fextract_fragment_length_ratios package

Submodules

fextract_fragment_length_ratios.plugin module

class lbfextract.fextract_fragment_length_ratios.plugin.CliHook

Bases: object

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

extract_fragment_length_ratios

Given a set of genomic intervals having the same length w, the extract_fragment_length_ratios extracts the fragment length ratios of the proportion of reads contained in two different parts of the fragment length distribution at each position.

\[\mathbf{c} = \left( \frac{\sum_{i \in [n,m)} \mathbf{d}^{l}_{i}}{\sum_{j \in [o, p)} \mathbf{d}^{l}_{j}} \right)^{w}_{l=0}\]

in which \(\mathbf{d}\) is the fragment length distribution at position \(l\), \(n,m\) the start and the end of the range of fragment lengths used in the nominator and \(o,p\) are the start and end of the range of fragment lengths used in the denominator.

get_command() → Command | List[Command]

class lbfextract.fextract_fragment_length_ratios.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

lbfextract.fextract_fragment_length_ratios.plugin.validate_nominator_denominator(ctx, param, value)

Module contents