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#!/usr/bin/env python
# Copyright (c) 2006, The Regents of the University of California, through
# Lawrence Berkeley National Laboratory (subject to receipt of any required
# approvals from the U.S. Dept. of Energy). All rights reserved.
# This software is distributed under the new BSD Open Source License.
# <http://www.opensource.org/licenses/bsd-license.html>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# (1) Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# (2) Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and or other materials provided with the distribution.
#
# (3) Neither the name of the University of California, Lawrence Berkeley
# National Laboratory, U.S. Dept. of Energy nor the names of its contributors
# may be used to endorse or promote products derived from this software
# without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import unittest
from weblogo.utils import (
ArgumentError,
Token,
crc32,
crc64,
group_count,
invert_dict,
isblank,
isfloat,
isint,
remove_whitespace,
resource_filename,
resource_stream,
resource_string,
)
class test_utils(unittest.TestCase):
def test_isfloat(self) -> None:
self.assertTrue(isfloat("0.5"))
self.assertTrue(isfloat(" 0"))
self.assertTrue(isfloat("+1000000000 "))
self.assertTrue(isfloat("2"))
self.assertTrue(isfloat("0000.2323"))
self.assertTrue(isfloat("0.1e-23"))
self.assertTrue(isfloat(" -0.5e+23"))
self.assertFalse(isfloat(None))
self.assertFalse(isfloat(""))
self.assertFalse(isfloat("asdad"))
self.assertFalse(isfloat("q34sd"))
self.assertFalse(isfloat("92384.kjdfghiksw"))
self.assertFalse(isfloat("adf!@#nn"))
def test_isint(self) -> None:
self.assertTrue(isint("0"))
self.assertTrue(isint("-1"))
self.assertTrue(isint("10"))
self.assertTrue(isint("100101012234"))
self.assertTrue(isint("000"))
self.assertFalse(isint(None))
self.assertFalse(isint(""))
self.assertFalse(isint("asdad"))
self.assertFalse(isint("q34sd"))
self.assertFalse(isint("0.23"))
self.assertFalse(isint("adf!@#nn"))
def test_remove_whitespace(self) -> None:
self.assertEqual(
remove_whitespace(" kjashd askjdh askjdh\tasdf"), "kjashdaskjdhaskjdhasdf"
)
def test_isblank(self) -> None:
blank = ("", " ", "\n", "\t \n\n")
not_blank = (" a",)
for s in blank:
self.assertTrue(isblank(s))
for s in not_blank:
self.assertFalse(isblank(s))
self.assertFalse(isblank(123))
def test_group_count(self) -> None:
test = "aaabbbbcccddea"
out = group_count(test)
self.assertEqual(
tuple(out), (("a", 3), ("b", 4), ("c", 3), ("d", 2), ("e", 1), ("a", 1))
)
def test_token(self) -> None:
t = Token("kind", "some data", 4, 3)
str(t)
r = repr(t)
t2 = eval(r)
self.assertEqual(t2.typeof, "kind")
def test_invert_dict(self) -> None:
d = dict(a=3, b=4)
invd = invert_dict(d)
self.assertTrue(3 in invd)
self.assertEqual(invd[3], "a")
def test_crc64(self) -> None:
self.assertEqual(crc64("IHATEMATH"), "E3DCADD69B01ADD1")
def test_crc32(self) -> None:
self.assertEqual(crc32("Test the CRC-32 of this string."), "%08X" % 1571220330)
def test_ArgumentValueError(self) -> None:
message = "Some message"
component = "whatsit"
try:
raise ArgumentError(message, component)
except ArgumentError as err:
self.assertEqual(err.msg, message)
self.assertEqual(err.key, component)
try:
raise ArgumentError(message, component, 10)
except ArgumentError as err:
self.assertEqual(err.msg, message)
self.assertEqual(err.key, component)
self.assertEqual(err.value, 10)
def test_resource(self) -> None:
fn = resource_filename(__name__, "data/cap.fa", __file__)
self.assertTrue(fn.endswith("data/cap.fa"))
f = resource_stream(__name__, "data/cap.fa", __file__)
f.close()
s = resource_string(__name__, "data/cap.fa", __file__).decode()
self.assertTrue(s.startswith(">aldB"))
tfile = """line 0
line 1
Blah
line 3
line 4
"""
if __name__ == "__main__":
unittest.main()
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