# Copyright 2009 by Tiago Antao <tiagoantao@gmail.com>.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Test GenePop."""


import os
import unittest
import warnings

from Bio import BiopythonDeprecationWarning
from Bio import MissingExternalDependencyError

with warnings.catch_warnings():
    warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
    from Bio.PopGen.GenePop.Controller import GenePopController

# Tests genepop related code. Note: this case requires genepop
# test_PopGen_GenePop_nodepend tests code that does not require genepop

found = False
for path in os.environ["PATH"].split(os.pathsep):
    try:
        for filename in os.listdir(path):
            if filename.startswith("Genepop"):
                found = True
    except OSError:
        pass  # Path doesn't exist - correct to pass
if not found:
    raise MissingExternalDependencyError(
        "Install GenePop if you want to use Bio.PopGen.GenePop."
    )


class AppTest(unittest.TestCase):
    """Tests genepop execution via biopython."""

    def test_allele_genotype_frequencies(self):
        """Test genepop execution on basic allele and genotype frequencies."""
        ctrl = GenePopController()
        path = os.path.join("PopGen", "big.gen")
        pop_iter, locus_iter = ctrl.calc_allele_genotype_freqs(path)
        # print("%s %s" % (pop, loci))
        # for popc in pop_iter:
        #    pop_name, loci_content = popc
        #    print(pop_name)
        #    for locus in loci_content:
        #        geno_list, hets, freq_fis = loci_content[locus]
        #        print(locus)
        #        print(hets)
        #        print(freq_fis)
        #        print(geno_list)
        #    print("")

    def test_calc_diversities_fis_with_identity(self):
        """Test calculations of diversities."""
        ctrl = GenePopController()
        path = os.path.join("PopGen", "big.gen")
        iter, avg_fis, avg_Qintra = ctrl.calc_diversities_fis_with_identity(path)
        liter = list(iter)
        self.assertEqual(len(liter), 37)
        self.assertEqual(liter[0][0], "Locus1")
        self.assertEqual(len(avg_fis), 10)
        self.assertEqual(len(avg_Qintra), 10)

    def test_estimate_nm(self):
        """Test Nm estimation."""
        ctrl = GenePopController()
        path = os.path.join("PopGen", "big.gen")
        (
            mean_sample_size,
            mean_priv_alleles,
            mig10,
            mig25,
            mig50,
            mig_corrected,
        ) = ctrl.estimate_nm(path)
        self.assertAlmostEqual(mean_sample_size, 28.0)
        self.assertAlmostEqual(mean_priv_alleles, 0.016129)
        self.assertAlmostEqual(mig10, 52.5578)
        self.assertAlmostEqual(mig25, 15.3006)
        self.assertAlmostEqual(mig50, 8.94583)
        self.assertAlmostEqual(mig_corrected, 13.6612)

    def test_fst_all(self):
        """Test genepop execution on all fst."""
        ctrl = GenePopController()
        path = os.path.join("PopGen", "c2line.gen")
        (allFis, allFst, allFit), itr = ctrl.calc_fst_all(path)
        results = list(itr)
        self.assertEqual(len(results), 3)
        self.assertEqual(results[0][0], "136255903")
        self.assertAlmostEqual(results[1][3], 0.335846)

    def test_haploidy(self):
        """Test haploidy."""
        ctrl = GenePopController()
        path = os.path.join("PopGen", "haplo.gen")
        (allFis, allFst, allFit), itr = ctrl.calc_fst_all(path)
        litr = list(itr)
        self.assertNotIsInstance(allFst, int)
        self.assertEqual(len(litr), 37)
        self.assertEqual(litr[36][0], "Locus37")


if __name__ == "__main__":
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)
