def test_missing_coverage_different_remap_counts(self):
sample = Sample(
MiseqRun(target_path='run1/Results/versionX'), 'sample42',
SampleFiles(coverage_scores=[{
'project': 'HCV',
'region': 'HCV1-E1',
'seed': 'HCV1-seed',
'on.score': '2'
}, {
'project': 'HCV',
'region': 'HCV2-E1',
'seed': 'HCV2-seed',
'on.score': '3'
}],
remap_counts=[{
'type': 'remap-1 HCV1-seed'
}, {
'type': 'remap-1 HCV2-seed'
}]),
SampleFiles(coverage_scores=[{
'project': 'HCV',
'region': 'HCV1-E1',
'seed': 'HCV1-seed',
'on.score': '2'
}],
remap_counts=[{
'type': 'remap-1 HCV1-seed'
}]))
expected_report = ''
expected_scenario_counts = {
Scenarios.REMAP_COUNTS_CHANGED:
[' run1:sample42 coverage: HCV HCV2-E1 3 => -\n']
}
report, scenario_counts, _ = compare_sample(
sample, Scenarios.REMAP_COUNTS_CHANGED)
self.assertEqual(expected_report, report)
self.assertEqual(expected_scenario_counts, scenario_counts)
def test_remap_counts_ignore_other_seeds(self):
sample = Sample(
MiseqRun(target_path='run1/Results/versionX'), 'sample42',
SampleFiles(coverage_scores=[{
'project': 'HIV',
'region': 'PR',
'seed': 'HIV1-seed',
'on.score': '3'
}],
remap_counts=[{
'type': 'remap-1 HIV1-seed'
}, {
'type': 'remap-1 HIV2-seed'
}, {
'type': 'remap-2 HIV2-seed'
}]),
SampleFiles(coverage_scores=[{
'project': 'HIV',
'region': 'PR',
'seed': 'HIV1-seed',
'on.score': '4'
}],
remap_counts=[{
'type': 'remap-1 HIV1-seed'
}, {
'type': 'remap-2 HIV1-seed'
}]))
expected_report = ''
expected_scenario_counts = {
Scenarios.REMAP_COUNTS_CHANGED:
[' run1:sample42 coverage: HIV PR 3 => 4\n']
}
report, scenario_counts, _ = compare_sample(
sample, Scenarios.REMAP_COUNTS_CHANGED)
self.assertEqual(expected_report, report)
self.assertEqual(expected_scenario_counts, scenario_counts)
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)