fextract_entropy package

Submodules

fextract_entropy.plugin module

class lbfextract.fextract_entropy.plugin.CliHook

Bases: object

This CliHook implements the CLI interface for the extract_entropy feature extraction method.

extract_entropy

Given a set of genomic intervals having the same length w, extract_entropy calculates the Entropy at each position, which can be represented as:

\[E_l = -\sum_{x \in X} P_l(x) log(P_l(x))\]

Where \(l\) represents the genomic position, \(P_l\) represents the fragment length distribution at position \(l\) and :math:`X`is the alphabet (fragment length range used)

get_command() → Command | List[Command]

class lbfextract.fextract_entropy.plugin.FextractHooks

Bases: object

plot_signal(signal: Signal, config: Any, extra_config: AppExtraConfig) → Figure

transform_all_intervals(single_intervals_transformed_reads: Signal, config: Any, extra_config: Any) → Signal

Parameters:

• single_intervals_transformed_reads – Signal object containing the signals per interval

• config – config specific to the function

• extra_config – extra configuration that may be used in the hook implementation

fextract_entropy.schemas module

fextract_entropy.signal_summarizers module

Module contents