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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
81 lines
3.0 KiB
Python
81 lines
3.0 KiB
Python
# Copyright 2015 by Kai Blin.
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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 EMBL module (using unittest framework)."""
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import unittest
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import warnings
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from os import path
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from Bio import BiopythonParserWarning
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from Bio import SeqIO
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class EMBLTests(unittest.TestCase):
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def test_embl_content_after_co(self):
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"""Test a ValueError is thrown by content after a CO line."""
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def parse_content_after_co():
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rec = SeqIO.read(path.join("EMBL", "xx_after_co.embl"), "embl")
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self.assertRaises(ValueError, parse_content_after_co)
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try:
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parse_content_after_co()
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except ValueError as e:
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self.assertEqual(str(e), "Unexpected content after SQ or CO line: 'XX'")
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else:
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self.assertTrue(
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False,
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"Error message without explanation raised by content after CO line",
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)
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def test_embl_0_line(self):
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"""Test SQ line with 0 length sequence."""
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# Biopython 1.67 and older would parse this file with a warning:
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# 'Expected sequence length 1740, found 1744 (TIR43YW1_CE).' and
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# the coordinates 1740 added to the sequence as four extra letters.
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with warnings.catch_warnings(record=True) as w:
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warnings.simplefilter("always")
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rec = SeqIO.read("EMBL/embl_with_0_line.embl", "embl")
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self.assertEqual(
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len(w),
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0,
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"Unexpected parser warnings: "
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+ "\n".join(str(warn.message) for warn in w),
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)
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self.assertEqual(len(rec), 1740)
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def test_embl_no_coords(self):
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"""Test sequence lines without coordinates."""
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# Biopython 1.68, 1.69 and 1.70 would ignore these lines
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# giving an unknown sequence!
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with warnings.catch_warnings(record=True) as w:
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warnings.simplefilter("always", BiopythonParserWarning)
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rec = SeqIO.read("EMBL/101ma_no_coords.embl", "embl")
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self.assertTrue(w, "Expected parser warning")
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self.assertEqual(
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[str(_.message) for _ in w],
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["EMBL sequence line missing coordinates"] * 3,
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)
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self.assertEqual(len(rec), 154)
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self.assertEqual(rec.seq[:10], "MVLSEGEWQL")
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self.assertEqual(rec.seq[-10:], "AKYKELGYQG")
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def test_embl_wrong_dr_line(self):
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"""Test files with wrong DR lines."""
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with warnings.catch_warnings(record=True) as w:
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warnings.simplefilter("always", BiopythonParserWarning)
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record = SeqIO.read("EMBL/RepBase23.02.embl", "embl")
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self.assertTrue(w, "Expected parser warning")
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self.assertEqual(
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[str(_.message) for _ in w], ["Malformed DR line in EMBL file."]
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)
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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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