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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 RNA go here. tests for functionality shared by DNA and RNA
# go in test_nucleotide_sequences.py
class TestRNA(unittest.TestCase):
def test_reverse_transcribe(self):
# without changes
self.assertEqual(RNA('').reverse_transcribe(), DNA(''))
self.assertEqual(RNA('A').reverse_transcribe(), DNA('A'))
self.assertEqual(RNA('.ACGW-').reverse_transcribe(), DNA('.ACGW-'))
# with changes
self.assertEqual(DNA('T'), RNA('U').reverse_transcribe())
self.assertEqual(DNA('TT'), RNA('UU').reverse_transcribe())
self.assertEqual(DNA('ATCTG'), RNA('AUCUG').reverse_transcribe())
self.assertEqual(DNA('TTTG'), RNA('UUUG').reverse_transcribe())
def test_reverse_transcribe_preserves_all_metadata(self):
im = IntervalMetadata(4)
im.add([(0, 2)], metadata={'gene': 'p53'})
seq = RNA('AGUU', metadata={'foo': 'bar'},
positional_metadata={'foo': range(4)},
interval_metadata=im)
exp = DNA('AGTT', metadata={'foo': 'bar'},
positional_metadata={'foo': range(4)},
interval_metadata=im)
self.assertEqual(seq.reverse_transcribe(), exp)
def test_reverse_transcribe_does_not_modify_input(self):
seq = RNA('AUAU')
self.assertEqual(seq.reverse_transcribe(), DNA('ATAT'))
self.assertEqual(seq, RNA('AUAU'))
def test_cannot_subclass(self):
with self.assertRaisesRegex(TypeError, "Subclassing disabled"):
class CustomSequence(RNA):
pass
if __name__ == '__main__':
unittest.main()
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