def test_pattern_replace_static(self):
result = transform.name_replace(self.sequences, '_REPLACE_',
'_DONE_')
result = list(result)
expected = self.create_sequences()
expected[1].id = 'test_DONE_2'
self.assertEqual(self.sequences, result)
def test_pattern_replace_anchored_nomatch(self):
sequences = [seqrecord('hello', 'A', description='hello friend')]
transformed = next(transform.name_replace(sequences, r'^hello$', 'bye'))
self.assertEqual(str(sequences[0].seq), str(transformed.seq))
self.assertEqual('hello', transformed.id)
self.assertEqual('hello friend', transformed.description)
def test_pattern_replace_static(self):
result = transform.name_replace(self.sequences, '_REPLACE_',
'_DONE_')
result = list(result)
expected = self.create_sequences()
expected[1].id = 'test_DONE_2'
self.assertEqual(self.sequences, result)
def test_pattern_replace_anchored_transform_id(self):
sequences = [
seqrecord(
'gi|351517969|ref|NW_003613580.1|',
'CAGTC',
description=
'gi|351517969|ref|NW_003613580.1| Cricetulus griseus unplaced genomic scaffold'
),
seqrecord('gi|351517969|ref|NW_003613580.1|',
'CAGTC',
description='gi|351517969|ref|NW_003613580.1|'),
seqrecord('gi|351517969|ref|NW_003613580.1|', 'CAGTC')
]
# capture the identifier after three groups of pipe-separated characters
transformed = list(
transform.name_replace(sequences, r'^(?:[^|]+\|){3}([^|]+)\|',
r'\1'))
self.assertEqual(str(sequences[0].seq), str(transformed[0].seq))
self.assertEqual('NW_003613580.1', transformed[0].id)
self.assertEqual(
'NW_003613580.1 Cricetulus griseus unplaced genomic scaffold',
transformed[0].description)
self.assertEqual(str(sequences[1].seq), str(transformed[1].seq))
self.assertEqual('NW_003613580.1', transformed[1].id)
self.assertEqual('NW_003613580.1', transformed[1].description)
self.assertEqual(str(sequences[2].seq), str(transformed[2].seq))
self.assertEqual('NW_003613580.1', transformed[2].id)
self.assertEqual('<unknown description>', transformed[2].description)
def test_pattern_replace_anchored_remove_from_description(self):
sequences = [seqrecord('Bra000001', 'CTTAT', description='Bra000001 Brassica rapa')]
transformed = next(transform.name_replace(sequences, r' .*$', ''))
self.assertEqual(str(sequences[0].seq), str(transformed.seq))
self.assertEqual('Bra000001', transformed.id)
self.assertEqual('Bra000001', transformed.description)
def test_pattern_replace_anchored_id_from_description(self):
sequences = [seqrecord('hg19_ct_UserTrack_3545_691', 'GATGG',
description='hg19_ct_UserTrack_3545_691 range=chr1:8121498-8121502 5\'pad=0 3\'pad=0 strand=+ repeatMasking=none')]
transformed = next(transform.name_replace(sequences, r'^\S+ range=(\S+)', r'\1'))
self.assertEqual(str(sequences[0].seq), str(transformed.seq))
self.assertEqual('chr1:8121498-8121502', transformed.id)
self.assertEqual('chr1:8121498-8121502 5\'pad=0 3\'pad=0 strand=+ repeatMasking=none', transformed.description)
def test_pattern_replace_case_insensitive(self):
"""
Substitutions are case insensitive
"""
result = transform.name_replace(self.sequences, '_replace_', '_DONE_')
result = list(result)
expected = self.create_sequences()
expected[1].id = 'test_DONE_2'
self.assertEqual(self.sequences, result)
def test_pattern_replace_group(self):
"""
Make sure capturing groups work
"""
result = transform.name_replace(self.sequences, '_(repl)ace_',
'_DONE-\\1_')
result = list(result)
expected = self.create_sequences()
expected[1].id = 'test_DONE-repl_2'
self.assertEqual(self.sequences, result)
def test_pattern_replace_case_insensitive(self):
"""
Substitutions are case insensitive
"""
result = transform.name_replace(self.sequences, '_replace_',
'_DONE_')
result = list(result)
expected = self.create_sequences()
expected[1].id = 'test_DONE_2'
self.assertEqual(self.sequences, result)
def test_pattern_replace_group(self):
"""
Make sure capturing groups work
"""
result = transform.name_replace(self.sequences, '_(repl)ace_',
'_DONE-\\1_')
result = list(result)
expected = self.create_sequences()
expected[1].id = 'test_DONE-repl_2'
self.assertEqual(self.sequences, result)
def test_pattern_replace_anchored_match(self):
sequences = [seqrecord('hello', 'A', description='hello friend'),
seqrecord('hello', 'A')]
transformed = list(transform.name_replace(sequences, r'^hello\b', 'bye'))
self.assertEqual(str(sequences[0].seq), str(transformed[0].seq))
self.assertEqual('bye', transformed[0].id)
self.assertEqual('bye friend', transformed[0].description)
self.assertEqual(str(sequences[1].seq), str(transformed[1].seq))
self.assertEqual('bye', transformed[1].id)
self.assertEqual('<unknown description>', transformed[1].description)
def test_pattern_replace_anchored_transform_id(self):
sequences = [seqrecord('gi|351517969|ref|NW_003613580.1|', 'CAGTC',
description='gi|351517969|ref|NW_003613580.1| Cricetulus griseus unplaced genomic scaffold'),
seqrecord('gi|351517969|ref|NW_003613580.1|', 'CAGTC',
description='gi|351517969|ref|NW_003613580.1|'),
seqrecord('gi|351517969|ref|NW_003613580.1|', 'CAGTC')]
# capture the identifier after three groups of pipe-separated characters
transformed = list(transform.name_replace(sequences, r'^(?:[^|]+\|){3}([^|]+)\|', r'\1'))
self.assertEqual(str(sequences[0].seq), str(transformed[0].seq))
self.assertEqual('NW_003613580.1', transformed[0].id)
self.assertEqual('NW_003613580.1 Cricetulus griseus unplaced genomic scaffold', transformed[0].description)
self.assertEqual(str(sequences[1].seq), str(transformed[1].seq))
self.assertEqual('NW_003613580.1', transformed[1].id)
self.assertEqual('NW_003613580.1', transformed[1].description)
self.assertEqual(str(sequences[2].seq), str(transformed[2].seq))
self.assertEqual('NW_003613580.1', transformed[2].id)
self.assertEqual('<unknown description>', transformed[2].description)
def test_pattern_replace_none(self):
result = transform.name_replace(self.sequences, 'ZZZ', 'MATCH')
result = list(result)
self.assertEqual(self.sequences, result)
def test_pattern_replace_none(self):
result = transform.name_replace(self.sequences, 'ZZZ', 'MATCH')
result = list(result)
self.assertEqual(self.sequences, result)
