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"""Tests for SeqIO NibIO module."""
import unittest
from io import BytesIO
from Bio import SeqIO
class TestNibReaderWriter(unittest.TestCase):
def test_read_even(self):
with open("Nib/test_even.fa") as handle:
record = SeqIO.read(handle, "fasta")
sequence = record.seq
with open("Nib/test_even_bigendian.nib", "rb") as handle:
record = SeqIO.read(handle, "nib")
self.assertEqual(sequence, record.seq)
with open("Nib/test_even_littleendian.nib", "rb") as handle:
record = SeqIO.read(handle, "nib")
self.assertEqual(sequence, record.seq)
def test_read_odd(self):
with open("Nib/test_odd.fa") as handle:
record = SeqIO.read(handle, "fasta")
sequence = record.seq
with open("Nib/test_odd_bigendian.nib", "rb") as handle:
record = SeqIO.read(handle, "nib")
self.assertEqual(sequence, record.seq)
with open("Nib/test_odd_littleendian.nib", "rb") as handle:
record = SeqIO.read(handle, "nib")
self.assertEqual(sequence, record.seq)
def test_write_even(self):
with open("Nib/test_even.fa") as handle:
record = SeqIO.read(handle, "fasta")
sequence = record.seq
handle = BytesIO()
n = SeqIO.write(record, handle, "nib")
self.assertEqual(n, 1)
handle.flush()
handle.seek(0)
record = SeqIO.read(handle, "nib")
handle.close()
self.assertEqual(sequence, record.seq)
def test_write_odd(self):
with open("Nib/test_odd.fa") as handle:
record = SeqIO.read(handle, "fasta")
sequence = record.seq
handle = BytesIO()
n = SeqIO.write(record, handle, "nib")
self.assertEqual(n, 1)
handle.flush()
handle.seek(0)
record = SeqIO.read(handle, "nib")
handle.close()
self.assertEqual(sequence, record.seq)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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