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Send filter warnings to stderr #862

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Mar 11, 2022
Merged

Send filter warnings to stderr #862

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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 @@ -623,7 +623,7 @@ def construct_filters(args, sequence_index):
is_vcf = filename_is_vcf(args.sequences)

if is_vcf: #doesn't make sense for VCF, ignore.
print("WARNING: Cannot use min_length for VCF files. Ignoring...")
print("WARNING: Cannot use min_length for VCF files. Ignoring...", file=sys.stderr)
else:
exclude_by.append((
filter_by_sequence_length,
Expand Down Expand Up @@ -1744,7 +1744,7 @@ def calculate_sequences_per_group(target_max_value, counts_per_group, allow_prob
)
except TooManyGroupsError as error:
if allow_probabilistic:
print(f"WARNING: {error}")
print(f"WARNING: {error}", file=sys.stderr)
sequences_per_group = _calculate_fractional_sequences_per_group(
target_max_value,
counts_per_group,
Expand Down
3 changes: 3 additions & 0 deletions tests/functional/filter.t
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Expand Up @@ -101,6 +101,7 @@ Explicitly use probabilistic subsampling to handle the case when there are more
> --subsample-seed 314159 \
> --probabilistic-sampling \
> --output-strains "$TMP/filtered_strains_probabilistic.txt" > /dev/null
WARNING: Asked to provide at most 5 sequences, but there are 8 groups.

Using the default probabilistic subsampling, should work the same as the previous case.

Expand All @@ -113,6 +114,7 @@ Using the default probabilistic subsampling, should work the same as the previou
> --subsample-max-sequences 5 \
> --subsample-seed 314159 \
> --output-strains "$TMP/filtered_strains_default.txt" > /dev/null
WARNING: Asked to provide at most 5 sequences, but there are 8 groups.

By setting the subsample seed above, we should get the same results for both runs.

Expand Down Expand Up @@ -394,6 +396,7 @@ Strains with ambiguous years or months should be dropped and logged.
> --subsample-max-sequences 5 \
> --output-strains "$TMP/filtered_strains.txt" \
> --output-log "$TMP/filtered_log.tsv" > /dev/null
WARNING: Asked to provide at most 5 sequences, but there are 6 groups.
$ grep "SG_018" "$TMP/filtered_log.tsv" | cut -f 1-2
SG_018\tskip_group_by_with_ambiguous_month (esc)
$ grep "COL/FLR_00024/2015" "$TMP/filtered_log.tsv" | cut -f 1-2
Expand Down