flexs.landscapes.tf_binding¶

Define TFBinding landscape and problem registry.

class flexs.landscapes.tf_binding.TFBinding(landscape_file)[source]¶

Bases: flexs.landscape.Landscape

A landscape of binding affinity of proposed 8-mer DNA sequences to a particular transcription factor.

We use experimental data from Barrera et al. (2016), a survey of the binding affinity of more than one hundred and fifty transcription factors (TF) to all possible DNA sequences of length 8.

flexs.landscapes.tf_binding.registry()[source]¶

Return a dictionary of problems of the form:

```python {

“problem name”: {
“params”: …,

where flexs.landscapes.TFBinding(**problem[“params”]) instantiates the transcription factor binding landscape for the given set of parameters.

Return type: Dict[str, Dict]
Returns: Problems in the registry.