# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Tests for Wise module."""

import doctest
import sys
import unittest

from io import StringIO

from Bio import Wise

if "requires_wise" in sys.modules:
    del sys.modules["requires_wise"]
import requires_wise  # noqa: E402


class TestWiseDryRun(unittest.TestCase):
    def setUp(self):
        self.old_stdout = sys.stdout
        sys.stdout = StringIO()

    def test_dnal(self):
        """Call dnal, and do a trivial check on its output."""
        Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
        # If test output is redirected to a file, the wrapper adds -quiet
        output = sys.stdout.getvalue().replace(" -quiet ", " ")
        self.assertTrue(
            output.startswith("dnal -kbyte 100000 seq1.fna seq2.fna"), output[:200]
        )

    def test_psw(self):
        """Call psw, and do a trivial check on its output."""
        Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
        # If test output is redirected to a file, the wrapper adds -quiet
        output = sys.stdout.getvalue().replace(" -quiet ", " ")
        self.assertTrue(
            output.startswith("psw -kbyte 4 seq1.faa seq2.faa"), output[:200]
        )

    def tearDown(self):
        sys.stdout = self.old_stdout


class TestWise(unittest.TestCase):
    def test_align(self):
        """Call dnal with optional arguments, and do a trivial check on the output."""
        temp_file = Wise.align(
            ["dnal"],
            ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"),
            kbyte=100000,
            force_type="DNA",
            quiet=True,
        )
        line = temp_file.readline().rstrip()
        if line == "Score 114":
            # Wise 2.4.1 includes a score line, even in quiet mode, ignore this
            line = temp_file.readline().rstrip()
        if (
            line
            == "ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC"
        ):
            # This is what we expect from wise 2.2.0 (and earlier)
            pass
        elif (
            line
            == "ENSG00000172135   AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC"
        ):
            # This is what we expect from wise 2.4.1
            pass
        else:
            # Bad!
            self.fail(line)


if __name__ == "__main__":
    unittest_suite = unittest.TestLoader().loadTestsFromName("test_Wise")
    doctest_suite = doctest.DocTestSuite(Wise)
    suite = unittest.TestSuite((unittest_suite, doctest_suite))
    runner = unittest.TextTestRunner(sys.stdout, verbosity=2)
    runner.run(suite)
