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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
62 lines
2.0 KiB
Python
62 lines
2.0 KiB
Python
"""Tests for SeqIO NibIO 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 TestNibReaderWriter(unittest.TestCase):
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def test_read_even(self):
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with open("Nib/test_even.fa") as handle:
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record = SeqIO.read(handle, "fasta")
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sequence = record.seq
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with open("Nib/test_even_bigendian.nib", "rb") as handle:
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record = SeqIO.read(handle, "nib")
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self.assertEqual(sequence, record.seq)
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with open("Nib/test_even_littleendian.nib", "rb") as handle:
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record = SeqIO.read(handle, "nib")
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self.assertEqual(sequence, record.seq)
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def test_read_odd(self):
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with open("Nib/test_odd.fa") as handle:
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record = SeqIO.read(handle, "fasta")
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sequence = record.seq
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with open("Nib/test_odd_bigendian.nib", "rb") as handle:
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record = SeqIO.read(handle, "nib")
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self.assertEqual(sequence, record.seq)
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with open("Nib/test_odd_littleendian.nib", "rb") as handle:
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record = SeqIO.read(handle, "nib")
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self.assertEqual(sequence, record.seq)
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def test_write_even(self):
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with open("Nib/test_even.fa") as handle:
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record = SeqIO.read(handle, "fasta")
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sequence = record.seq
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handle = BytesIO()
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n = SeqIO.write(record, handle, "nib")
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self.assertEqual(n, 1)
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handle.flush()
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handle.seek(0)
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record = SeqIO.read(handle, "nib")
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handle.close()
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self.assertEqual(sequence, record.seq)
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def test_write_odd(self):
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with open("Nib/test_odd.fa") as handle:
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record = SeqIO.read(handle, "fasta")
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sequence = record.seq
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handle = BytesIO()
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n = SeqIO.write(record, handle, "nib")
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self.assertEqual(n, 1)
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handle.flush()
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handle.seek(0)
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record = SeqIO.read(handle, "nib")
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handle.close()
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self.assertEqual(sequence, record.seq)
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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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