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