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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 io import StringIO
from weblogo.seq import protein_alphabet
from weblogo.seq_io import clustal_io, phylip_io, plain_io
from . import data_ref
class test_phylip_io(unittest.TestCase):
def test_read(self) -> None:
with data_ref("phylip_test_1.phy").open() as f:
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 10)
self.assertEqual(seqs[0].name, "Cow")
self.assertEqual(len(seqs[1]), 234)
def test_iterseq(self) -> None:
with data_ref("phylip_test_1.phy").open() as f:
n = 0
for seq in phylip_io.iterseq(f):
n += 1
assert n == 10
def test_parse_plain_fail(self) -> None:
# should fail with parse error
f = StringIO(plain_io.example)
self.assertRaises(ValueError, phylip_io.read, f)
def test_parse_phylip_test_2(self) -> None:
with data_ref("phylip_test_2.phy").open() as f:
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 20)
self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
self.assertEqual(seqs[1].name, "Hesperorni")
def test_parse_clustal_fail(self) -> None:
# should fail with parse error
f = StringIO(clustal_io.example)
self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)
def test_parse_phylip_test_3(self) -> None:
with data_ref("phylip_test_3.phy").open() as f:
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 20)
self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT")
self.assertEqual(seqs[1].name, "Hesperorni")
def test_parse_phylip_test_4(self) -> None:
with data_ref("phylip_test_4.phy").open() as f:
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 25)
self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG")
self.assertEqual(seqs[2].name, "ddrasa")
def test_parse_phylip_test_5(self) -> None:
with data_ref("phylip_test_5.phy").open() as f:
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 6)
self.assertEqual(len(seqs[0]), 50)
self.assertEqual(
str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGG"
)
self.assertEqual(seqs[2].name, "ddrasa")
def test_parse_wrong_phylip_codes_1(self) -> None:
with data_ref("phylip_test_6.corrupt.phy").open() as f:
self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)
def test_parse_wrong_phylip_codes_2(self) -> None:
with data_ref("phylip_test_7.corrupt.phy").open() as f:
self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet)
def test_parse_phylip_dna(self) -> None:
with data_ref("dna.phy").open() as f:
seqs = phylip_io.read(f)
self.assertEqual(len(seqs), 10)
self.assertEqual(len(seqs[0]), 705)
self.assertEqual(str(seqs[1][0:10]), "ATGGCACACC")
self.assertEqual(seqs[2].name, "Chicken")
if __name__ == "__main__":
unittest.main()
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