#!/usr/bin/env python

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#  Lawrence Berkeley National Laboratory (subject to receipt of any required
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import unittest
from io import StringIO

from weblogo.seq import nucleic_alphabet
from weblogo.seq_io import msf_io, plain_io

from . import data_stream


class test_msf_io(unittest.TestCase):
    def test_parse_msf(self) -> None:
        f = data_stream("dna.msf")
        seqs = msf_io.read(f)
        self.assertEqual(len(seqs), 10)
        self.assertEqual(seqs[1].name, "Carp")
        self.assertEqual(len(seqs[1]), 705)
        self.assertEqual(str(seqs[2][0:10]), "ATGGCCAACC")
        f.close()

    def test_parse_msf2(self) -> None:
        f = data_stream("cox2.msf")
        seqs = msf_io.read(f)
        self.assertEqual(len(seqs), 5)
        self.assertEqual(seqs[1].name, "cox2_crifa")
        self.assertEqual(len(seqs[1]), 166)
        self.assertEqual(str(seqs[2][0:10]), "MSFILTFWMI")
        f.close()

    def test_parse_1beo(self) -> None:
        f = data_stream("1beo.msf")
        msf_io.read(f)
        f.close()

    """ Wrong alphabet should throw a parsing error """

    def test_parse_error(self) -> None:
        f = data_stream("cox2.msf")
        self.assertRaises(ValueError, msf_io.read, f, nucleic_alphabet)
        f.close()

    def test_parse_fasta_fail2(self) -> None:
        # should fail with parse error
        f = data_stream("globin.fa")
        self.assertRaises(ValueError, msf_io.read, f)
        f.close()

    def test_parse_plain_fail(self) -> None:
        # should fail with parse error
        f = StringIO(plain_io.example)
        self.assertRaises(ValueError, msf_io.read, f)
        f.close()

    def test_parse_phylip_fail(self) -> None:
        # should fail with parse error
        f = data_stream("phylip_test_2.phy")
        self.assertRaises(ValueError, msf_io.read, f)
        f.close()

    def test_iter(self) -> None:
        f = data_stream("1beo.msf")
        for seq in msf_io.iterseq(f):
            pass
        f.close()


if __name__ == "__main__":
    unittest.main()