def test_master_mix_dunder():
# Just quickly call all the dunders to make sure they're doing something.
# The `test_reaction_...()` tests make sure these methods actually work.
mm = MasterMix()
mm.solvent = 'w'
# `__repr__()`
assert repr(mm) == "MasterMix('w')"
# `__getitem__()`
mm['x'].volume = '1 µL'
assert mm.reaction['x'].volume == '1 µL'
# `__iter__()`
for reagent, expected in zip(mm, ['w', 'x']):
assert reagent.name == expected
# `__contains__()`
assert 'w' in mm
assert 'x' in mm
assert 'y' not in mm
# `__len__()`
assert len(mm) == 2
# `__delitem__()`
del mm['x']
assert len(mm) == 1
def test_master_mix_setattr():
mm = MasterMix()
mm.volume = '1 µL'
assert mm.reaction.volume == '1 µL'
mm.solvent = 'w'
assert mm.reaction.solvent == 'w'
def test_master_mix_replace_text():
mm = MasterMix.from_text("""\
Reagent Stock Volume MM?
========= ===== ======== ===
water to 10 µL yes
long name 10x 1 µL yes
""")
assert str(mm) == """\
Reagent Stock Volume
──────────────────────────
water 9.00 µL
long name 10x 1.00 µL
──────────────────────────
10.00 µL"""
mm.replace_text('long ', '')
assert str(mm) == """\
Reagent Stock Volume
────────────────────────
water 9.00 µL
name 10x 1.00 µL
────────────────────────
10.00 µL"""
mm.replace_text('name', 'extra long name')
assert str(mm) == """\
def test_master_mix_format_text_0_volume_reagent():
mm = MasterMix.from_text("""\
Reagent Stock Volume MM?
======== ===== ======= ===
water to 3 µL yes
buffer 3x 1 µL yes
cofactor 3x 1 µL yes
enzyme 3x 1 µL no
""")
mm.num_reactions = 2
mm.extra_fraction = 0
mm.extra_reactions = 0
assert str(mm) == """\
Reagent Stock Volume 2x
─────────────────────────────────
buffer 3x 1.00 µL 2.00 µL
cofactor 3x 1.00 µL 2.00 µL
enzyme 3x 1.00 µL
─────────────────────────────────
3.00 µL 2.00 µL/rxn"""
mm['buffer'].volume = 0.001, 'µL'
assert str(mm) == """\
Reagent Stock Volume 2x
─────────────────────────────────
water 1.00 µL 2.00 µL
cofactor 3x 1.00 µL 2.00 µL
enzyme 3x 1.00 µL
─────────────────────────────────
3.00 µL 2.00 µL/rxn"""
mm['buffer'].volume = -0.001, 'µL'
assert str(mm) == """\
def test_master_mix_format_text(format):
mm = MasterMix.from_text("""\
Reagent Stock Volume MM?
======= ===== ======== ===
water to 10 µL yes
buffer 10x 1 µL yes
enzyme 5x 2 µL no
""")
mm.num_reactions = 1
assert format(mm) == """\
Reagent Stock Volume
────────────────────────
water 7.00 µL
buffer 10x 1.00 µL
enzyme 5x 2.00 µL
────────────────────────
10.00 µL"""
mm.num_reactions = 2
mm.extra_fraction = 0
mm.extra_reactions = 0
assert format(mm) == """\
Reagent Stock Volume 2x
──────────────────────────────────
water 7.00 µL 14.00 µL
buffer 10x 1.00 µL 2.00 µL
enzyme 5x 2.00 µL
──────────────────────────────────
10.00 µL 8.00 µL/rxn"""
mm.show_master_mix = False
mm.show_1x = True
mm.show_totals = True
assert format(mm) == """\
Reagent Stock Volume
────────────────────────
water 7.00 µL
buffer 10x 1.00 µL
enzyme 5x 2.00 µL
────────────────────────
10.00 µL"""
mm.show_master_mix = True
mm.show_1x = False
mm.show_totals = True
assert format(mm) == """\
Reagent Stock 2x
────────────────────────
water 14.00 µL
buffer 10x 2.00 µL
enzyme 5x
────────────────────────
8.00 µL/rxn"""
mm.show_master_mix = True
mm.show_1x = True
mm.show_totals = False
assert format(mm) == """\
def test_master_mix_getattr_raises():
mm = MasterMix()
with pytest.raises(AttributeError, match="'MasterMix' object has no attribute 'undefined'"):
mm.undefined
# Try to trick to code that munges the error message.
with pytest.raises(AttributeError, match="'MasterMix' object has no attribute 'Reaction'"):
mm.Reaction
def hydroxide_hydrolysis():
rxn = MasterMix("""\
Reagent Stock Volume
============= ====== ========
water to 10 µL
IVTT reaction 2.5 µL
EDTA 500 mM 1.25 µL
NaOH 1 M 1.67 µL
""")
return f"""\
def rnase_digestion():
rxn = MasterMix("""\
Reagent Stock Volume
============= ====== ========
water to 10 µL
IVTT reaction 2.5 µL
EDTA 500 mM 1.25 µL
RNase A 1.0 µL
""")
return f"""\
def carbonate_hydrolysis():
rxn = MasterMix("""\
Reagent Stock Volume
======================== ====== ========
water to 10 µL
IVTT reaction 2.5 µL
EDTA 500 mM 1.25 µL
sodium carbonate, pH 9.2 100 mM 5 µL
""")
return f"""\
def test_master_mix_scale(params):
mm = MasterMix()
mm.num_reactions = params['n']
mm.solvent = 'w'
mm.volume = params['vol_rxn']
mm['x'].volume = params['vol_x']
mm['w'].master_mix = True
mm['x'].master_mix = True
if 'fraction' in params:
mm.extra_fraction = params['fraction']
assert mm.extra_percent == pytest.approx(params['fraction'] * 100)
if 'percent' in params:
mm.extra_percent = params['percent']
assert mm.extra_fraction == pytest.approx(params['percent'] / 100)
if 'reactions' in params:
mm.extra_reactions = params['reactions']
if 'min_vol' in params:
mm.extra_min_volume = params['min_vol']
assert mm.get_scale() == pytest.approx(params['expected'])
def get_reaction(self):
rxn = MasterMix(self.buffers[self.transfer_type])
rxn.extra_percent = 20
rxn.extra_min_volume = '1 µL'
if isinstance(self.samples, int):
rxn.num_reactions = self.samples
else:
rxn['DNA'].name = ','.join(self.samples)
rxn.num_reactions = len(self.samples)
if x := self.num_spots:
rxn.num_reactions = x
def test_master_mix_format_text_scale_header():
mm = MasterMix.from_text("""\
Reagent Stock Volume MM?
======= ===== ======== ===
water to 10 µL yes
buffer 10x 1 µL yes
enzyme 5x 2 µL no
""")
# Scale is an exact integer ending with zero.
mm.num_reactions = 10
mm.extra_percent = 0
assert str(mm) == """\
Reagent Stock Volume 10x
──────────────────────────────────
water 7.00 µL 70.00 µL
buffer 10x 1.00 µL 10.00 µL
enzyme 5x 2.00 µL
──────────────────────────────────
10.00 µL 8.00 µL/rxn"""
# Scale is an exact integer not ending with zero.
mm.extra_percent = 10
assert str(mm) == """\
Reagent Stock Volume 11x
──────────────────────────────────
water 7.00 µL 77.00 µL
buffer 10x 1.00 µL 11.00 µL
enzyme 5x 2.00 µL
──────────────────────────────────
10.00 µL 8.00 µL/rxn"""
# Scale is exactly represented with one decimal point.
mm.extra_percent = 11
assert str(mm) == """\
Reagent Stock Volume 11.1x
──────────────────────────────────
water 7.00 µL 77.70 µL
buffer 10x 1.00 µL 11.10 µL
enzyme 5x 2.00 µL
──────────────────────────────────
10.00 µL 8.00 µL/rxn"""
# Scale is not exactly represented with one decimal point.
mm.extra_percent = 11.1
assert str(mm) == """\
def test_master_mix_format_text_no_solvent():
mm = MasterMix.from_text("""\
Reagent Stock Volume MM?
======== ===== ======= ===
buffer 3x 1 µL yes
cofactor 3x 1 µL yes
enzyme 3x 1 µL no
""")
mm.num_reactions = 1
assert str(mm) == """\
Reagent Stock Volume
────────────────────────
buffer 3x 1.00 µL
cofactor 3x 1.00 µL
enzyme 3x 1.00 µL
────────────────────────
3.00 µL"""
mm.num_reactions = 2
mm.extra_fraction = 0
mm.extra_reactions = 0
assert str(mm) == """\
def test_master_mix_pickle():
from pickle import loads, dumps
# Just checking that this doesn't raise.
loads(dumps(MasterMix()))
args = docopt.docopt(__doc__)
try:
n = float(args['<num_rxns>'])
templates_str = 'DNA'
except ValueError:
templates = args['<num_rxns>'].split(',')
templates_str = ','.join(templates)
n = len(templates)
n_aliquots = int(ceil(n / 2))
s30 = MasterMix.from_text("""\
Reagent Stock Volume MM?
======= ===== ====== ===
water 1.2 µL yes
A 10x 1 µL yes
B 2.5x 4 µL yes
C 3.33x 3 µL yes
DNA 75 nM 0.8 µL
""")
s30.num_reactions = n
s30['DNA'].name = templates_str
protocol = Protocol()
protocol += f"""\
Thaw {plural(n_aliquots):# S30 extract aliquot/s} [1].
"""
protocol += f"""\
Setup the S30 extract reaction:
def parse_reaction(reaction_input):
if isinstance(reaction_input, dict):
return {k: MasterMix(v) for k, v in reaction_input.items()}
else:
return MasterMix(reaction_input)
#!/usr/bin/env python3
import stepwise
from inform import plural
from stepwise import Protocol, Step, Footnote, MasterMix
p = Protocol()
n = 6
loading_buf = MasterMix("""\
Reagent Stock Volume MM?
====================== ===== ========= ===
water to 5.0 µL y
Bolt LDS sample buffer 4x 2.5 µL y
Bolt reducing agent 10x 1.0 µL y
""")
loading_buf.num_reactions = 2 * n
loading_buf.extra_percent = 50
protein_samples = MasterMix("""\
Reagent Stock Volume MM?
========================= ========= ========== ===
water to 10.0 µL y
loading buffer master mix 2x 5.0 µL y
BSA 500 ng/µL 1.0 µL y
""")
protein_samples.num_reactions = n
protein_samples.extra_percent = 10
dna_samples = MasterMix("""\
Reagent Stock Volume MM?
Amplification − + + + − − +
expected?
"""
p += f"""\
Attach HUH-tagged DNA to the dCas9 RNP.
{huh}
- Incubate at 37°C for 15 min.
"""
bal31 = MasterMix("""\
Reagent Stock Volume MM?
================ ====== ======== ===
water to 50 µL yes
dCas9-PCV2-DNA 100 nM 10 µL
NEBuffer 3.1 [2] 10x 5 µL yes
BAL-31 1 U/µL 1 µL
""")
bal31.hold_ratios.volume = '20 µL'
bal31.num_reactions = 3
p += f"""\
Setup {plural(bal31.num_reactions):# BAL-31 digestion/s} [1]:
{bal31}
- Incubate at 30°C for 10 min.
- Add EGTA to 30 mM
- Incubate at 65°C for 10 min.
"""