dae.genomic_resources.statistics package

Submodules

dae.genomic_resources.statistics.base_statistic module

class dae.genomic_resources.statistics.base_statistic.Statistic(statistic_id: str, description: str)

Bases: object

Base class genomic resource statistics.

Statistics are generated using task graphs and aggregate values from a large amount of data. Each statistic should have a clearly defined single unit of data to process (for example, a nucleotide in a reference genome).

abstract add_value(value: Any) → None

Add a value to the statistic.

description: str

abstract static deserialize(content: str) → Statistic

Create a statistic from serialized data.

finish() → None

Perform final calculations for the statistic.

This step is optional.

This is called when resource iteration is complete.

Can also be used when creating more complex resources via deserialization.

abstract merge(other: Statistic) → None

Merge the values from another statistic in place.

abstract serialize() → str

Return a serialized version of this statistic.

statistic_id: str

dae.genomic_resources.statistics.min_max module

class dae.genomic_resources.statistics.min_max.MinMaxValue(score_id: str, min_value: float = nan, max_value: float = nan, count: int = 0)

Bases: Statistic

Statistic that calculates Min and Max values in a genomic score.

add_count(count: int = 1) → None

add_value(value: float | None) → None

Add a value to the statistic.

static deserialize(content: str) → MinMaxValue

Create a statistic from serialized data.

merge(other: Statistic) → None

Merge the values from another statistic in place.

serialize() → str

Return a serialized version of this statistic.

class dae.genomic_resources.statistics.min_max.MinMaxValueStatisticMixin

Bases: object

static get_min_max_file(score_id: str) → str

Module contents