tracts.tracts_data.TractsData

class TractsData(population, autosome_bins, autosome_data_mapped, allosome_bins=None, allosome_length=None, female_data_mapped=None, male_data_mapped=None, num_females=None, num_males=None)

Bases: object

Observed tract-length histogram data for a population, mapped to a demographic model’s population ordering, for autosomes and (optionally) allosomes.

population

The population providing chromosome lengths and sample sizes.

Type:

Population

autosome_bins

Bin edges for the autosomal tract-length histogram.

Type:

np.ndarray

autosome_data_mapped

Observed autosomal tract counts per population, indexed to match the demographic model’s population ordering.

Type:

list of list

allosome_bins

Bin edges for the allosomal tract-length histogram. None if allosomal data is not available.

Type:

np.ndarray | None

allosome_length

Length of the X chromosome in Morgans. None if allosomal data is not available.

Type:

float | None

female_data_mapped

Observed X-chromosome tract counts for females per population, indexed to match the demographic model’s population ordering. None if allosomal data is not available.

Type:

list of list | None

male_data_mapped

Observed X-chromosome tract counts for males per population, indexed to match the demographic model’s population ordering. None if allosomal data is not available.

Type:

list of list | None

num_females

Number of female samples. None if allosomal data is not available.

Type:

int | None

num_males

Number of male samples. None if allosomal data is not available.

Type:

int | None

allosome_bins: ndarray | None = None

allosome_length: float | None = None

autosome_bins: ndarray

autosome_data_mapped: list

female_data_mapped: list | None = None

classmethod from_population(population, p_dict, npts, exclude_tracts_below_cM=0, include_allosomes=True)

Extracts and maps tract-length histograms from a population, for autosomes and, if requested, allosomes.

Parameters:

• population (Population) – The population to extract tract-length histograms from.

• p_dict (dict) – A dictionary mapping population labels to their corresponding indices in the demographic model.

• npts (int) – Number of bins for the tract-length histograms.

• exclude_tracts_below_cM (float) – Minimum tract length in centimorgans to include in the histograms.

• include_allosomes (bool) – Whether to also extract and map allosomal (X-chromosome) tract-length histograms. If False, allosome_bins and the other allosome-related attributes are left as None.

Returns:

The extracted and mapped tract-length histogram data.

Return type:

TractsData

property has_allosome_data: bool

Whether allosomal tract-length data is available (allosome_bins is not None).

male_data_mapped: list | None = None

num_females: int | None = None

num_males: int | None = None

population: Population