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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.
# ----------------------------------------------------------------------------
from unittest import TestCase, main
from skbio.io.format._sequence_feature_vocabulary import (
_parse_loc_str, _parse_section_default, _serialize_location)
from skbio.io import FileFormatError
from skbio.metadata import IntervalMetadata
class Tests(TestCase):
def test_parse_section_default(self):
lines = [
['FOO blah blah',
' blah'],
['FOO=blah',
' blah'],
['FOO']]
kwargs = [{'join_delimiter': '=', 'return_label': False},
{'label_delimiter': '=', 'join_delimiter': '',
'return_label': True},
{'label_delimiter': '=', 'join_delimiter': '=',
'return_label': True}]
expects = ['blah blah=blah',
('FOO', 'blahblah'),
('FOO', '')]
for i, j, k in zip(lines, kwargs, expects):
self.assertEqual(k, _parse_section_default(i, **j))
def test_parse_loc_str(self):
examples = [
'9', # a single base in the presented sequence
'3..8',
'<3..8',
'3..>8',
'complement(3..>8)',
'complement(join(3..>5,<7..9))',
'join(J00194.1:1..9,3..8)',
'join(3..8,J00194.1:1..9)',
'1.9',
'1^2']
expects = [
([(8, 9)], [(False, False)], {'strand': '+'}),
([(2, 8)], [(False, False)], {'strand': '+'}),
([(2, 8)], [(True, False)], {'strand': '+'}),
([(2, 8)], [(False, True)], {'strand': '+'}),
([(2, 8)], [(False, True)], {'strand': '-'}),
([(2, 5), (6, 9)], [(False, True), (True, False)],
{'strand': '-'}),
([(2, 8)], [(False, False)], {'strand': '+'}),
([(2, 8)], [(False, False)], {'strand': '+'}),
([(0, 9)], [(False, False)], {'strand': '+'}),
([(0, 1)], [(False, False)], {'strand': '+'})]
for example, expect in zip(examples, expects):
parsed = _parse_loc_str(example)
self.assertEqual(parsed, expect)
def test_parse_loc_str_invalid(self):
examples = [
'abc',
'3-8']
for example in examples:
with self.assertRaisesRegex(FileFormatError,
'Could not parse location string: '
'"%s"' % example):
_parse_loc_str(example)
def test_serialize_location(self):
imd = IntervalMetadata(9)
i1 = imd.add([(0, 1)])
self.assertEqual(_serialize_location(i1), '1')
i2 = imd.add([(0, 2)], [(True, True)])
self.assertEqual(_serialize_location(i2), '<1..>2')
i3 = imd.add([(0, 2)], [(False, True)])
self.assertEqual(_serialize_location(i3), '1..>2')
i4 = imd.add([(0, 2)], [(True, False)])
self.assertEqual(_serialize_location(i4), '<1..2')
i5 = imd.add([(0, 2), (3, 9)], metadata={'strand': '-'})
self.assertEqual(_serialize_location(i5),
'complement(join(1..2,4..9))')
i6 = imd.add([(0, 2), (3, 9)],
[(True, False), (False, True)],
metadata={'strand': '-'})
self.assertEqual(_serialize_location(i6),
'complement(join(<1..2,4..>9))')
if __name__ == '__main__':
main()
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