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Filter priority hotfix #530

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merged 2 commits into from
Apr 7, 2020
Merged

Filter priority hotfix #530

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ebc1764
Tests: Failing test for filter priorities regression
tsibley Apr 7, 2020
8139f32
filter: Restore default priority of 0 for missing sequences
tsibley Apr 7, 2020
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4 changes: 2 additions & 2 deletions augur/filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,10 +56,10 @@ def write_vcf(input_filename, output_filename, dropped_samps):
def read_priority_scores(fname):
try:
with open(fname) as pfile:
return {
return defaultdict(float, {
elems[0]: float(elems[1])
for elems in (line.strip().split() for line in pfile.readlines())
}
})
except Exception as e:
print(f"ERROR: missing or malformed priority scores file {fname}", file=sys.stderr)
raise e
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2 changes: 2 additions & 0 deletions tests/test_filter.py
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Expand Up @@ -44,6 +44,8 @@ def test_read_priority_scores_valid(self, mock_priorities_file_valid):
)

assert priorities == {"strain1": 5, "strain2": 6, "strain3": 8}
assert priorities["strain1"] == 5
assert priorities["strain42"] == 0, "Default priority is 0 for unlisted sequences"

def test_read_priority_scores_malformed(self, mock_priorities_file_malformed):
with pytest.raises(ValueError):
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