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src/b/i/biopython-HEAD/Tests/test_PopGen_GenePop.py   biopython(Download)
 
from Bio import MissingExternalDependencyError
from Bio.PopGen.GenePop.Controller import GenePopController
 
#Tests genepop related code. Note: this case requires genepop
    def test_allele_genotype_frequencies(self):
        """Test genepop execution on basic allele and genotype frequencies.
        """
        ctrl = GenePopController()
        pop_iter, locus_iter = ctrl.calc_allele_genotype_freqs("PopGen" + os.sep + "big.gen")
    def test_calc_diversities_fis_with_identity(self):
        """Test calculations of diversities ...
        """
        ctrl = GenePopController()
        iter, avg_fis, avg_Qintra = ctrl.calc_diversities_fis_with_identity(
    def test_estimate_nm(self):
        """Test Nm estimation.
        """
        ctrl = GenePopController()
        mean_sample_size, mean_priv_alleles, mig10, mig25, mig50, mig_corrected =\
    def test_fst_all(self):
        """Test genepop execution on all fst.
        """
        ctrl = GenePopController()
        (allFis, allFst, allFit), itr = ctrl.calc_fst_all("PopGen" + os.sep + "c2line.gen")

src/b/i/biopython-1.63/Tests/test_PopGen_GenePop.py   biopython(Download)
 
from Bio import MissingExternalDependencyError
from Bio.PopGen.GenePop.Controller import GenePopController
 
#Tests genepop related code. Note: this case requires genepop
    def test_allele_genotype_frequencies(self):
        """Test genepop execution on basic allele and genotype frequencies.
        """
        ctrl = GenePopController()
        pop_iter, locus_iter = ctrl.calc_allele_genotype_freqs("PopGen" + os.sep + "big.gen")
    def test_calc_diversities_fis_with_identity(self):
        """Test calculations of diversities ...
        """
        ctrl = GenePopController()
        iter, avg_fis, avg_Qintra = ctrl.calc_diversities_fis_with_identity(
    def test_estimate_nm(self):
        """Test Nm estimation.
        """
        ctrl = GenePopController()
        mean_sample_size, mean_priv_alleles, mig10, mig25, mig50, mig_corrected =\
    def test_fst_all(self):
        """Test genepop execution on all fst.
        """
        ctrl = GenePopController()
        (allFis, allFst, allFit), itr = ctrl.calc_fst_all("PopGen" + os.sep + "c2line.gen")