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.
-
estimate_nm
(self)¶ Estimate Nm. Just a simple bridge.
-
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_fis
(self)¶ Calculate identity-base average Fis.
-
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.
-