Class GenePopController

Initializes the controller.

genepop_dir is the directory where GenePop is.

The binary should be called Genepop (capital G)

Hardy-Weinberg test for heterozygote deficiency.

Returns a population iterator containg
    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)

Hardy-Weinberg test for heterozygote deficiency.

Returns a population iterator containg
    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)

Hardy-Weinberg test based on probability.

 Returns 2 iterators and a final tuple:

1. Returns a loci iterator containing
     b. 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)
     c. Result of Fisher's test (Chi2, deg freedom, prob)
2. Returns a population iterator containg
     a. 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)
     b. Result of Fisher's test (Chi2, deg freedom, prob)
3. (Chi2, deg freedom, prob)

Global Hardy-Weinberg test for heterozygote deficiency.

Returns a triple with:
  An list per population containg
    (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 containg
    (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)

Global Hardy-Weinberg test for heterozygote excess.

Returns a triple with:
  An list per population containg
    (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 containg
    (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)

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

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.

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.

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.