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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.
#
from io import StringIO
import pytest
from weblogo.seq import protein_alphabet, rna_alphabet
from weblogo.seq_io import fasta_io, plain_io
def test_read_example() -> None:
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
# print seqs
assert len(seqs) == 1
assert not seqs[0].name
# print seqs[0]
assert len(seqs[0]) == 450
def test_write_seq() -> None:
f = StringIO(plain_io.example)
seqs = plain_io.read(f)
fout = StringIO()
plain_io.write(fout, seqs)
fout.seek(0)
seqs2 = plain_io.read(fout)
# print seqs[0].alphabet !=seqs2[0].alphabet
assert seqs[0].alphabet == seqs2[0].alphabet
assert seqs[0] == seqs2[0]
assert seqs == seqs2
def test_parse_fasta_fail() -> None:
# should fail with parse error
with pytest.raises(ValueError):
f = StringIO(fasta_io.example)
plain_io.read(f, protein_alphabet)
with pytest.raises(ValueError):
f = StringIO(plain_io.example)
plain_io.read(f, rna_alphabet)
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