fextract_fragment_length_distribution_in_batch package

Submodules

fextract_fragment_length_distribution_in_batch.plugin module

class lbfextract.fextract_fragment_length_distribution_in_batch.plugin.CliHook[source]

Bases: object

get_command() → Command[source]
class lbfextract.fextract_fragment_length_distribution_in_batch.plugin.FextractHooks[source]

Bases: object

fetch_reads(path_to_bam: Path, path_to_bed: Path, config: Any, extra_config: Any) → IntervalIteratorFld[source]
Parameters:

  • path_to_bam – path to the bam file

  • path_to_bed – path to the bed file with the regions to be filtered

  • config – configuration file containing the configuration object required by the fetch_reads function

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

Returns:

ReadsPerIntervalContainer object containing all the ReadsPerInterval objects in all the intervals contained in the bed file

plot_signal(signal: Signal, extra_config: Any, config: PlotConfig) → dict[str, Path][source]
Parameters:

  • signal – Signal object containing the signals per interval

  • config – object containing the configuration to create the plots

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

save_signal(signal: Signal, config: Any, extra_config: Any) → Path[source]
Parameters:

  • signal – Signal object containing the signals per interval

  • config – config specific to the save signal hook

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

transform_all_intervals(single_intervals_transformed_reads: IntervalIteratorFld, config: Any, extra_config: Any) → Signal[source]
Parameters:

  • single_intervals_transformed_reads – Signal object containing the signals per interval

  • config – config specific to the transform_all_intervals hook

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

transform_single_intervals(transformed_reads: IntervalIteratorFld, config: SingleSignalTransformerConfig, extra_config: Any) → IntervalIteratorFld[source]
Parameters:

  • transformed_reads – ReadsPerIntervalContainer containing a list of ReadsPerInterval which are basically lists with information about start and end of the interval

  • config – config specific to the function

  • extra_config – config containing context information plus extra parameters

class lbfextract.fextract_fragment_length_distribution_in_batch.plugin.IntervalIteratorFld(df: DataFrame, path_to_bam: Path, multiple_iterators: bool, extra_bases: int, flip_based_on_strand: bool | None = None)[source]

Bases: object

set_signal_transformer(signal_transformer)[source]
lbfextract.fextract_fragment_length_distribution_in_batch.plugin.identity(x)[source]
lbfextract.fextract_fragment_length_distribution_in_batch.plugin.optimize_tensor_subsampling(tensor, n)[source]
lbfextract.fextract_fragment_length_distribution_in_batch.plugin.subsample_fragment_lengths(x, n)[source]

Module contents