# Copyright 2007 by Tiago Antao . 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. """Tests for PopGen GenePop nodepend module.""" import os import unittest from Bio.PopGen import GenePop from Bio.PopGen.GenePop import FileParser import tempfile class RecordTest(unittest.TestCase): """Record tests.""" def test_record_basic(self): """Basic test on Record.""" r = GenePop.Record() self.assertIsInstance(r.marker_len, int) self.assertIsInstance(r.comment_line, str) self.assertIsInstance(r.loci_list, list) self.assertIsInstance(r.populations, list) class ParserTest(unittest.TestCase): """Parser tests.""" def setUp(self): files = [ "c2line.gen", "c3line.gen", "c2space.gen", "c3space.gen", "haplo3.gen", "haplo2.gen", ] self.handles = [] for filename in files: self.handles.append(open(os.path.join("PopGen", filename))) self.pops_indivs = [ (3, [4, 3, 5]), (3, [4, 3, 5]), (3, [4, 3, 5]), (3, [4, 3, 5]), (3, [4, 3, 5]), (3, [4, 3, 5]), ] self.num_loci = [3, 3, 3, 3, 3, 3] self.marker_len = [2, 3, 2, 3, 3, 2] self.pop_names = ["4", "b3", "5"] def tearDown(self): for handle in self.handles: handle.close() def test_record_parser(self): """Basic operation of the Record Parser.""" for index in range(len(self.handles)): handle = self.handles[index] rec = GenePop.read(handle) self.assertTrue( str(rec).startswith( "Generated by createGenePop.py - (C) Tiago Antao\n" "136255903\n" "136257048\n" "136257636\n" "Pop\n" ), "Did not expect this:\n%s" % rec, ) self.assertIsInstance(rec, GenePop.Record) self.assertEqual(len(rec.loci_list), self.num_loci[index]) self.assertEqual(rec.marker_len, self.marker_len[index]) self.assertEqual(len(rec.populations), self.pops_indivs[index][0]) self.assertEqual(rec.pop_list, self.pop_names) for i in range(self.pops_indivs[index][0]): self.assertEqual(len(rec.populations[i]), self.pops_indivs[index][1][i]) def test_wrong_file_parser(self): """Testing the ability to deal with wrongly formatted files.""" with open(os.path.join("PopGen", "README")) as f: try: rec = GenePop.read(f) raise Exception("Should have raised exception") except ValueError: pass class FileParserTest(unittest.TestCase): """File parser tests.""" def setUp(self): self.files = [ os.path.join("PopGen", x) for x in [ "c2line.gen", "c3line.gen", "c2space.gen", "c3space.gen", "haplo3.gen", "haplo2.gen", ] ] self.pops_indivs = [ (3, [4, 3, 5]), (3, [4, 3, 5]), (3, [4, 3, 5]), (3, [4, 3, 5]), (3, [4, 3, 5]), (3, [4, 3, 5]), ] self.num_loci = [3, 3, 3, 3, 3, 3] def test_file_record_parser(self): """Basic operation of the File Record Parser.""" for index in range(len(self.files)): fname = self.files[index] rec = FileParser.read(fname) self.assertIsInstance(rec, FileParser.FileRecord) self.assertTrue( str(rec).startswith( "Generated by createGenePop.py - (C) Tiago Antao\n" "136255903\n" "136257048\n" "136257636\n" "Pop\n" ), "Did not expect this:\n%s" % rec, ) self.assertEqual(len(rec.loci_list), self.num_loci[index]) for skip in range(self.pops_indivs[index][0]): if rec.skip_population() is False: raise Exception("Not enough populations") if rec.skip_population() is True: raise Exception("Too much populations") for i in range(self.pops_indivs[index][0]): continue rec._handle.close() # TODO - Needs a proper fix def test_wrong_file_parser(self): """Testing the ability to deal with wrongly formatted files.""" with open(os.path.join("PopGen", "README")) as f: try: rec = GenePop.read(f) raise Exception("Should have raised exception") except ValueError: pass def test_remove_features(self): """Testing the ability to remove population/loci via class methods.""" for index in range(len(self.files)): fname = self.files[index] ftemp = tempfile.NamedTemporaryFile(mode="w+", delete=False) ftemp.close() rec = FileParser.read(fname) rec.remove_loci_by_position([0], ftemp.name) with open(ftemp.name) as ft: ft.seek(0) rec2 = GenePop.read(iter(ft)) self.assertEqual(rec.loci_list[1:], rec2.loci_list) rec.remove_locus_by_position(0, ftemp.name) with open(ftemp.name) as ft: ft.seek(0) rec3 = GenePop.read(iter(ft)) self.assertEqual(rec.loci_list[1:], rec3.loci_list) rec.remove_locus_by_name(rec.loci_list[0], ftemp.name) with open(ftemp.name) as ft: ft.seek(0) rec4 = GenePop.read(iter(ft)) self.assertEqual(rec.loci_list[1:], rec4.loci_list) rec.remove_loci_by_name([rec.loci_list[0]], ftemp.name) with open(ftemp.name) as ft: ft.seek(0) rec5 = GenePop.read(iter(ft)) self.assertEqual(rec.loci_list[1:], rec5.loci_list) os.remove(ftemp.name) rec._handle.close() class UtilsTest(unittest.TestCase): """Utils tests.""" def setUp(self): # All files have to have at least 3 loci and 2 pops files = ["c2line.gen"] self.handles = [] for filename in files: self.handles.append(open(os.path.join("PopGen", filename))) def tearDown(self): for handle in self.handles: handle.close() def test_utils(self): """Basic operation of GenePop Utils.""" for index in range(len(self.handles)): handle = self.handles[index] rec = GenePop.read(handle) initial_pops = len(rec.populations) initial_loci = len(rec.loci_list) first_loci = rec.loci_list[0] rec.remove_population(0) self.assertEqual(len(rec.populations), initial_pops - 1) rec.remove_locus_by_name(first_loci) self.assertEqual(len(rec.loci_list), initial_loci - 1) self.assertNotEqual(rec.loci_list[0], first_loci) rec.remove_locus_by_position(0) self.assertEqual(len(rec.loci_list), initial_loci - 2) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)