thtools.utils.autoconfig

thtools.utils.autoconfig(ths, rbs, triggers, set_size=1, model=<nupack.model.Model object>, names=None, const_rna=None)

Quick configuration of ToeholdTests, assuming every RNA has the concentration of thtools.utils.ASSUMED_STRAND_CONC.

Parameters
thsstr

The toehold switch

rbsstr

The ribosome binding site whose slice of the toehold switch will be autodetected

triggersCollection[str]

An array-like of the triggers to test the toehold switch against

set_sizeint, default=1

How many triggers to test combinatorically against the toehold switch at a time.

modelnupack.Model, default=nupack.Model()

The thermodynamic model to use.

namesCollection[str], optional

The names of each trigger.

const_rnaIterable, optional

A list of any constant RNAs.

Returns
A fully configured ToeholdTest instance.

Examples

>>> import thtools as tt
>>> ths = "UUAGCCGCUGUCACACGCACAGGGAUUUACAAAAAGAGGAGAGUAAAAUGCUGUGCGUGCACCAUAAAACGAACAUAGAC"
>>> rbs = "AGAGGAGA"
>>> triggers = ["CUGUGCGUGUGACAGCGGCUGA", "CUAUACAAUCUACUGUCUUUCC", "UGUACAGCCUCCUAGCUUUCC"]
>>> my_test = tt.autoconfig(ths, rbs, triggers)
>>> my_result = my_test.run(max_size=3, n_samples=100)
>>> my_result.specificity # gives as decimal, not percentage
0.9999999587733204