def test_near_index():
'''Test binding near index for circular templates.'''
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
template = template.circularize()
seq = DNA('aggccctttcgtctcgcgcgttt')
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
print fwd_matches
print loc[0]
print loc[1]
assert_true(len(fwd_matches) == len(loc[0]))
assert_true(len(rev_matches) == len(loc[1]))
for match in loc[0]:
expected = match + len(seq)
if expected > len(template):
expected -= len(template)
assert_true(expected in fwd_indices)
for match in loc[1]:
expected = match + len(seq)
if expected > len(template):
expected -= len(template)
assert_true(expected in rev_indices)
def test_near_index():
'''Test binding near index for circular templates.'''
current_path = os.path.dirname(__file__)
template = seqio.read_dna(
os.path.join(current_path, "pMODKan-HO-pACT1GEV.ape"))
template = template.circularize()
seq = DNA('aggccctttcgtctcgcgcgttt')
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
print fwd_matches
print loc[0]
print loc[1]
assert_true(len(fwd_matches) == len(loc[0]))
assert_true(len(rev_matches) == len(loc[1]))
for match in loc[0]:
expected = match + len(seq)
if expected > len(template):
expected -= len(template)
assert_true(expected in fwd_indices)
for match in loc[1]:
expected = match + len(seq)
if expected > len(template):
expected -= len(template)
assert_true(expected in rev_indices)
def test_multiple_priming():
''' test multiple binding sites '''
current_path = os.path.dirname(__file__)
template = seqio.read_dna(
os.path.join(current_path, "pMODKan-HO-pACT1GEV.ape"))
template = template.circularize()
seq = DNA('cgccagggttttcccagtcacgac')
template = template.linearize()
template = template + seq + DNA("AGGCGTATGC") + seq
template = (template + DNA("GGGGGGG") + seq.reverse_complement() +
DNA("GGAAAG"))
template = template.circularize()
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_matches) == len(loc[0]))
assert_true(len(rev_matches) == len(loc[1]))
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
def test_multiple_priming():
''' test multiple binding sites '''
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
template = template.circularize()
seq = DNA('cgccagggttttcccagtcacgac')
template = template.linearize()
template = template + seq + DNA("AGGCGTATGC") + seq
template = (template + DNA("GGGGGGG") + seq.reverse_complement() +
DNA("GGAAAG"))
template = template.circularize()
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_matches) == len(loc[0]))
assert_true(len(rev_matches) == len(loc[1]))
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
def test_overhang():
''' test forward priming '''
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
seq = DNA('cgccagggttttcccagtcacgac')
overhang = DNA('ggggggg')
seq2 = overhang + seq
primer = Primer(seq2, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_indices) == len(loc[0]))
assert_true(len(rev_indices) == len(loc[1]))
# FIXME: Add match length check for all these cases.
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
# Test forward priming.
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
seq = DNA('ACAAGAGAGATTGGGAAGGAAAGGATCA')
overhang = DNA('ggggggg')
seq2 = overhang + seq
primer = Primer(seq2, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_indices) == len(loc[0]))
assert_true(len(rev_indices) == len(loc[1]))
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
def test_overhang():
''' test forward priming '''
current_path = os.path.dirname(__file__)
template = seqio.read_dna(
os.path.join(current_path, "pMODKan-HO-pACT1GEV.ape"))
seq = DNA('cgccagggttttcccagtcacgac')
overhang = DNA('ggggggg')
seq2 = overhang + seq
primer = Primer(seq2, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_indices) == len(loc[0]))
assert_true(len(rev_indices) == len(loc[1]))
# FIXME: Add match length check for all these cases.
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
# Test forward priming.
current_path = os.path.dirname(__file__)
template = seqio.read_dna(
os.path.join(current_path, "pMODKan-HO-pACT1GEV.ape"))
seq = DNA('ACAAGAGAGATTGGGAAGGAAAGGATCA')
overhang = DNA('ggggggg')
seq2 = overhang + seq
primer = Primer(seq2, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_indices) == len(loc[0]))
assert_true(len(rev_indices) == len(loc[1]))
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
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_construction():
plasmid_path = os.path.join(os.path.dirname(__file__), 'gibson_test.fasta')
f1_path = os.path.join(os.path.dirname(__file__), 'fragment_1.fasta')
f2_path = os.path.join(os.path.dirname(__file__), 'fragment_2.fasta')
f3_path = os.path.join(os.path.dirname(__file__), 'fragment_3.fasta')
f3_linear_path = os.path.join(os.path.dirname(__file__),
'fragment_3_linear.fasta')
plasmid = seqio.read_dna(plasmid_path).circularize()
f1 = seqio.read_dna(f1_path)
f2 = seqio.read_dna(f2_path)
f3 = seqio.read_dna(f3_path)
f3_linear = seqio.read_dna(f3_linear_path)
gibsoned_circular = reaction.gibson([f1, f2, f3])
gibsoned_linear = reaction.gibson([f1, f2, f3_linear], linear=True)
#
expected_length = len(plasmid)
gibsoned_circular_length = len(gibsoned_circular)
gibsoned_linear_length = len(gibsoned_linear)
assert_equal(gibsoned_circular_length, expected_length)
assert_equal(gibsoned_linear_length, expected_length)
assert_equal(gibsoned_circular.topology, 'circular')
assert_equal(gibsoned_linear.topology, 'linear')
assert(plasmid.is_rotation(gibsoned_circular))
try:
assert_equal(str(plasmid), str(gibsoned_linear))
except AssertionError:
assert_equal(str(plasmid), str(gibsoned_linear.flip()))
# Should fail with circular input
assert_raises(ValueError, reaction.gibson, [f1.circularize()])
# Should fail if compatible end can't be found
assert_raises(Exception, reaction.gibson, [f1, f3[50:-50]], linear=True)
normal = [f1, f2, f3]
rotated = [f1, f2, f3.reverse_complement()]
# Gibson should work regardless of fragment orientation
assert_true(reaction.gibson(normal).is_rotation(reaction.gibson(rotated)))
# A redundant fragment shouldn't affect the outcome
assert_equal(reaction.gibson([f1, f2, f3]),
reaction.gibson([f1, f2, f2, f3]))
# A fragment that can't circularize should raise a ValueError
assert_raises(ValueError, reaction.gibson, [f1, f2, f3[:-80]])
def test_construction():
plasmid_path = os.path.join(os.path.dirname(__file__), 'gibson_test.fasta')
f1_path = os.path.join(os.path.dirname(__file__), 'fragment_1.fasta')
f2_path = os.path.join(os.path.dirname(__file__), 'fragment_2.fasta')
f3_path = os.path.join(os.path.dirname(__file__), 'fragment_3.fasta')
f3_linear_path = os.path.join(os.path.dirname(__file__),
'fragment_3_linear.fasta')
plasmid = seqio.read_dna(plasmid_path).circularize()
f1 = seqio.read_dna(f1_path)
f2 = seqio.read_dna(f2_path)
f3 = seqio.read_dna(f3_path)
f3_linear = seqio.read_dna(f3_linear_path)
gibsoned_circular = reaction.gibson([f1, f2, f3])
gibsoned_linear = reaction.gibson([f1, f2, f3_linear], linear=True)
#
expected_length = len(plasmid)
gibsoned_circular_length = len(gibsoned_circular)
gibsoned_linear_length = len(gibsoned_linear)
assert_equal(gibsoned_circular_length, expected_length)
assert_equal(gibsoned_linear_length, expected_length)
assert_equal(gibsoned_circular.topology, 'circular')
assert_equal(gibsoned_linear.topology, 'linear')
assert (plasmid.is_rotation(gibsoned_circular))
try:
assert_equal(str(plasmid), str(gibsoned_linear))
except AssertionError:
assert_equal(str(plasmid), str(gibsoned_linear.flip()))
# Should fail with circular input
assert_raises(ValueError, reaction.gibson, [f1.circularize()])
# Should fail if compatible end can't be found
assert_raises(Exception, reaction.gibson, [f1, f3[50:-50]], linear=True)
normal = [f1, f2, f3]
rotated = [f1, f2, f3.reverse_complement()]
# Gibson should work regardless of fragment orientation
assert_true(reaction.gibson(normal).is_rotation(reaction.gibson(rotated)))
# A redundant fragment shouldn't affect the outcome
assert_equal(reaction.gibson([f1, f2, f3]),
reaction.gibson([f1, f2, f2, f3]))
# A fragment that can't circularize should raise a ValueError
assert_raises(ValueError, reaction.gibson, [f1, f2, f3[:-80]])
def test_min_primer_length():
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
# Test forward priming
seq = DNA('cgccagggttttcccagtcacgac')
seq = seq[:15]
primer = Primer(seq, 50.6)
assert_raises(analysis._sequence.anneal.PrimerLengthError, analysis.anneal,
template, primer, min_len=16)
def test_min_tm():
current_path = os.path.dirname(__file__)
template = seqio.read_dna(
os.path.join(current_path, "pMODKan-HO-pACT1GEV.ape"))
# Test forward priming
# Tm should be ~40 C
seq = DNA('CTTCTATCGAACAA')
primer = Primer(seq, seq.tm())
matches = analysis.anneal(template, primer, min_tm=60.0)
assert_true(len(matches[0]) == 0)
matches = analysis.anneal(template, primer, min_tm=30.0)
assert_true(len(matches[0]) > 0)
def test_min_tm():
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
# Test forward priming
# Tm should be ~40 C
seq = DNA('CTTCTATCGAACAA')
primer = Primer(seq, seq.tm())
matches = analysis.anneal(template, primer, min_tm=60.0)
assert_true(len(matches[0]) == 0)
matches = analysis.anneal(template, primer, min_tm=30.0)
assert_true(len(matches[0]) > 0)
def test_min_primer_length():
current_path = os.path.dirname(__file__)
template = seqio.read_dna(
os.path.join(current_path, "pMODKan-HO-pACT1GEV.ape"))
# Test forward priming
seq = DNA('cgccagggttttcccagtcacgac')
seq = seq[:15]
primer = Primer(seq, 50.6)
assert_raises(analysis._sequence.anneal.PrimerLengthError,
analysis.anneal,
template,
primer,
min_len=16)
def test_no_priming():
''' test no priming '''
current_path = os.path.dirname(__file__)
template = seqio.read_dna(
os.path.join(current_path, "pMODKan-HO-pACT1GEV.ape"))
seq = DNA('ggaggagggcggcgaggcgagcgacggaggggga')
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
loc = template.locate(seq)
assert_true(len(fwd_matches) == len(loc[0]))
assert_true(len(rev_matches) == len(loc[1]))
for match in loc[0]:
assert_true(match + len(seq) in fwd_matches)
for match in loc[1]:
assert_true(match + len(seq) in rev_matches)
def test_no_priming():
''' test no priming '''
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
seq = DNA('ggaggagggcggcgaggcgagcgacggaggggga')
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
loc = template.locate(seq)
assert_true(len(fwd_matches) == len(loc[0]))
assert_true(len(rev_matches) == len(loc[1]))
for match in loc[0]:
assert_true(match + len(seq) in fwd_matches)
for match in loc[1]:
assert_true(match + len(seq) in rev_matches)
def test_basic():
current_path = os.path.dirname(__file__)
template = seqio.read_dna(os.path.join(current_path,
"pMODKan-HO-pACT1GEV.ape"))
# Test forward priming.
seq = DNA('cgccagggttttcccagtcacgac')
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
# fwd_lens = [match[1] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
# rev_lens = [match[1] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_matches) == len(loc[0]))
assert_true(len(rev_matches) == len(loc[1]))
# Top strand matches
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
# Top strand matches
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
# Test reverse priming
seq = DNA('ACAAGAGAGATTGGGAAGGAAAGGATCA')
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_indices) == len(loc[0]))
assert_true(len(rev_indices) == len(loc[1]))
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
def test_basic():
current_path = os.path.dirname(__file__)
template = seqio.read_dna(
os.path.join(current_path, "pMODKan-HO-pACT1GEV.ape"))
# Test forward priming.
seq = DNA('cgccagggttttcccagtcacgac')
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
# fwd_lens = [match[1] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
# rev_lens = [match[1] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_matches) == len(loc[0]))
assert_true(len(rev_matches) == len(loc[1]))
# Top strand matches
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
# Top strand matches
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
# Test reverse priming
seq = DNA('ACAAGAGAGATTGGGAAGGAAAGGATCA')
primer = Primer(seq, 50.6)
matches = analysis.anneal(template, primer)
fwd_matches, rev_matches = matches
fwd_indices = [match[0] for match in fwd_matches]
rev_indices = [match[0] for match in rev_matches]
loc = template.locate(seq)
assert_true(len(fwd_indices) == len(loc[0]))
assert_true(len(rev_indices) == len(loc[1]))
for match in loc[0]:
assert_true(match + len(seq) in fwd_indices)
for match in loc[1]:
assert_true(match + len(seq) in rev_indices)
def read_reference(self, path):
'''Read in sequencing reference sequence.'''
seq = seqio.read_dna(path)
return seq
def read_reference(self, path):
'''Read in sequencing reference sequence.'''
seq = seqio.read_dna(path)
return seq
