def test_left_overhang_default_behavior(self, gfp):
"""Without setting overhangs, should raise run time error."""
design = Design()
design.settings.template(gfp)
design.settings.left_sequence("AGGCGGCTGA" + gfp[20:40])
with pytest.raises(Primer3PlusRunTimeError):
design.run()
def test_gfp(gfp, iter_random_primer):
fwd_primers = list(iter_random_primer(25, gfp[:250], 16))
rev_primers = list(iter_random_primer(25, rc(gfp)[:250], 16))
primers = fwd_primers + rev_primers
# from itertools import product
#
# for f, r in product(fwd_primers, rev_primers):
# design = Design()
# design.settings.left_sequence(f)
# design.settings.right_sequence(r)
# design.settings.task('check_primers')
# design.settings.template(gfp)
# design.run()
region_ok = check_primers(gfp, primers)
# print(region_ok[:1])
design = Design()
design.settings.template(gfp)
print(region_ok)
design.settings.pair_region_list(region_ok[:10])
design.settings.product_size([50, 2000])
pairs, explain = design.run()
print(explain)
print(pairs)
def test_left_overhang(self, gfp):
design = Design()
design.settings.template(gfp)
design.settings.left_sequence("AGGCGGCTGA" + gfp[0:20])
design.settings.use_overhangs()
pairs, explain = design.run_and_optimize(5)
print(explain)
assert pairs
def test_set(gfp):
design = Design()
design.settings.template(gfp)
design.settings.left_sequence(gfp[60:85])
design.settings.as_generic_task()
results = design.run()
print(results)
assert results
def test_right_overhang_default_behavior(self, gfp):
"""Without setting overhangs, should raise run time error."""
design = Design()
design.settings.template(gfp)
rseq = "AAAAAA" + rc(gfp[200:220])
design.settings.right_sequence(rseq)
with pytest.raises(Primer3PlusRunTimeError):
design.run()
def test_right_overhang(self, gfp):
design = Design()
design.settings.template(gfp)
rseq = "AGGCGGCTGA" + rc(gfp[200:225])
design.settings.right_sequence(rseq)
design.settings.use_overhangs()
pairs, explain = design.run_and_optimize(5)
assert pairs
def test_both_overhangs(self, gfp):
design = Design()
design.settings.template(gfp)
lseq = "TTTTTT" + gfp[10:30]
rseq = rc(gfp[200:220] + "AAAAAAA")
design.settings.left_sequence(lseq)
design.settings.right_sequence(rseq)
design.settings.use_overhangs()
pairs, explain = design.run_and_optimize(5)
assert pairs
def test_long_right_primer(self, gfp):
design = Design()
design.settings.template(gfp)
design.settings.right_sequence(rc(gfp[-50:]))
design.PRIMER_MAX_TM.value = 75.0
design.PRIMER_MAX_SIZE = 35
design.PRIMER_PICK_ANYWAY = 1
design.settings.long_ok()
pairs, explain = design.run_and_optimize(10)
print(explain)
assert pairs
def test_run_and_optimize_basic(gfp, iter_random_primer):
fwd = gfp[:25]
rev = reverse_complement(gfp[-25:])
design = Design()
design.settings.template(gfp)
design.settings.left_sequence(fwd)
design.settings.right_sequence(rev)
design.settings.task("check_primers")
pairs, explain = design.run()
assert not pairs
pairs, explain = design.run_and_optimize(15)
print(explain)
assert pairs
def test_set_long_primers_with_included_and_size(self, gfp):
design = Design()
design.settings.template(gfp)
left = gfp[10:60]
design.settings.left_sequence(left)
design.settings.included((10, 400))
design.settings.product_size((400, 400))
design.settings.long_ok()
design.settings.use_overhangs()
design.settings.pick_anyway()
pairs, explain = design.run_and_optimize(15)
assert pairs
def test_set_long_right_primers_with_included_and_size(self, gfp):
design = Design()
design.settings.template(gfp)
right = rc(gfp[-100:-20])
design.settings.right_sequence(right)
design.settings.included((len(gfp) - 50 - 300, 300))
design.settings.product_size((250, 250))
design.settings.long_ok()
design.settings.use_overhangs()
design.settings.pick_anyway()
pairs, explain = design.run_and_optimize(15)
print(pairs)
assert pairs
def test_set_long_overhang(self, gfp):
design = Design()
design.settings.template(gfp)
design.settings.left_sequence(gfp[0:50])
design.PRIMER_MAX_TM.value = 75.0
design.PRIMER_MAX_SIZE = 35
design.PRIMER_PICK_ANYWAY = 1
design.settings.left_overhang("AAAAAAAAA")
design.settings.long_ok()
design.settings.use_overhangs()
design.settings.pick_anyway()
pairs, explain = design.run()
print(explain)
import json
print(json.dumps(pairs[0]["LEFT"], indent=1))
assert pairs
def test_long_left_primer_with_overhangs(self, gfp):
"""We expect no errors with setting long left primers.
The settings should automatically readjust the product length to
match and the 'SEQUENCE', 'OVERHANG', and 'location' and
'PRODUCT_SIZE' results should automatically be adjusted.
"""
design = Design()
design.settings.template(gfp)
design.settings.left_sequence(gfp[:50])
design.settings.product_size((len(gfp), len(gfp)))
loverhang = "TTTTTTT"
roverhang = "GGGAGAG"
design.settings.left_overhang(loverhang)
design.settings.right_overhang(roverhang)
design.settings.long_ok()
design.settings.use_overhangs()
design.settings.pick_anyway()
pairs, explain = design.run()
pprint(pairs)
assert pairs
for pair in pairs.values():
assert pair["PAIR"]["PRODUCT_SIZE"] == len(gfp)
assert pair["RIGHT"]["OVERHANG"] == roverhang
assert pair["LEFT"]["OVERHANG"] == loverhang
assert pair["LEFT"]["SEQUENCE"] == gfp[:50]
lloc = pair["LEFT"]["location"]
rloc = pair["RIGHT"]["location"]
assert lloc[0] == 0
assert lloc[1] == 50
assert rloc[0] == len(gfp) - 1
assert pairs
def test_long_right_primer_default_behavior(self, gfp):
design = Design()
design.settings.template(gfp)
design.settings.right_sequence(rc(gfp[-50:]))
design.PRIMER_MAX_TM.value = 75.0
design.PRIMER_MAX_SIZE = 35
design.PRIMER_PICK_ANYWAY = 1
with pytest.raises(Primer3PlusRunTimeError):
design.run_and_optimize(10)
def test_as_str(self, gfp):
design = Design()
design.settings.template(gfp).excluded(gfp[100:300])
pairs, explain = design.run()
assert pairs
def test_as_list_of_tuples(self, gfp):
design = Design()
design.settings.template(gfp).excluded([(100, 300)])
pairs, explain = design.run()
assert pairs
def test_as_list(self, gfp):
design = Design()
design.settings.template(gfp).excluded([100, 300])
print(design.SEQUENCE_EXCLUDED_REGION)
pairs, explain = design.run()
assert pairs
def test_product_size_list(gfp):
design = Design()
design.settings.template(gfp)
design.settings.product_size([(50, 100), (200, 300)])
design.run()
def test_as_str(self, gfp):
design = Design()
design.settings.template(gfp).included(gfp[100:300])
print(design.SEQUENCE_INCLUDED_REGION)
pairs, explain = design.run()
assert pairs
def test_raises_value_error(self, gfp):
design = Design()
design.settings.template(gfp).included([None, 100])
print(design.SEQUENCE_INCLUDED_REGION)
with pytest.raises(TypeError):
design.run()
def test_as_tuple(self, gfp):
design = Design()
design.settings.template(gfp).included((100, 100))
print(design.SEQUENCE_INCLUDED_REGION)
pairs, explain = design.run()
assert pairs
def test_raises_value_error(self, gfp):
design = Design()
with pytest.raises(TypeError):
design.settings.template(gfp).included([100, 100, 100])
def test_init():
design = Design()
