def test_very_big_diff(self):
source_sequences = {
'R1':
'LOREMIPSUMDOLORSITAMETCONSECTETURADIPISCINGELITCRASMOLESTIE'
'ODIOVELMAXIMUSELEMENTUMMASSAPURUSFRINGILLALIGULANONSUSCIPIT'
'FELISDUIUTLACUS' * 3
}
new_sequence = source_sequences['R1']
new_sequence = new_sequence[:10] + 'CETUS' + new_sequence[15:]
project_config = self.build_config({'P-A-KX-R1-seed': new_sequence})
expected_report = """\
ERROR: changed references:
P-A-KX-R1-seed
- LOREMIPSUMDOLORSITAMETCONSECTETURADIPISCINGELITCRASMOLESTIEODIOVE
? ^^^^^
+ LOREMIPSUMCETUSSITAMETCONSECTETURADIPISCINGELITCRASMOLESTIEODIOVE
? ^^^^^
LMAXIMUSELEMENTUMMAS[244 matching characters]VELMAXIMUSELEMENTUMM
ASSAPURUSFRINGILLALIGULANONSUSCIPITFELISDUIUTLACUS
"""
report, error_count = compare_config(['P-A-KX-R1-seed'],
project_config,
source_sequences,
name_part=3)
assert expected_report == report
assert 1 == error_count
def test_match(self):
sequences = {'R1': 'ACTGATA'}
project_config = self.build_config('PROJ1',
{'P-A-KX-R1-seed': 'ACTGATA'})
expected_report = """\
P-A-KX-R1-seed
==
0 differences
"""
report = ''.join(compare_config('PROJ1', project_config, sequences))
self.assertEqual(expected_report, report)
def test_match(self):
sequences = {'KX1234': 'ACTGATA'} # {accession_num: seq}
project_config = self.build_config({'P-A-KX-KX1234-seed': 'ACTGATA'})
expected_report = """\
Matching references: P-A-KX-KX1234-seed
"""
report, error_count = compare_config(['P-A-KX-KX1234-seed'],
project_config,
sequences,
name_part=3)
assert expected_report == report
assert 0 == error_count
def test_dashes(self):
sequences = {'R1': 'ACT---GATT'}
project_config = self.build_config({'P-A-KX-R1-seed': 'ACTGATT'})
expected_report = """\
Matching references: P-A-KX-R1-seed
"""
report, error_count = compare_config(['P-A-KX-R1-seed'],
project_config,
sequences,
name_part=3)
assert expected_report == report
assert 0 == error_count
def test(self):
sequences = {'R1': 'ACTGATT'}
project_config = self.build_config('PROJ1',
{'P-A-KX-R1-seed': 'ACTGATT',
'P-A-KY-R2-seed': 'TTT'})
expected_report = """\
P-A-KX-R1-seed
==
P-A-KY-R2-seed
missing
1 differences
"""
report = ''.join(compare_config('PROJ1', project_config, sequences))
self.assertEqual(expected_report, report)
def test_missing_from_source(self):
sequences = {'R1': 'ACTGATT'}
project_config = self.build_config({
'P-A-KX-R1-seed': 'ACTGATT',
'P-A-KY-R2-seed': 'TTT'
})
expected_report = """\
Matching references: P-A-KX-R1-seed
ERROR: references missing from source: P-A-KY-R2-seed
"""
report, error_count = compare_config(
['P-A-KX-R1-seed', 'P-A-KY-R2-seed'],
project_config,
sequences,
name_part=3)
assert expected_report == report
assert 1 == error_count
def test_diff(self):
source_sequences = {'R1': 'ACTGATT'}
project_config = self.build_config({'P-A-KX-R1-seed': 'ACTGATA'})
expected_report = """\
ERROR: changed references:
P-A-KX-R1-seed
- ACTGATT
? ^
+ ACTGATA
? ^
"""
report, error_count = compare_config(['P-A-KX-R1-seed'],
project_config,
source_sequences,
name_part=3)
assert expected_report == report
assert 1 == error_count
def test_many_matches(self):
sequences = {'R1': 'ACTGATT', 'R2': 'TTT', 'R3': 'A', 'R4': 'A'}
project_config = self.build_config({
'P-A-KX-R1-seed': 'ACTGATT',
'P-A-KY-R2-seed': 'TTT',
'P-A-KY-R3-seed': 'A',
'P-A-KY-R4-seed': 'A'
})
expected_report = """\
Matching references: P-A-KX-R1-seed, P-A-KY-R2-seed, P-A-KY-R3-seed,
P-A-KY-R4-seed
"""
report, error_count = compare_config([
'P-A-KX-R1-seed', 'P-A-KY-R2-seed', 'P-A-KY-R3-seed',
'P-A-KY-R4-seed'
],
project_config,
sequences,
name_part=3)
assert expected_report == report
assert 0 == error_count