def db(mock_plugins):
MOCK_CONFIG = {
'use': 'mock',
'database': {
'mock': {
'type': 'excel',
'dir': str(MOCK_DB),
}
}
}
return load_db(config=MOCK_CONFIG)
def check(use=None):
db = load_db(use)
n_total = len(db)
n_passed = 0
for tag, construct in tqdm(db.items()):
try:
construct.check()
n_passed += 1
except CheckError as err:
err.report()
print(f"{n_total} sequences found.")
print(f"{n_passed} passed all checks.")
def query(tags, attrs):
db = load_db()
print('\t'.join(['tag', *attrs]))
for tag in tags:
try:
hit = db[tag]
except QueryError:
print(tag)
continue
row = []
for attr in attrs:
try:
row.append(getattr(hit, attr))
except (QueryError, AttributeError):
row.append('')
print('\t'.join(str(x) for x in [hit.tag, *row]))
def get_db(self):
if self._db is None:
self._db = freezerbox.load_db()
return self._db
def __bareinit__(self):
self.db = freezerbox.load_db()
args = docopt.docopt(__doc__)
p = stepwise.Protocol()
huh = stepwise.MasterMix.from_text("""\
Reagent Stock Volume MM?
========== ====== ======== ===
water to 10 µL yes
buffer 10x 1 µL yes
dCas9-PCV2 1 µM 1 µL yes
sgRNA 1 µM 1 µL yes
EDTA 500 mM 1 µL
DNA 200 nM 5 µL
""")
db = freezerbox.load_db()
dna = args['<dna>']
dna_nM = min([round(db[x].conc_nM) for x in dna])
huh.num_reactions = int(args['--num-reactions'] or len(dna))
huh.extra_min_volume = '0.5 µL'
huh['buffer'].name = args['--buffer']
huh['dCas9-PCV2'].hold_conc.stock_conc = args['--cas9-stock-conc'], 'µM'
huh['sgRNA'].hold_conc.stock_conc = 10, 'µM'
huh['EDTA'].hold_stock_conc.conc = 30 / 2.5 * float(
args['--buffer-divalent-conc']), 'mM'
huh['DNA'].hold_conc.stock_conc = dna_nM, 'nM'
huh['DNA'].name = ','.join(dna)
def test_load_db_err(config, error):
with error:
load_db(config=config)
def test_ignore_external_freezerbox_db():
import freezerbox
db = freezerbox.load_db()
assert db.name == "WARNING: ACCESSING EXTERNAL DATABASE"