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SNPio Version 1.2.1

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@btmartin721 btmartin721 released this 07 Jan 07:08
· 7 commits to master since this release
v1.2.1
2de8348

Changelog

Version 1.2.1 (2025-01-06)

Features

  • Improved the PopGenStatistics class to include new functionality to calculate genetic distances between populations and Tajima's D per locus:

    • calculate genetic distances between populations using the neis_genetic_distance() method. The method calculates Nei's genetic distance between populations and returns a pandas DataFrame with the genetic distances.
    • Tajima's D per locus using the tajimas_d method. The method calculates Tajima's D per locus and returns a pandas Series with the Tajima's D values.

  • The PopGenStatistics class now has the following public methods:

    • neis_genetic_distance()
    • tajimas_d()
    • calculate_d_statistics()
    • detect_fst_outliers()
    • observed_heterozygosity()
    • expected_heterozygosity()
    • observed_heterozygosity_per_population()
    • expected_heterozygosity_per_population()
    • nucleotide_diversity()
    • nucleotide_diversity_per_population()
    • summary_statistics()
    • amova()
    • weir_cockerham_fst_between_populations()
    • plot_d_statistics()

  • The AMOVA method now returns a dictionary with the AMOVA results. Its functionality has been greatly extended to follow Excoffier et al. (1992) and Excoffier et al. (1999) methods.

    • The method now calculates the variance components (within populations, within regions among popoulations, and among regions), Phi-statistics, and p-values via bootstrapping for the AMOVA analysis.
    • A regionmap dictionary is now required to map populations to regions/groups.

Enhancements

  • Improved the PopGenStatistics class to include new functionality to calculate observed and expected heterozygosity per population and nucleotide diversity per population.
  • Improved the PopGenStatistics class to include new functionality to calculate Weir and Cockerham's Fst between populations.
  • Improved aesthetics of the Fst heatmap plot.
  • Improved the PopGenStatistics class to include new functionality to plot D-statistics.
  • Improved the PopGenStatistics class to include new functionality to plot Fst outliers.
    • Two ways:
      • DBSCAN clustering method
      • Bootstrapping method
  • Improved the PopGenStatistics class to include new functionality to plot summary statistics.

Deprecations

The following method have been deprecated:

  • wrights_fst(): Use weir_cockerham_fst_between_populations() instead.

Bug Fixes

  • Fixed bug where the PopGenStatistics class did not have the verbose and debug attributes.
  • Fixed bug where the PopGenStatistics class did not have the genotype_data attribute.
  • Fixed warnings in snpio.plotting.plotting.Plotting class with the font family.
  • Fixed bug with VCFReader class when a non-tabix-indexed and uncompressed VCF file was read. The bug caused an error when reading an uncompressed VCF file.

Version 1.2.0 (2024-11-07)

Features

  • Added new functionality to calculate several population genetic statistics using the PopGenStatistics class, including:

    • Wright's Fst
    • nucleotide diversity
    • expected and observed heterozygosity
    • Fst outliers
    • Patterson's, Partitioned, and D-Foil D-statistic tests
    • AMOVAs (Analysis of Molecular Variance)

  • The PopGenStatistics class now has the following methods:

    • calculate_d_statistics()
    • detect_fst_outliers()
    • observed_heterozygosity()
    • expected_heterozygosity()
    • nucleotide_diversity()
    • wrights_fst()
    • summary_statistics()
    • amova()

Bootstrapping is performed for D-statistics and Fst outliers, and the results are saved as CSV files. The results are also returned as pandas DataFrames and dictionaries. The D-statistics are plotted, and the Fst outliers are plotted and saved as a CSV file. The summary statistics are plotted and returned as a dictionary.

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