fextract_batch_coverage package

Submodules

fextract_batch_coverage.plugin module

class lbfextract.fextract_batch_coverage.plugin.CliHook

Bases: object

get_command() → Command | List[Command]

class lbfextract.fextract_batch_coverage.plugin.FextractHooks

Bases: object

fetch_reads(path_to_bam: Path, path_to_bed: Path, config: Any, extra_config: Any) → IntervalIterator

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

load_fetched_reads(config: Any, extra_config: AppExtraConfig) → DataFrame

Parameters:

• config – config specific to the function

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

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

Parameters:

• signal – Signal object containing the signals per interval

• config – object containing the parameters of the plot

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

save_fetched_reads(reads_per_interval_container: IntervalIterator, config: Any, extra_config: Any) → None

Hook implementing the strategy to save the reads fetched from the intervals :param reads_per_interval_container: ReadsPerIntervalContainer containing information about the genomic region

and the reads mapping to it

Parameters:

• config – object contaiing the configuration for saving the reads

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

Returns:

None

save_signal(signal: Signal, config: Any, extra_config: Any) → None

Parameters:

• signal – Signal object containing the signals per interval

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

transform_all_intervals(single_intervals_transformed_reads: IntervalIterator, 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

transform_single_intervals(transformed_reads: IntervalIterator, config: Any, extra_config: Any) → IntervalIterator

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_batch_coverage.plugin.IntervalIterator(df: DataFrame, path_to_bam: Path, multiple_iterators: bool, extra_bases: int, flanking_window: int, flip_based_on_strand: bool | None = None)

Bases: object

set_signal_summarizer(signal_summarizer)

set_signal_transformer(signal_transformer)

lbfextract.fextract_batch_coverage.plugin.extract_coverage(coverage_extractor, transformed_reads)

lbfextract.fextract_batch_coverage.plugin.identity(x, axis=None)

fextract_batch_coverage.schemas module

class lbfextract.fextract_batch_coverage.schemas.PlotConfig(config_dict: dict | None = None)

Bases: Config

annotation_center_line: str = None

apply_savgol: bool = None

bottom: int = None

color: str = None

flanking: int = None

general_font_size: int = None

savgol_polyorder: int = None

savgol_window_length: int = None

schema = <Schema({'title_font_size': Coerce(int, msg='title_font_size should be a integer'), 'general_font_size': Coerce(int, msg='general_font_size should be a integer'), 'tf_to_annotate': typing.List[str], 'ylabel': <class 'str'>, 'flanking': Coerce(int, msg='flanking should be a integer'), 'annotation_center_line': <class 'str'>, 'apply_savgol': <class 'bool'>, 'savgol_window_length': Coerce(int, msg='savgol_window_length should be a integer'), 'savgol_polyorder': Coerce(int, msg='savgol_polyorder should be a integer'), 'color': <class 'str'>, 'xlabel': <class 'str'>, 'window_center': Coerce(int, msg='window_center should be a integer'), 'top': Coerce(int, msg='top should be a integer'), 'bottom': Coerce(int, msg='bottom should be a integer')}, extra=PREVENT_EXTRA, required=False) object>

tf_to_annotate: List[str] = None

title_font_size: int = None

top: int = None

window_center: int = None

xlabel: str = None

ylabel: str = None

Module contents