def test_same_consensus(self):
source_seqs = {('R1-seed', 'R1'): make_nuc_rows('ACACAC')}
target_seqs = {('R1-seed', 'R1'): make_nuc_rows('ACACAC')}
coverage_scores = [{
'seed': 'R1-seed',
'region': 'R1',
'project': 'R1',
'on.score': '4'
}]
sample = Sample(
MiseqRun(target_path='run1/Results/versionX'), 'sample42',
SampleFiles(region_consensus=source_seqs,
coverage_scores=coverage_scores),
SampleFiles(region_consensus=target_seqs,
coverage_scores=coverage_scores))
expected_diffs = []
expected_scenarios = {}
diffs = []
scenarios = defaultdict(list)
compare_consensus(
sample, diffs, Scenarios.MAIN_CONSENSUS_CHANGED
| Scenarios.OTHER_CONSENSUS_CHANGED, scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_scenarios, scenarios)
def test_other_consensus_change(self):
source_seqs = {('R1-seed', 'R1', '0.250'): 'ACACAC'}
target_seqs = {('R1-seed', 'R1', '0.250'): 'ACACAT'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42',
SampleFiles(),
SampleFiles())
expected_diffs = ['run1:sample42 consensus: R1-seed R1 0.250',
'- ACACAC',
'? ^',
'+ ACACAT',
'? ^']
expected_scenarios = {}
diffs = []
scenarios = defaultdict(list)
compare_consensus(
sample,
source_seqs,
target_seqs,
diffs,
Scenarios.NONE,
scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_scenarios, scenarios)
def test_consensus_change_diff(self):
source_seqs = {('R1-seed', 'R1'): make_nuc_rows('ACACAC')}
target_seqs = {('R1-seed', 'R1'): make_nuc_rows('ACACAT')}
coverage_scores = [{
'seed': 'R1-seed',
'region': 'R1',
'project': 'R1',
'on.score': '4'
}]
sample = Sample(
MiseqRun(target_path='run1/Results/versionX'), 'sample42',
SampleFiles(region_consensus=source_seqs,
coverage_scores=coverage_scores),
SampleFiles(region_consensus=target_seqs,
coverage_scores=coverage_scores))
expected_diffs = [
'run1:sample42 consensus: R1-seed R1 MAX', '- ACACAC', '? ^',
'+ ACACAT', '? ^'
]
expected_scenarios = {}
diffs = []
scenarios = defaultdict(list)
compare_consensus(sample, diffs, Scenarios.NONE, scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_scenarios, scenarios)
def test_consensus_trailing_change(self):
source_seqs = {('R1-seed', 'R1'): make_nuc_rows('ACTTAC------GTAC')}
target_seqs = {('R1-seed', 'R1'): make_nuc_rows('ACTTAC')}
coverage_scores = [{
'seed': 'R1-seed',
'region': 'R1',
'project': 'R1',
'on.score': '4'
}]
sample = Sample(
MiseqRun(target_path='run1/Results/versionX'), 'sample42',
SampleFiles(region_consensus=source_seqs,
coverage_scores=coverage_scores),
SampleFiles(region_consensus=target_seqs,
coverage_scores=coverage_scores))
expected_diffs = [
'run1:sample42 consensus: R1-seed R1 MAX', '- ACTTAC------GTAC',
'+ ACTTAC'
]
expected_consensus_distances = [
ConsensusDistance(region='R1',
cutoff='MAX',
distance=4,
pct_diff=25)
]
diffs = []
scenarios = defaultdict(list)
consensus_distances = compare_consensus(sample, diffs, Scenarios.NONE,
scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_consensus_distances, consensus_distances)
def test_one_consensus_changes(self):
source_seqs = {
('R1-seed', 'R1', 'MAX'): 'ACACACGT',
('R2-seed', 'R2', 'MAX'): 'ACACACGT'
}
target_seqs = {
('R1-seed', 'R1', 'MAX'): 'ACACACGT',
('R2-seed', 'R2', 'MAX'): 'ACACAMGT'
}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42', SampleFiles(), SampleFiles())
expected_diffs = [
'run1:sample42 consensus: R2-seed R2 MAX', '- ACACACGT',
'? ^', '+ ACACAMGT', '? ^'
]
expected_consensus_distances = [
ConsensusDistance(region='R1',
cutoff='MAX',
distance=0,
pct_diff=0),
ConsensusDistance(region='R2',
cutoff='MAX',
distance=1,
pct_diff=12.5)
]
diffs = []
scenarios = defaultdict(list)
consensus_distances = compare_consensus(sample, source_seqs,
target_seqs, diffs,
Scenarios.NONE, scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_consensus_distances, consensus_distances)
def test_consensus_trailing_change(self):
source_seqs = {('R1-seed', 'R1', 'MAX'): 'ACTTAC------GTAC'}
target_seqs = {('R1-seed', 'R1', 'MAX'): 'ACTTAC'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42',
SampleFiles(),
SampleFiles())
expected_diffs = ['run1:sample42 consensus: R1-seed R1 MAX',
'- ACTTAC------GTAC',
'+ ACTTAC']
expected_consensus_distances = [ConsensusDistance(region='R1',
cutoff='MAX',
distance=4,
pct_diff=25)]
diffs = []
scenarios = defaultdict(list)
consensus_distances = compare_consensus(
sample,
source_seqs,
target_seqs,
diffs,
Scenarios.NONE,
scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_consensus_distances, consensus_distances)
def test_one_consensus_changes(self):
source_seqs = {('R1-seed', 'R1', 'MAX'): 'ACACACGT',
('R2-seed', 'R2', 'MAX'): 'ACACACGT'}
target_seqs = {('R1-seed', 'R1', 'MAX'): 'ACACACGT',
('R2-seed', 'R2', 'MAX'): 'ACACAMGT'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42',
SampleFiles(),
SampleFiles())
expected_diffs = ['run1:sample42 consensus: R2-seed R2 MAX',
'- ACACACGT',
'? ^',
'+ ACACAMGT',
'? ^']
expected_consensus_distances = [ConsensusDistance(region='R1',
cutoff='MAX',
distance=0,
pct_diff=0),
ConsensusDistance(region='R2',
cutoff='MAX',
distance=1,
pct_diff=12.5)]
diffs = []
scenarios = defaultdict(list)
consensus_distances = compare_consensus(
sample,
source_seqs,
target_seqs,
diffs,
Scenarios.NONE,
scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_consensus_distances, consensus_distances)
def test_same_consensus(self):
source_seqs = {('R1-seed', 'R1', 'MAX'): 'ACACAC'}
target_seqs = {('R1-seed', 'R1', 'MAX'): 'ACACAC'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42', SampleFiles(), SampleFiles())
expected_diffs = []
expected_scenarios = {}
diffs = []
scenarios = defaultdict(list)
compare_consensus(
sample, source_seqs, target_seqs, diffs,
Scenarios.MAIN_CONSENSUS_CHANGED
| Scenarios.OTHER_CONSENSUS_CHANGED, scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_scenarios, scenarios)
def test_other_consensus_change(self):
source_seqs = {('R1-seed', 'R1', '0.250'): 'ACACAC'}
target_seqs = {('R1-seed', 'R1', '0.250'): 'ACACAT'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42', SampleFiles(), SampleFiles())
expected_diffs = [
'run1:sample42 consensus: R1-seed R1 0.250', '- ACACAC',
'? ^', '+ ACACAT', '? ^'
]
expected_scenarios = {}
diffs = []
scenarios = defaultdict(list)
compare_consensus(sample, source_seqs, target_seqs, diffs,
Scenarios.NONE, scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_scenarios, scenarios)
def test_same_consensus(self):
source_seqs = {('R1-seed', 'R1', 'MAX'): 'ACACAC'}
target_seqs = {('R1-seed', 'R1', 'MAX'): 'ACACAC'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42',
SampleFiles(),
SampleFiles())
expected_diffs = []
expected_scenarios = {}
diffs = []
scenarios = defaultdict(list)
compare_consensus(
sample,
source_seqs,
target_seqs,
diffs,
Scenarios.MAIN_CONSENSUS_CHANGED | Scenarios.OTHER_CONSENSUS_CHANGED,
scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_scenarios, scenarios)
def test_consensus_added(self):
source_seqs = {}
target_seqs = {('R1-seed', 'R1', 'MAX'): 'ACTTAC'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42', SampleFiles(), SampleFiles())
expected_diffs = [
'run1:sample42 consensus: R1-seed R1 MAX', '+ ACTTAC'
]
expected_consensus_distances = []
diffs = []
scenarios = defaultdict(list)
consensus_distances = compare_consensus(sample, source_seqs,
target_seqs, diffs,
Scenarios.NONE, scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_consensus_distances, consensus_distances)
def test_consensus_added(self):
source_seqs = {}
target_seqs = {('R1-seed', 'R1', 'MAX'): 'ACTTAC'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42',
SampleFiles(),
SampleFiles())
expected_diffs = ['run1:sample42 consensus: R1-seed R1 MAX',
'+ ACTTAC']
expected_consensus_distances = []
diffs = []
scenarios = defaultdict(list)
consensus_distances = compare_consensus(
sample,
source_seqs,
target_seqs,
diffs,
Scenarios.NONE,
scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_consensus_distances, consensus_distances)
def test_consensus_trailing_change(self):
source_seqs = {('R1-seed', 'R1', 'MAX'): 'ACTTAC------GTAC'}
target_seqs = {('R1-seed', 'R1', 'MAX'): 'ACTTAC'}
sample = Sample(MiseqRun(target_path='run1/Results/versionX'),
'sample42', SampleFiles(), SampleFiles())
expected_diffs = [
'run1:sample42 consensus: R1-seed R1 MAX', '- ACTTAC------GTAC',
'+ ACTTAC'
]
expected_consensus_distances = [
ConsensusDistance(region='R1',
cutoff='MAX',
distance=4,
pct_diff=25)
]
diffs = []
scenarios = defaultdict(list)
consensus_distances = compare_consensus(sample, source_seqs,
target_seqs, diffs,
Scenarios.NONE, scenarios)
self.assertEqual(expected_diffs, diffs)
self.assertEqual(expected_consensus_distances, consensus_distances)
