Bio.PopGen.GenePop.EasyController module¶

Control GenePop through an easier interface.

This interface is less efficient than the standard GenePopControler

class Bio.PopGen.GenePop.EasyController.EasyController(fname, genepop_dir=None)¶

Bases: object

Define a class for an easier interface with the GenePop program.

__init__(self, fname, genepop_dir=None)¶

Initialize the controller.

genepop_dir is the directory where GenePop is.

The binary should be called Genepop (capital G)

get_basic_info(self)¶: Obtain the population list and loci list from the file.

test_hw_pop(self, pop_pos, test_type='probability')¶: Perform Hardy-Weinberg test on the given position.

test_hw_global(self, test_type='deficiency', enum_test=True, dememorization=10000, batches=20, iterations=5000)¶: Perform Hardy-Weinberg global Heterozygote test.

test_ld_all_pair(self, locus1, locus2, dememorization=10000, batches=20, iterations=5000)¶: Test for linkage disequilibrium for each pair of loci in each population.

get_heterozygosity_info(self, pop_pos, locus_name)¶

Return the heterozygosity info for a certain locus on a population.

Returns (Expected homozygotes, observed homozygotes, Expected heterozygotes, observed heterozygotes)

get_genotype_count(self, pop_pos, locus_name)¶: Return the genotype counts for a certain population and locus.

get_fis(self, pop_pos, locus_name)¶

Return the Fis for a certain population and locus.

Below CW means Cockerham and Weir and RH means Robertson and Hill.

Returns a pair:

dictionary [allele] = (repetition count, frequency, Fis CW ) with information for each allele
a triple with total number of alleles, Fis CW, Fis RH

get_alleles(self, pop_pos, locus_name)¶: Return the alleles for a certain population and locus.

get_alleles_all_pops(self, locus_name)¶: Return the alleles for a certain population and locus.

get_allele_frequency(self, pop_pos, locus_name)¶: Calculate the allele frequency for a certain locus on a population.

get_multilocus_f_stats(self)¶

Return the multilocus F stats.

Explain averaging. Returns Fis(CW), Fst, Fit

get_f_stats(self, locus_name)¶

Return F stats for a locus.

Returns Fis(CW), Fst, Fit, Qintra, Qinter

get_avg_fst_pair(self)¶: Calculate Allele size-base average Fis for all population pairs.

get_avg_fst_pair_locus(self, locus)¶: Calculate Allele size-base average Fis for all population pairs of the given locus.

calc_ibd(self, is_diplo=True, stat='a', scale='Log', min_dist=1e-05)¶: Calculate isolation by distance statistics for Diploid or Haploid.