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21d5f670d6
* avoid yield * alternative --------- Co-authored-by: Michiel de Hoon <mdehoon@tkx249.genome.gsc.riken.jp>
96 lines
3.5 KiB
Python
96 lines
3.5 KiB
Python
# Copyright 2019 Damien Goutte-Gattat. All rights reserved.
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#
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Tests for the SeqIO Gck module."""
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import unittest
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from io import BytesIO
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from Bio import SeqIO
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class TestGckWithArtificialData(unittest.TestCase):
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def setUp(self):
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with open("Gck/artificial.gck", "rb") as f:
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self.buffer = f.read()
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def test_read(self):
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"""Read an artificial sample file."""
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h = BytesIO(self.buffer)
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record = SeqIO.read(h, "gck")
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self.assertEqual("ACGTACGTACGT", record.seq)
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self.assertEqual("Sample construct", record.description)
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self.assertEqual("linear", record.annotations["topology"])
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self.assertEqual(2, len(record.features))
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self.assertEqual(2, record.features[0].location.start)
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self.assertEqual(6, record.features[0].location.end)
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self.assertEqual(1, record.features[0].location.strand)
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self.assertEqual("misc_feature", record.features[0].type)
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self.assertEqual("FeatureA", record.features[0].qualifiers["label"][0])
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self.assertEqual(7, record.features[1].location.start)
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self.assertEqual(11, record.features[1].location.end)
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self.assertEqual(-1, record.features[1].location.strand)
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self.assertEqual("CDS", record.features[1].type)
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self.assertEqual("FeatureB", record.features[1].qualifiers["label"][0])
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h.close()
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def munge_buffer(self, position, value):
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mod_buffer = bytearray(self.buffer)
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if isinstance(value, list):
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mod_buffer[position : position + len(value) - 1] = value
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else:
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mod_buffer[position] = value
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return BytesIO(mod_buffer)
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def test_conflicting_lengths(self):
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"""Read a file with incorrect length."""
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# Change the sequence length as indicated in the sequence packet
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h = self.munge_buffer(0x1C, [0x00, 0x00, 0x20, 0x15])
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with self.assertRaisesRegex(ValueError, "Conflicting sequence length values"):
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SeqIO.read(h, "gck")
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h.close()
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# Change the sequence length as indicated in the features packet
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h = self.munge_buffer(0x36, [0x00, 0x00, 0x20, 0x15])
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with self.assertRaisesRegex(ValueError, "Conflicting sequence length values"):
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SeqIO.read(h, "gck")
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h.close()
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# Change the number of features
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h = self.munge_buffer(0x3B, 0x30)
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with self.assertRaisesRegex(
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ValueError, "Features packet size inconsistent with number of features"
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):
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SeqIO.read(h, "gck")
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h.close()
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# Change the number of restriction sites
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h = self.munge_buffer(0x137, 0x30)
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with self.assertRaisesRegex(
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ValueError, "Sites packet size inconsistent with number of sites"
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):
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SeqIO.read(h, "gck")
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h.close()
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class TestGckWithImproperHeader(unittest.TestCase):
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def test_read(self):
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"""Read a file with an incomplete header."""
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stream = BytesIO(b"tiny")
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with self.assertRaisesRegex(
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ValueError, "Improper header, cannot read 24 bytes from stream"
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):
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SeqIO.read(stream, "gck")
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stream.close()
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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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