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#!/usr/bin/env python
# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
import unittest
from io import StringIO
from weblogo.seq_io import array_io, fasta_io
class test_array_io(unittest.TestCase):
def test_read_example(self) -> None:
f = StringIO(array_io.example)
seqs = array_io.read(f)
# print(seqs)
self.assertEqual(len(seqs), 8)
self.assertEqual(seqs[0].name, "")
self.assertEqual(len(seqs[1]), 60)
def test_write_seq(self) -> None:
f = StringIO(array_io.example)
seqs = array_io.read(f)
fout = StringIO()
array_io.write(fout, seqs)
fout.seek(0)
seqs2 = array_io.read(fout)
self.assertEqual(seqs, seqs2)
def test_fail(self) -> None:
# Lengths differ
example = """
-SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
-EPC-RDEN
"""
f = StringIO(example)
self.assertRaises(ValueError, array_io.read, f)
def test_read_fasta(self) -> None:
f = StringIO(fasta_io.example)
self.assertRaises(ValueError, array_io.read, f)
if __name__ == "__main__":
unittest.main()
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