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__(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()
Obtain the population list and loci list from the file.
- test_hw_pop(pop_pos, test_type='probability')
Perform Hardy-Weinberg test on the given position.
- test_hw_global(test_type='deficiency', enum_test=True, dememorization=10000, batches=20, iterations=5000)
Perform Hardy-Weinberg global Heterozygote test.
- test_ld_all_pair(locus1, locus2, dememorization=10000, batches=20, iterations=5000)
Test for linkage disequilibrium for each pair of loci in each population.
- estimate_nm()
Estimate Nm. Just a simple bridge.
- get_heterozygosity_info(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(pop_pos, locus_name)
Return the genotype counts for a certain population and locus.
- get_fis(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(pop_pos, locus_name)
Return the alleles for a certain population and locus.
- get_alleles_all_pops(locus_name)
Return the alleles for a certain population and locus.
- get_allele_frequency(pop_pos, locus_name)
Calculate the allele frequency for a certain locus on a population.
- get_multilocus_f_stats()
Return the multilocus F stats.
Explain averaging. Returns Fis(CW), Fst, Fit
- get_f_stats(locus_name)
Return F stats for a locus.
Returns Fis(CW), Fst, Fit, Qintra, Qinter
- get_avg_fis()
Calculate identity-base average Fis.
- get_avg_fst_pair()
Calculate Allele size-base average Fis for all population pairs.
- get_avg_fst_pair_locus(locus)
Calculate Allele size-base average Fis for all population pairs of the given locus.
- calc_ibd(is_diplo=True, stat='a', scale='Log', min_dist=0.00001)
Calculate isolation by distance statistics for Diploid or Haploid.