thtools.core.ToeholdResult

class thtools.core.ToeholdResult

Data container for the result of a ToeholdTest.

Not intended to be constructed manually.

Note

All activation and unbinding values are given as decimals, not percentages.

See also

ToeholdTest

A class to test different trigger sets against the toehold switch for activation probability, in order to find its specificity.

Attributes
trigger_setsCollection[Collection[str]]

The trigger sets that were tested.

namesCollection[str | Collection[str]]

The names of each trigger set in trigger_sets. If a collection of names is given for each trigger set, they will be joined with ‘+’ signs. This can also be set through the names parameter of ToeholdTest or passed to an argument to one of the methods defined here.

activationnp.ndarray[np.float64]

An array of the activation by each trigger set.

rbs_unbindingnp.ndarray[np.float64]

An array of the RBS unbinding by each trigger set.

aug_unbindingnp.ndarray[np.float64]

An array of the AUG unbinding by each trigger set.

post_aug_unbindingnp.ndarray[np.float64]

An array of the post-AUG unbinding by each trigger set.

activation_senp.ndarray[np.float64]

The standard error of each value in the activation attribute array.

specificitynp.ndarray[np.float64]

The level of specificity to the highest activating trigger set.

specificity_senp.ndarray[np.float64]

The standard error of the specificity attribute.

target_indexint

The index of the trigger_sets with the highest activation probability.

target_setCollection[str]

The item in the trigger_sets with the highest activation probability.

targetstr | Collection[str]

Same as target_set, but if the trigger_set only contains a single RNA, this is the RNA sequence.

target_namestr

The name of the trigger_set with the highest activation probability.

target_activationfloat

The switch activation probability with the target trigger set.

target_activation_sefloat

The standard error of the switch activation probability with the target trigger set.

unix_createddatetime.datetime

UNIX timestamp of the creation of the ToeholdResult.

datestr
metadict
pretty_metastr
prettify(dp, names, show_unbinding)

Alias to str(self). Get the result as its prettytable.PrettyTable in string form, with added metadata.

Parameters
dpint, optional

The decimal places to limit the display to.

namesCollection[str | Collection[str]], optional

The names of each trigger set in trigger_sets.

show_unbindingbool, default = True

Whether to display the individual unbinding probability of the RBS, start codon and post-start codon region

tabulate(dp, names, show_unbinding)

Create a prettytable.PrettyTable of the result.

Parameters
dpint, optional

The decimal places to limit the display to.

namesCollection[str | Collection[str]], optional

The names of each trigger set in trigger_sets.

show_unbindingbool, default = True

Whether to display the individual unbinding probability of the RBS, start codon and post-start codon region

to_csv(dp, names, show_unbinding, **kwargs)

Get the result as a CSV with added metadata.

Parameters
dpint, optional

The decimal places to limit the display to.

namesCollection[str | Collection[str]], optional

The names of each trigger set in trigger_sets.

show_unbindingbool, default = True

Whether to display the individual unbinding probability of the RBS, start codon and post-start codon region

**kwargs

Extra arguments to be passed to csv.writer() via the PrettyTable.prettytable instance.

to_df(dp, names, show_unbinding, **kwargs)

Get the result as a pandas DataFrame.

Parameters
dpint, optional

The decimal places to limit the display to.

namesCollection[str | Collection[str]], optional

The names of each trigger set in trigger_sets.

show_unbindingbool, default = True

Whether to display the individual unbinding probability of the RBS, start codon and post-start codon region

**kwargs

Extra arguments to be passed to the pandas.DataFrame instance.

to_html(dp, names, show_unbinding, **kwargs)

Get the result as a HTML table.

Parameters
dpint, optional

The decimal places to limit the display to.

namesCollection[str | Collection[str]], optional

The names of each trigger set in trigger_sets.

show_unbindingbool, default = True

Whether to display the individual unbinding probability of the RBS, start codon and post-start codon region

**kwargs

Extra arguments to be passed to the PrettyTable.prettytable instance.

to_json(dp, names, show_unbinding, **kwargs)

Get the result as a JSON string.

Parameters
dpint, optional

The decimal places to limit the display to.

namesCollection[str | Collection[str]], optional

The names of each trigger set in trigger_sets.

show_unbindingbool, default = True

Whether to display the individual unbinding probability of the RBS, start codon and post-start codon region

**kwargs

Extra arguments to be passed to the PrettyTable.prettytable instance.