biopython

v1.71.0

biopython v1.71.0 Bio.PopGen.GenePop.Controller.GenePopController

Initializes the controller.

genepop_dir is the directory where GenePop is.

The binary should be called Genepop (capital G)

Link to this section Summary

Functions

__init__()
_calc_ibd()

Calculates isolation by distance statistics

_test_global_hz_both()

Global Hardy-Weinberg test for heterozygote deficiency/excess

_test_pop_hz_both()

Hardy-Weinberg test for heterozygote deficiency/excess

calc_allele_genotype_freqs()

Calculates allele and genotype frequencies per locus and per sample

calc_fst_all()

Executes GenePop and gets Fst/Fis/Fit (all populations)

calc_ibd_diplo()

Calculates isolation by distance statistics for diploid data

calc_ibd_haplo()

Calculates isolation by distance statistics for haploid data

test_global_hz_deficiency()

Global Hardy-Weinberg test for heterozygote deficiency

test_global_hz_excess()

Global Hardy-Weinberg test for heterozygote excess

test_pop_hz_deficiency()

Hardy-Weinberg test for heterozygote deficiency

test_pop_hz_excess()

Hardy-Weinberg test for heterozygote deficiency

test_pop_hz_prob()

Hardy-Weinberg test based on probability

Link to this section Functions

Link to this function __init__()
Link to this function _calc_ibd()

Calculates isolation by distance statistics.

Link to this function _test_global_hz_both()

Global Hardy-Weinberg test for heterozygote deficiency/excess.

Returns a triple with:

  • A list per population containing (pop_name, P-val, SE, switches). Some pops have a None if the info is not available. SE might be none (for enumerations).
  • A list per loci containing (locus_name, P-val, SE, switches). Some loci have a None if the info is not available. SE might be none (for enumerations).
  • Overall results (P-val, SE, switches).
Link to this function _test_pop_hz_both()

Hardy-Weinberg test for heterozygote deficiency/excess.

Returns a population iterator containing a dictionary where dictionary[locus]=(P-val, SE, Fis-WC, Fis-RH, steps).

Some loci have a None if the info is not available. SE might be none (for enumerations).

Link to this function calc_allele_genotype_freqs()

Calculates allele and genotype frequencies per locus and per sample.

Parameters:

  • fname - file name

Returns tuple with 2 elements:

  • Population iterator with

    • population name
    • Locus dictionary with key = locus name and content tuple as Genotype List with (Allele1, Allele2, observed, expected) (expected homozygotes, observed hm, expected heterozygotes, observed ht) Allele frequency/Fis dictionary with allele as key and (count, frequency, Fis Weir & Cockerham)
    • Totals as a pair
    • count
    • Fis Weir & Cockerham,
    • Fis Robertson & Hill

  • Locus iterator with

    • Locus name
    • allele list

    • Population list with a triple

      • population name
      • list of allele frequencies in the same order as allele list above
      • number of genes

Will create a file called fname.INF

Link to this function calc_fst_all()

Executes GenePop and gets Fst/Fis/Fit (all populations)

Parameters:

  • fname - file name

Returns:

  • (multiLocusFis, multiLocusFst, multiLocus Fit),
  • Iterator of tuples (Locus name, Fis, Fst, Fit, Qintra, Qinter)

Will create a file called fname.FST.

This does not return the genotype frequencies.

Link to this function calc_ibd_diplo()

Calculates isolation by distance statistics for diploid data.

See _calc_ibd for parameter details.

Note that each pop can only have a single individual and the individual name has to be the sample coordinates.

Link to this function calc_ibd_haplo()

Calculates isolation by distance statistics for haploid data.

See _calc_ibd for parameter details.

Note that each pop can only have a single individual and the individual name has to be the sample coordinates.

Link to this function test_global_hz_deficiency()

Global Hardy-Weinberg test for heterozygote deficiency.

Returns a triple with:

  • An list per population containing (pop_name, P-val, SE, switches). Some pops have a None if the info is not available. SE might be none (for enumerations).
  • An list per loci containing (locus_name, P-val, SE, switches). Some loci have a None if the info is not available. SE might be none (for enumerations).
  • Overall results (P-val, SE, switches).
Link to this function test_global_hz_excess()

Global Hardy-Weinberg test for heterozygote excess.

Returns a triple with:

  • A list per population containing (pop_name, P-val, SE, switches). Some pops have a None if the info is not available. SE might be none (for enumerations).
  • A list per loci containing (locus_name, P-val, SE, switches). Some loci have a None if the info is not available. SE might be none (for enumerations).
  • Overall results (P-val, SE, switches)
Link to this function test_pop_hz_deficiency()

Hardy-Weinberg test for heterozygote deficiency.

Returns a population iterator containing a dictionary wehre dictionary[locus]=(P-val, SE, Fis-WC, Fis-RH, steps).

Some loci have a None if the info is not available. SE might be none (for enumerations).

Link to this function test_pop_hz_excess()

Hardy-Weinberg test for heterozygote deficiency.

Returns a population iterator containing a dictionary where dictionary[locus]=(P-val, SE, Fis-WC, Fis-RH, steps).

Some loci have a None if the info is not available. SE might be none (for enumerations).

Link to this function test_pop_hz_prob()

Hardy-Weinberg test based on probability.

Returns 2 iterators and a final tuple:

  1. Returns a loci iterator containing:

    • A dictionary[pop_pos]=(P-val, SE, Fis-WC, Fis-RH, steps). Some pops have a None if the info is not available. SE might be none (for enumerations).
    • Result of Fisher’s test (Chi2, deg freedom, prob).

  2. Returns a population iterator containing:

    • A dictionary[locus]=(P-val, SE, Fis-WC, Fis-RH, steps). Some loci have a None if the info is not available. SE might be none (for enumerations).
    • Result of Fisher’s test (Chi2, deg freedom, prob).
  3. Final tuple (Chi2, deg freedom, prob).