def helper(name):
in_path = examples / name
out_path = tmp_path / in_path.name
in_dna = snap.parse(examples / name)
snap.write(out_path, in_dna)
out_dna = snap.parse(out_path)
print('input...')
yield in_dna
print('output...')
yield out_dna
def test_extract_traces(examples, tmp_path):
dna = snap.parse(examples / 'puc19_bsai_abc.dna')
dna.extract_traces(tmp_path)
assert (tmp_path / 'puc19_bsai_a.ztr').exists()
assert (tmp_path / 'puc19_bsai_b.ztr').exists()
assert (tmp_path / 'puc19_bsai_c.ztr').exists()
def test_replace_target(examples):
dna = snap.parse(examples / 'puc19_bsai_ab.dna')
assert dna.count_traces() == count_seq_blocks(dna) == 2
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_b']
dna.replace_trace(examples / 'puc19_bsai_b', examples / 'puc19_bsai_c.ab1')
assert dna.count_traces() == count_seq_blocks(dna) == 2
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_c']
def test_sort_traces(examples):
dna = snap.parse(examples / 'puc19_bsai_abc.dna')
assert dna.count_traces() == count_seq_blocks(dna) == 3
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_b', 'puc19_bsai_c']
dna.sort_traces(reverse=True)
assert dna.count_traces() == count_seq_blocks(dna) == 3
assert dna.trace_names == ['puc19_bsai_c', 'puc19_bsai_b', 'puc19_bsai_a']
def test_insert_trace(examples):
dna = snap.parse(examples / 'puc19_bsai_ab.dna')
assert dna.count_traces() == count_seq_blocks(dna) == 2
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_b']
dna.insert_trace(1, examples / 'puc19_bsai_c.ab1')
assert dna.count_traces() == count_seq_blocks(dna) == 3
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_c', 'puc19_bsai_b']
def test_remove_trace_dups(examples):
dna = snap.parse(examples / 'puc19_bsai_ab.dna')
dna.append_trace(examples / 'puc19_bsai_a.ab1')
assert dna.count_traces() == count_seq_blocks(dna) == 3
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_b', 'puc19_bsai_a']
dna.remove_trace('puc19_bsai_a')
assert dna.count_traces() == count_seq_blocks(dna) == 1
assert dna.trace_names == ['puc19_bsai_b']
def test_remove_feature(examples):
dna = snap.parse(examples / 't7_promoter.dna')
assert dna.count_features() == 1
dna.remove_feature('T7 promoter')
assert dna.count_features() == 0
with pytest.raises(snap.FeatureNotFound):
dna.remove_feature('T7 promoter')
with pytest.raises(snap.FeatureNotFound):
dna.remove_feature('Does not exist')
def test_add_feature(examples):
dna = snap.parse(examples / 't7_promoter.dna')
assert dna.count_features() == 1
feat = snap.Feature()
feat.name = 'Blah'
feat.segments = [snap.FeatureSegment()]
feat.segments[0].range = 2, 18
feat.segments[0].color = '#ff0000'
dna.add_feature(feat)
assert dna.count_features() == 2
def test_clear_traces(examples):
dna = snap.parse(examples / 'puc19_bsai_abc.dna')
assert dna.count_traces() == count_seq_blocks(dna) == 3
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_b', 'puc19_bsai_c']
dna.clear_traces()
assert dna.count_traces() == count_seq_blocks(dna) == 0
assert dna.trace_names == []
# Not an error to clar an empty sequence.
dna.clear_traces()
assert dna.count_traces() == count_seq_blocks(dna) == 0
assert dna.trace_names == []
def test_remove_trace(examples):
dna = snap.parse(examples / 'puc19_bsai_abc.dna')
assert dna.count_traces() == count_seq_blocks(dna) == 3
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_b', 'puc19_bsai_c']
dna.remove_trace('puc19_bsai_b')
assert dna.count_traces() == count_seq_blocks(dna) == 2
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_c']
dna.remove_trace('puc19_bsai_c')
assert dna.count_traces() == count_seq_blocks(dna) == 1
assert dna.trace_names == ['puc19_bsai_a']
dna.remove_trace(examples / 'puc19_bsai_a.ab1')
assert dna.count_traces() == count_seq_blocks(dna) == 0
assert dna.trace_names == []
with pytest.raises(ValueError):
dna.remove_trace('xxx')
def test_add_trace(examples):
dna = snap.parse(examples / 'puc19_bsai.dna')
assert dna.count_traces() == count_seq_blocks(dna) == 0
assert dna.trace_names == []
dna.add_trace(examples / 'puc19_bsai_a.ab1')
assert dna.count_traces() == count_seq_blocks(dna) == 1
assert dna.trace_names == ['puc19_bsai_a']
dna.add_trace(examples / 'puc19_bsai_a.ab1')
assert dna.count_traces() == count_seq_blocks(dna) == 1
assert dna.trace_names == ['puc19_bsai_a']
dna.add_trace(examples / 'puc19_bsai_b.ab1')
assert dna.count_traces() == count_seq_blocks(dna) == 2
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_b']
dna.add_trace(examples / 'puc19_bsai_b.ab1')
assert dna.count_traces() == count_seq_blocks(dna) == 2
assert dna.trace_names == ['puc19_bsai_a', 'puc19_bsai_b']
suggested by NEB above, which is interesting because this
sequence is presumably optimized to be short (as it’s already
on the long-side for a PCR primer).
It’s also worth noting that the aaaaaat 3’ of the SD sequence
creates a 6 bp spacing, 1 bp longer than ideal. Again, it’s not
clear what the rationale for this is."""), ),
),
Block(
name={
k: " ".join(["Zif268"] + ([] if k == 'wt' else [k.upper()]))
for k in names
},
sequence={
k: reverse_translate(
snap.parse(f'zif268_{k}.prot').protein_sequence,
forbidden_seqs=restriction_sites,
include_stop=False,
)
for k in names
},
type='CDS',
color=colors['blue'],
directionality='forward',
is_translated=True,
),
# 3' BsaI site for Golden Gate cloning.
Block('tGAGACCa'),
]
def test_trace_names(examples, path, names):
dna = snap.parse(examples / path)
assert dna.trace_names == names
def test_have_trace(examples, path, name, has_trace):
dna = snap.parse(examples / path)
assert dna.has_trace(name) == has_trace
def test_count_traces(examples, path, count):
dna = snap.parse(examples / path)
assert dna.count_traces() == count
def test_get_feature(examples):
dna = snap.parse(examples / 't7_promoter.dna')
feat = dna.get_feature("T7 promoter")
assert feat.name == "T7 promoter"
assert feat.type == 'promoter'
def test_clear_features(examples):
dna = snap.parse(examples / 't7_promoter.dna')
assert dna.count_features() == 1
dna.clear_features()
assert dna.count_features() == 0
def _seq_from_tag(dir, tag):
if path := _path_from_tag(dir, tag):
return snap.parse(path).dna_sequence
def get_plasmid_seq(tag):
dna = snap.parse(get_plasmid_path(tag))
return DnaSeq(dna.sequence)