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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/excess. 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) |
Global Hardy-Weinberg test for heterozygote deficiency/excess. Returns a triple with: A 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) A 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) |
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. |
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