MetaInformAnt/src/metainformant/dna/population/__init__.py at main · docxology/MetaInformAnt · GitHub

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"""Population genetics analysis sub-package."""

from __future__ import annotations

from . import analysis, core, visualization, visualization_core, visualization_stats

# Re-export public functions from analysis.py
from .analysis import (
    calculate_fst,
    calculate_fu_li_d,
    calculate_ld_decay,
    calculate_nucleotide_diversity,
    calculate_segregating_sites,
    calculate_summary_statistics,
    calculate_tajima_d,
    calculate_wattersons_theta,
    detect_population_structure,
    detect_selection,
    estimate_population_size,
    mcdonald_kreitman_test,
)

# Re-export public functions from core.py
from .core import (
    allele_frequencies,
    expected_heterozygosity,
    fay_wu_h_from_sequences,
    fixation_index,
    fu_and_li_d_star_from_sequences,
    fu_and_li_f_star_from_sequences,
    hardy_weinberg_allele_freqs,
    hudson_fst,
    linkage_disequilibrium,
    nucleotide_diversity,
    observed_heterozygosity,
    segregating_sites,
    tajimas_d,
    wattersons_theta,
)

__all__ = [
    "analysis",
    "core",
    "visualization",
    "visualization_core",
    "visualization_stats",
    # core.py
    "allele_frequencies",
    "expected_heterozygosity",
    "fay_wu_h_from_sequences",
    "fixation_index",
    "fu_and_li_d_star_from_sequences",
    "fu_and_li_f_star_from_sequences",
    "hardy_weinberg_allele_freqs",
    "hudson_fst",
    "linkage_disequilibrium",
    "nucleotide_diversity",
    "observed_heterozygosity",
    "segregating_sites",
    "tajimas_d",
    "wattersons_theta",
    # analysis.py
    "calculate_fst",
    "calculate_fu_li_d",
    "calculate_ld_decay",
    "calculate_nucleotide_diversity",
    "calculate_segregating_sites",
    "calculate_summary_statistics",
    "calculate_tajima_d",
    "calculate_wattersons_theta",
    "detect_population_structure",
    "detect_selection",
    "estimate_population_size",
    "mcdonald_kreitman_test",
]