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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 unittest
from Bio.PopGen import GenePop
from Bio.PopGen.GenePop import FileParser
class RecordTest(unittest.TestCase):
def test_record_basic(self):
"""Basic test on Record
"""
r = GenePop.Record()
assert isinstance(r.marker_len, int)
assert isinstance(r.comment_line, str)
assert isinstance(r.loci_list, list)
assert isinstance(r.populations, list)
class ParserTest(unittest.TestCase):
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)
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]
assert rec.pop_list == self.pop_names
for i in range(self.pops_indivs[index][0]):
assert 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", "fdist1")) as f:
try:
rec = GenePop.read(f)
raise Exception("Should have raised exception")
except ValueError:
pass
class FileParserTest(unittest.TestCase):
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)
assert isinstance(rec, FileParser.FileRecord)
assert 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
assert len(rec.populations[i]) == \
self.pops_indivs[index][1][i]
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", "fdist1")) as f:
try:
rec = GenePop.read(f)
raise Exception("Should have raised exception")
except ValueError:
pass
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 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)
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__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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