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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import unittest
from skbio import DNA, RNA
from skbio.metadata import IntervalMetadata
# tests specific to DNA go here. tests for functionality shared by DNA and RNA
# go in test_nucleotide_sequences.py
class TestDNA(unittest.TestCase):
def test_transcribe(self):
# without changes
self.assertEqual(DNA('').transcribe(), RNA(''))
self.assertEqual(DNA('A').transcribe(), RNA('A'))
self.assertEqual(DNA('.ACGW-').transcribe(), RNA('.ACGW-'))
# with changes
self.assertEqual(DNA('T').transcribe(), RNA('U'))
self.assertEqual(DNA('TT').transcribe(), RNA('UU'))
self.assertEqual(DNA('ATCTG').transcribe(), RNA('AUCUG'))
self.assertEqual(DNA('TTTG').transcribe(), RNA('UUUG'))
def test_transcribe_preserves_all_metadata(self):
im = IntervalMetadata(4)
im.add([(0, 2)], metadata={'gene': 'p53'})
exp = RNA('AGUU', metadata={'foo': 'bar'},
positional_metadata={'foo': range(4)},
interval_metadata=im)
seq = DNA('AGTT', metadata={'foo': 'bar'},
positional_metadata={'foo': range(4)},
interval_metadata=im)
self.assertEqual(seq.transcribe(), exp)
def test_transcribe_does_not_modify_input(self):
seq = DNA('ATAT')
self.assertEqual(seq.transcribe(), RNA('AUAU'))
self.assertEqual(seq, DNA('ATAT'))
def test_cannot_subclass(self):
with self.assertRaisesRegex(TypeError, "Subclassing disabled"):
class CustomSequence(DNA):
pass
if __name__ == '__main__':
unittest.main()
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