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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 Sequence, DNA, RNA, Protein
from skbio import read
from skbio.util import get_data_path
from skbio.io import QSeqFormatError
from skbio.io.format.qseq import _qseq_to_generator, _qseq_sniffer
import numpy as np
def _drop_kwargs(kwargs, *args):
for arg in args:
if arg in kwargs:
kwargs.pop(arg)
class TestQSeqBase(unittest.TestCase):
def setUp(self):
self.valid_files = [
(get_data_path('qseq_single_seq_sanger'), [
{'variant': 'sanger'},
{'phred_offset': 33},
], [
{'id': 'sanger_1:3:34:-30:30#0/2',
'sequence': 'ACGTACGTACGTACGTACGTACGTACTTTTTTTTTTACGTACGTACG'
'TACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC',
'quality': [26, 26, 29, 31, 33, 34, 36, 37, 38, 39, 41, 42,
43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,
67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
91, 92, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93,
93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93,
93, 93, 93, 93, 93, 93, 93, 93, 93, 93],
'machine_name': 'sanger',
'run_number': 1,
'lane_number': 3,
'tile_number': 34,
'x': -30,
'y': 30,
'index': 0,
'read_number': 2}
]),
(get_data_path('qseq_multi_seq_illumina1.3'), [
{'variant': 'illumina1.3'},
{'phred_offset': 64}
], [
{'id': 'illumina_1:3:34:-30:30#0/1',
'sequence': 'ACG....ACGTAC',
'quality': [50, 53, 2, 2, 2, 2, 50, 2, 3, 5, 6, 7, 8],
'machine_name': 'illumina',
'run_number': 1,
'lane_number': 3,
'tile_number': 34,
'x': -30,
'y': 30,
'index': 0,
'read_number': 1},
{'id': 'illumina_1:3:35:-30:30#0/2',
'sequence': 'ACGTA.AATAAAC',
'quality': [39, 37, 20, 33, 1, 33, 38, 40, 55, 49, 1, 1, 38],
'machine_name': 'illumina',
'run_number': 1,
'lane_number': 3,
'tile_number': 35,
'x': -30,
'y': 30,
'index': 0,
'read_number': 2}
]),
(get_data_path('qseq_multi_seq_illumina1.3'), [
{'variant': 'illumina1.3', 'filter': False, 'seq_num': 1},
{'phred_offset': 64, 'filter': False, 'seq_num': 2},
{'variant': 'illumina1.3', 'filter': False, 'seq_num': 3,
'constructor': Protein},
{'phred_offset': 64, 'filter': False, 'seq_num': 4,
'constructor': DNA},
], [
{'id': 'illumina_1:3:34:-30:30#0/1',
'sequence': 'ACG....ACGTAC',
'quality': [50, 53, 2, 2, 2, 2, 50, 2, 3, 5, 6, 7, 8],
'machine_name': 'illumina',
'run_number': 1,
'lane_number': 3,
'tile_number': 34,
'x': -30,
'y': 30,
'index': 0,
'read_number': 1},
{'id': 'illumina_1:3:34:30:-30#0/1',
'sequence': 'CGGGCATTGCA',
'quality': [3, 7, 7, 7, 3, 33, 51, 36, 7, 3, 1],
'machine_name': 'illumina',
'run_number': 1,
'lane_number': 3,
'tile_number': 34,
'x': 30,
'y': -30,
'index': 0,
'read_number': 1},
{'id': 'illumina_1:3:35:-30:30#0/2',
'sequence': 'ACGTA.AATAAAC',
'quality': [39, 37, 20, 33, 1, 33, 38, 40, 55, 49, 1, 1, 38],
'machine_name': 'illumina',
'run_number': 1,
'lane_number': 3,
'tile_number': 35,
'x': -30,
'y': 30,
'index': 0,
'read_number': 2},
{'id': 'illumina_1:3:35:30:-30#0/3',
'sequence': 'CATTTAGGA.TGCA',
'quality': [52, 42, 38, 44, 43, 1, 6, 46, 43, 11, 39, 40, 54,
13],
'machine_name': 'illumina',
'run_number': 1,
'lane_number': 3,
'tile_number': 35,
'x': 30,
'y': -30,
'index': 0,
'read_number': 3}
])
]
self.invalid_files = [
(get_data_path('whitespace_only'), [
{},
{'variant': 'sanger'}
], [
'blank line',
], QSeqFormatError),
(get_data_path('tsv_10_fields'), [
{},
{'variant': 'sanger'},
{'variant': 'solexa'}
], [
'read',
'[1, 3]'
], QSeqFormatError),
(get_data_path('tsv_8_fields'), [
{},
{'variant': 'sanger'},
{'variant': 'solexa'}
], [
'8',
'10 or 11'
], QSeqFormatError),
(get_data_path('qseq_invalid_filter'), [
{},
{'phred_offset': 33},
{'variant': 'solexa'},
{'variant': 'illumina1.3'},
{'variant': 'illumina1.8'}
], [
'filter',
'0 or 1',
], QSeqFormatError),
(get_data_path('qseq_invalid_read'), [
{},
{'phred_offset': 33},
{'variant': 'solexa'},
{'variant': 'illumina1.3'},
{'variant': 'illumina1.8'}
], [
'read',
'[1, 3]',
], QSeqFormatError),
(get_data_path('qseq_invalid_x'), [
{},
{'phred_offset': 33},
{'variant': 'solexa'},
{'variant': 'illumina1.3'},
{'variant': 'illumina1.8'}
], [
'x',
'integer',
], QSeqFormatError),
(get_data_path('qseq_invalid_y'), [
{},
{'phred_offset': 33},
{'variant': 'solexa'},
{'variant': 'illumina1.3'},
{'variant': 'illumina1.8'}
], [
'y',
'integer',
], QSeqFormatError),
(get_data_path('qseq_invalid_lane'), [
{},
{'phred_offset': 33},
{'variant': 'solexa'},
{'variant': 'illumina1.3'},
{'variant': 'illumina1.8'}
], [
'lane',
'positive integer',
], QSeqFormatError),
(get_data_path('qseq_invalid_tile'), [
{},
{'phred_offset': 33},
{'variant': 'solexa'},
{'variant': 'illumina1.3'},
{'variant': 'illumina1.8'}
], [
'tile',
'positive integer',
], QSeqFormatError)
]
class TestQSeqToGenerator(TestQSeqBase):
def setUp(self):
super(TestQSeqToGenerator, self).setUp()
self.valid_files += [
(get_data_path('empty'), [{}, {'variant': 'sanger'}], [])
]
self.invalid_files += [
(get_data_path('qseq_single_seq_sanger'), [
{'variant': 'illumina1.3'},
{'variant': 'illumina1.8'}
], [
'out of range',
'[0, 62]'
], ValueError)
]
def test_invalid_files(self):
for invalid, kwargs, errors, etype in self.invalid_files:
with self.assertRaises(etype) as cm:
for kwarg in kwargs:
_drop_kwargs(kwarg, 'seq_num')
list(_qseq_to_generator(invalid, **kwarg))
for e in errors:
self.assertIn(e, str(cm.exception))
def test_valid_files(self):
for valid, kwargs, components in self.valid_files:
for kwarg in kwargs:
_drop_kwargs(kwarg, 'seq_num')
constructor = kwarg.get('constructor', Sequence)
expected = [
constructor(
c['sequence'],
metadata={'id': c['id'],
'machine_name': c['machine_name'],
'run_number': c['run_number'],
'lane_number': c['lane_number'],
'tile_number': c['tile_number'],
'x': c['x'],
'y': c['y'],
'index': c['index'],
'read_number': c['read_number']},
positional_metadata={
'quality': np.array(c['quality'], dtype=np.uint8)})
for c in components]
observed = list(_qseq_to_generator(valid, **kwarg))
self.assertEqual(len(expected), len(observed))
for o, e in zip(observed, expected):
self.assertEqual(o, e)
class TestQSeqToSequences(TestQSeqBase):
def test_invalid_files(self):
for constructor in [Sequence, DNA, RNA, Protein]:
for invalid, kwargs, errors, etype in self.invalid_files:
with self.assertRaises(etype) as cm:
for kwarg in kwargs:
_drop_kwargs(kwarg, 'constructor', 'filter')
read(invalid, format='qseq', verify=False,
into=constructor, **kwarg)
for e in errors:
self.assertIn(e, str(cm.exception))
def test_valid_files(self):
for constructor in [Sequence, DNA, RNA, Protein]:
for valid, kwargs, components in self.valid_files:
for observed_kwargs in kwargs:
expected_kwargs = {}
# Currently not validating the alphabet for qseq
# files that are read in for this test.
if hasattr(constructor, 'alphabet'):
observed_kwargs['validate'] = False
expected_kwargs['validate'] = False
_drop_kwargs(observed_kwargs, 'constructor', 'filter')
seq_num = observed_kwargs.get('seq_num', 1)
c = components[seq_num - 1]
expected = constructor(
c['sequence'],
metadata={'id': c['id'],
'machine_name': c['machine_name'],
'run_number': c['run_number'],
'lane_number': c['lane_number'],
'tile_number': c['tile_number'],
'x': c['x'],
'y': c['y'],
'index': c['index'],
'read_number': c['read_number']},
positional_metadata={
'quality': np.array(c['quality'], np.uint8)},
**expected_kwargs)
observed = read(valid, into=constructor,
format='qseq', verify=False,
**observed_kwargs)
self.assertEqual(observed, expected)
class TestQSeqSniffer(TestQSeqBase):
def setUp(self):
super(TestQSeqSniffer, self).setUp()
self.invalid_files += [
(get_data_path('empty'), None, None, None)
]
def test_qseq_sniffer_valid_files(self):
for valid, _, _ in self.valid_files:
self.assertEqual(_qseq_sniffer(valid), (True, {}))
def test_qseq_sniffer_invalid_files(self):
for invalid, _, _, _ in self.invalid_files:
self.assertEqual(_qseq_sniffer(invalid), (False, {}))
if __name__ == '__main__':
unittest.main()
|
