#!/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
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#  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():
    f = StringIO(plain_io.example)
    seqs = plain_io.read(f)
    # print seqs
    assert len(seqs) == 1
    assert seqs[0].name is None
    # print seqs[0]
    assert len(seqs[0]) == 450


def test_write_seq():
    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():
    # 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)