def test_get_slice_list_of_ints(self):
span = Span(8, 22, 10, cyclic=True)
x = list(range(20, 140))
y = span.get_slice(x)
print(list(span.get_slice_iter(x)))
print(y)
assert y == [x[_s] for _s in list(span)]
span = Span(8, 22, 10, cyclic=True)
x = tuple(range(20, 140))
y = span.get_slice(x)
assert y == tuple([x[_s] for _s in list(span)])
def test_get_slice_seqrecord(self):
seq = SeqRecord(Seq("AGGGTGTGTGCGA"))
span = Span(8, 22, len(seq), cyclic=True)
seq2 = span.get_slice(seq)
assert isinstance(seq2, SeqRecord)
assert isinstance(seq2.seq, Seq)
print(seq2)
def pcr_amplify(
fwd: SeqRecord,
rev: SeqRecord,
template: SeqRecord,
cyclic: bool,
cyclic_buffer: int = 100,
name: str = None,
return_matches: bool = False,
):
original_template = template
if cyclic:
template = template + template + template[:cyclic_buffer]
fwd_matches, rev_matches = anneal(str(template.seq), [str(fwd.seq), str(rev.seq)])
products_by_sequence = {}
for f, r in itertools.product(fwd_matches, rev_matches):
i = f["top_strand_slice"][0]
j = r["top_strand_slice"][1]
try:
span = Span(
i,
j,
length=len(original_template.seq),
cyclic=cyclic,
ignore_wrap=True,
)
except IndexError as e:
if not cyclic:
continue
else:
raise e
f_rec = new_sequence(
f["overhang"], name=fwd.name + "_overhang", auto_annotate=True
)
r_rec = new_sequence(
rc(r["overhang"]), name=rev.name + "_overhang", auto_annotate=True
)
product = span.get_slice(original_template)
# annotate(template_chunk, name="source: {}".format(template_name[:40]))
if len(f_rec.seq):
product = f_rec + product
if len(r_rec.seq):
product = product + r_rec
if not name:
name = original_template.name or original_template.id
name += "[{}:{}]".format(span.a, span.b)
# annotate(product, name=name)
if len(product) <= len(original_template.seq):
products_by_sequence[str(product.seq)] = (product, span.a, span.b)
product_list = list(products_by_sequence.values())
product_list.sort(key=lambda x: (x[1], len(product)))
if return_matches:
return product_list, fwd_matches, rev_matches
return product_list
def test_get_slice_str(self):
span = Span(8, 22, 10, cyclic=True)
x = "abcdefghijklmnopqrstuv"
y = span.get_slice(x)
print(y)