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https://github.com/biopython/biopython.git
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57056bbfc4
Reverted unwanted changes (mostly arrays in tests, but also some whitespace in doctests). Remaining changes are standardising spacing between module docstring and imports, and lower-case \x<hex> in strings.
110 lines
3.8 KiB
Python
110 lines
3.8 KiB
Python
# Copyright 2009 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Test GenePop."""
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import os
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import unittest
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import warnings
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from Bio import BiopythonDeprecationWarning
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from Bio import MissingExternalDependencyError
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
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from Bio.PopGen.GenePop.Controller import GenePopController
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# Tests genepop related code. Note: this case requires genepop
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# test_PopGen_GenePop_nodepend tests code that does not require genepop
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found = False
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for path in os.environ["PATH"].split(os.pathsep):
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try:
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for filename in os.listdir(path):
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if filename.startswith("Genepop"):
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found = True
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except OSError:
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pass # Path doesn't exist - correct to pass
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if not found:
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raise MissingExternalDependencyError(
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"Install GenePop if you want to use Bio.PopGen.GenePop."
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)
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class AppTest(unittest.TestCase):
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"""Tests genepop execution via biopython."""
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def test_allele_genotype_frequencies(self):
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"""Test genepop execution on basic allele and genotype frequencies."""
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ctrl = GenePopController()
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path = os.path.join("PopGen", "big.gen")
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pop_iter, locus_iter = ctrl.calc_allele_genotype_freqs(path)
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# print("%s %s" % (pop, loci))
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# for popc in pop_iter:
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# pop_name, loci_content = popc
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# print(pop_name)
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# for locus in loci_content:
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# geno_list, hets, freq_fis = loci_content[locus]
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# print(locus)
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# print(hets)
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# print(freq_fis)
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# print(geno_list)
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# print("")
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def test_calc_diversities_fis_with_identity(self):
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"""Test calculations of diversities."""
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ctrl = GenePopController()
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path = os.path.join("PopGen", "big.gen")
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iter, avg_fis, avg_Qintra = ctrl.calc_diversities_fis_with_identity(path)
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liter = list(iter)
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self.assertEqual(len(liter), 37)
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self.assertEqual(liter[0][0], "Locus1")
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self.assertEqual(len(avg_fis), 10)
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self.assertEqual(len(avg_Qintra), 10)
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def test_estimate_nm(self):
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"""Test Nm estimation."""
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ctrl = GenePopController()
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path = os.path.join("PopGen", "big.gen")
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(
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mean_sample_size,
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mean_priv_alleles,
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mig10,
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mig25,
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mig50,
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mig_corrected,
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) = ctrl.estimate_nm(path)
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self.assertAlmostEqual(mean_sample_size, 28.0)
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self.assertAlmostEqual(mean_priv_alleles, 0.016129)
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self.assertAlmostEqual(mig10, 52.5578)
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self.assertAlmostEqual(mig25, 15.3006)
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self.assertAlmostEqual(mig50, 8.94583)
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self.assertAlmostEqual(mig_corrected, 13.6612)
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def test_fst_all(self):
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"""Test genepop execution on all fst."""
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ctrl = GenePopController()
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path = os.path.join("PopGen", "c2line.gen")
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(allFis, allFst, allFit), itr = ctrl.calc_fst_all(path)
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results = list(itr)
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self.assertEqual(len(results), 3)
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self.assertEqual(results[0][0], "136255903")
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self.assertAlmostEqual(results[1][3], 0.335846)
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def test_haploidy(self):
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"""Test haploidy."""
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ctrl = GenePopController()
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path = os.path.join("PopGen", "haplo.gen")
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(allFis, allFst, allFit), itr = ctrl.calc_fst_all(path)
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litr = list(itr)
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self.assertNotIsInstance(allFst, int)
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self.assertEqual(len(litr), 37)
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self.assertEqual(litr[36][0], "Locus37")
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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