mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 21:53:47 +08:00
57056bbfc4
Reverted unwanted changes (mostly arrays in tests, but also some whitespace in doctests). Remaining changes are standardising spacing between module docstring and imports, and lower-case \x<hex> in strings.
130 lines
4.0 KiB
Python
130 lines
4.0 KiB
Python
# Copyright 1999 by Jeffrey Chang. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests for Bio.File module."""
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import os.path
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import shutil
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import tempfile
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import unittest
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from io import StringIO
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from Bio import bgzf
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from Bio import File
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class RandomAccess(unittest.TestCase):
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"""Random access tests."""
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def test_plain(self):
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"""Test plain text file."""
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with File._open_for_random_access("Quality/example.fastq") as handle:
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self.assertIn("r", handle.mode)
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self.assertIn("b", handle.mode)
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def test_bgzf(self):
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"""Test BGZF compressed file."""
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with File._open_for_random_access("Quality/example.fastq.bgz") as handle:
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self.assertIsInstance(handle, bgzf.BgzfReader)
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def test_gzip(self):
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"""Test gzip compressed file."""
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self.assertRaises(
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ValueError, File._open_for_random_access, "Quality/example.fastq.gz"
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)
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class AsHandleTestCase(unittest.TestCase):
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"""Tests for as_handle function."""
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def setUp(self):
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"""Initialise temporary directory."""
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# Create a directory to work in
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self.temp_dir = tempfile.mkdtemp(prefix="biopython-test")
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def tearDown(self):
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"""Remove temporary directory."""
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shutil.rmtree(self.temp_dir)
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def _path(self, *args):
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return os.path.join(self.temp_dir, *args)
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def test_handle(self):
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"""Test as_handle with a file-like object argument."""
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p = self._path("test_file.fasta")
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with open(p, "wb") as fp:
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with File.as_handle(fp) as handle:
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self.assertEqual(
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fp,
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handle,
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"as_handle should "
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"return argument when given a "
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"file-like object",
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)
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self.assertFalse(handle.closed)
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self.assertFalse(
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handle.closed,
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"Exiting as_handle given a file-like object "
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"should not close the file",
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)
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def test_string_path(self):
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"""Test as_handle with a string path argument."""
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p = self._path("test_file.fasta")
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mode = "wb"
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with File.as_handle(p, mode=mode) as handle:
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self.assertEqual(p, handle.name)
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self.assertEqual(mode, handle.mode)
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self.assertFalse(handle.closed)
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self.assertTrue(handle.closed)
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def test_path_object(self):
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"""Test as_handle with a pathlib.Path object."""
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from pathlib import Path
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p = Path(self._path("test_file.fasta"))
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mode = "wb"
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with File.as_handle(p, mode=mode) as handle:
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self.assertEqual(str(p.absolute()), handle.name)
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self.assertEqual(mode, handle.mode)
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self.assertFalse(handle.closed)
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self.assertTrue(handle.closed)
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def test_custom_path_like_object(self):
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"""Test as_handle with a custom path-like object."""
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class CustomPathLike:
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def __init__(self, path):
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self.path = path
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def __fspath__(self):
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return self.path
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p = CustomPathLike(self._path("test_file.fasta"))
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mode = "wb"
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with File.as_handle(p, mode=mode) as handle:
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self.assertEqual(p.path, handle.name)
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self.assertEqual(mode, handle.mode)
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self.assertFalse(handle.closed)
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self.assertTrue(handle.closed)
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def test_stringio(self):
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"""Testing passing StringIO handles."""
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s = StringIO()
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with File.as_handle(s) as handle:
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self.assertIs(s, handle)
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class BaseClassTests(unittest.TestCase):
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"""Tests for _IndexedSeqFileProxy base class."""
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def test_instance_exception(self):
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self.assertRaises(TypeError, File._IndexedSeqFileProxy)
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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