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# Copyright 2007 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.
import os
import sys
import unittest
from Bio.PopGen import GenePop
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests.
"""
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
tests = [RecordTest, ParserTest, UtilsTest]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class RecordTest(unittest.TestCase):
def t_record_basic(self):
"""Basic test on Record
"""
r = GenePop.Record()
assert type(r.marker_len) == int
assert type(r.comment_line) == str
assert type(r.loci_list) == list
assert type(r.populations) == list
class ParserTest(unittest.TestCase):
def setUp(self):
files = ["c2line.gen", "c3line.gen", "c2space.gen", "c3space.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])
]
self.num_loci = [3, 3, 3, 3]
self.marker_len = [2, 3, 2, 3]
def tearDown(self):
for handle in self.handles:
handle.close()
def t_record_parser(self):
"""Basic operation of the Record Parser.
"""
for index in range(len(self.handles)):
handle = self.handles[index]
rec = GenePop.parse(handle)
assert isinstance(rec, GenePop.Record)
assert len(rec.loci_list) == self.num_loci[index]
assert rec.marker_len == self.marker_len[index]
assert len(rec.populations) == self.pops_indivs[index][0]
for i in range(self.pops_indivs[index][0]):
assert len(rec.populations[i]) == \
self.pops_indivs[index][1][i]
def t_wrong_file_parser(self):
"""Testing the ability to deal with wrongly formatted files
"""
f = open(os.path.join("PopGen", "fdist1"))
try:
rec = GenePop.parse(f)
raise Error("Should have raised exception")
except ValueError:
pass
f.close()
class UtilsTest(unittest.TestCase):
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 t_utils(self):
"""Basic operation of GenePop Utils.
"""
for index in range(len(self.handles)):
handle = self.handles[index]
rec = GenePop.parse(handle)
initial_pops = len(rec.populations)
initial_loci = len(rec.loci_list)
first_loci = rec.loci_list[0]
rec.remove_population(0)
assert len(rec.populations) == initial_pops - 1
rec.remove_locus_by_name(first_loci)
assert len(rec.loci_list) == initial_loci - 1
assert rec.loci_list[0] <> first_loci
rec.remove_locus_by_position(0)
assert len(rec.loci_list) == initial_loci - 2
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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