Tm), raise ValueError
too_short = DNA('at')
assert_raises(ValueError, design.primer, too_short, tm=72)
# Should design different primers (sometimes) if ending on GC is preferred
diff_template = DNA('GATCGATCGATACGATCGATATGCGATATGATCGATAT')
nogc = design.primer(diff_template,
tm=72,
min_len=10,
tm_undershoot=1,
tm_overshoot=3,
end_gc=False,
tm_parameters='cloning',
overhang=None)
withgc = design.primer(diff_template,
tm=72,
min_len=10,
tm_undershoot=1,
tm_overshoot=3,
end_gc=True,
tm_parameters='cloning',
overhang=None)
assert_not_equal(nogc, withgc)
# Should raise ValueError if it's impossible to create an end_gc primer
end_at_template = DNA('ATGCGATACGATACGCGATATGATATATatatatat' +
'ATAAaaaaaaaaaattttttttTTTTTTTTTTTTTT' +
'TTTTTTTTTT')
assert_raises(ValueError,
design.primer,
end_at_template,
end_gc=True,
tm=72)