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_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) == """\
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: