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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.
"""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)
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