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[MRG] adjust output of gather to indicate weighted/unweighted results #1819

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merged 2 commits into from
Feb 2, 2022
Merged

[MRG] adjust output of gather to indicate weighted/unweighted results #1819

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0bf6584
add checks in tests
ctb Feb 2, 2022
ec7e297
Merge branch 'latest' into add/abund_print
ctb Feb 2, 2022
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5 changes: 4 additions & 1 deletion src/sourmash/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -791,7 +791,10 @@ def gather(args):
print_results(f'(truncated gather because --num-results={args.num_results})')

p_covered = (1 - weighted_missed) * 100
print_results(f'the recovered matches hit {p_covered:.1f}% of the query')
if is_abundance:
print_results(f'the recovered matches hit {p_covered:.1f}% of the abundance-weighted query')
else:
print_results(f'the recovered matches hit {p_covered:.1f}% of the query (unweighted)')
print_results('')
if gather_iter.scaled != query.minhash.scaled:
print_results(f'WARNING: final scaled was {gather_iter.scaled}, vs query scaled of {query.minhash.scaled}')
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4 changes: 4 additions & 0 deletions tests/test_sourmash.py
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Expand Up @@ -4034,6 +4034,8 @@ def test_gather_abund_1_1(runtmp, linear_gather, prefetch_gather):
assert '50.4% 80.0% 1.9 tests/test-data/genome-s11.fa.gz' in out
assert 'genome-s12.fa.gz' not in out

assert "the recovered matches hit 100.0% of the abundance-weighted query" in out


def test_gather_abund_10_1(runtmp, prefetch_gather, linear_gather):
c = runtmp
Expand Down Expand Up @@ -4069,6 +4071,7 @@ def test_gather_abund_10_1(runtmp, prefetch_gather, linear_gather):
assert '91.0% 100.0% 14.5 tests/test-data/genome-s10.fa.gz' in out
assert '9.0% 80.0% 1.9 tests/test-data/genome-s11.fa.gz' in out
assert 'genome-s12.fa.gz' not in out
assert "the recovered matches hit 100.0% of the abundance-weighted query" in out

# check the calculations behind the above output by looking into
# the CSV.
Expand Down Expand Up @@ -4136,6 +4139,7 @@ def test_gather_abund_10_1_ignore_abundance(runtmp, linear_gather, prefetch_gath

print(out)
print(err)
assert "the recovered matches hit 100.0% of the query (unweighted)" in out

# when we project s10x10-s11 (r2+r3), 10:1 abundance,
# onto s10 and s11 genomes with gather --ignore-abundance, we get:
Expand Down