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feat(mask): allow empty mask file, warn not error #1287

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feat(mask): allow empty mask file, warn not error #1287

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2 changes: 2 additions & 0 deletions CHANGES.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,15 @@
### Features

* mask: Add `--mask-gaps` option to `augur mask` to allow masking of gaps at terminals via `--mask-gaps terminals` or all gaps via `--mask-gaps all`. [#1286][] (@corneliusroemer)
* mask: Warn on empty mask file instead of error. Introduced to allow empty stub files when setting up builds and to prevent necessary workflow changes when all mask sites are removed. [#1287][] (@corneliusroemer)

### Bug fixes

* distance: Improve documentation by describing how gaps get treated as indels and how users can ignore specific characters in distance calculations. [#1285][] (@huddlej)

[#1285]: https://github.com/nextstrain/augur/pull/1285
[#1286]: https://github.com/nextstrain/augur/pull/1286
[#1287]: https://github.com/nextstrain/augur/pull/1286

## 22.3.0 (14 August 2023)

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3 changes: 1 addition & 2 deletions augur/mask.py
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Expand Up @@ -231,8 +231,7 @@ def run(args):
print("ERROR: File {} does not exist!".format(args.mask_file))
sys.exit(1)
if os.path.getsize(args.mask_file) == 0:
print("ERROR: {} is an empty file.".format(args.mask_file))
sys.exit(1)
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The pytest failure isn't very clear, but it fails on this test:

augur/tests/test_mask.py

Lines 257 to 261 in 2810abe

def test_run_handle_empty_mask_file(self, vcf_file, bed_file, argparser):
open(bed_file, "w").close()
args = argparser("-s %s --mask %s" % (vcf_file, bed_file))
with pytest.raises(SystemExit):
mask.run(args)

Failing there makes sense because a SystemExit is no longer raised. However, by warning and letting augur mask continue to run with an empty mask file, there is a new error downstream:

augur/mask.py:244: in run
    mask_sites.update(load_mask_sites(args.mask_file))
augur/utils.py:531: in load_mask_sites
    mask_sites = read_bed_file(mask_file)
augur/utils.py:479: in read_bed_file
    bed = pd.read_csv(bed_file, sep='\t', header=None, usecols=[1,2],
…/site-packages/pandas/util/_decorators.py:211: in wrapper
    return func(*args, **kwargs)
…/site-packages/pandas/util/_decorators.py:331: in wrapper
    return func(*args, **kwargs)
…/site-packages/pandas/io/parsers/readers.py:950: in read_csv
    return _read(filepath_or_buffer, kwds)
…/site-packages/pandas/io/parsers/readers.py:605: in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
…/site-packages/pandas/io/parsers/readers.py:1442: in __init__
    self._engine = self._make_engine(f, self.engine)
…/site-packages/pandas/io/parsers/readers.py:1753: in _make_engine
    return mapping[engine](f, **self.options)
…/site-packages/pandas/io/parsers/c_parser_wrapper.py:79: in __init__
    self._reader = parsers.TextReader(src, **kwds)

>   ???
E   pandas.errors.EmptyDataError: No columns to parse from file

pandas/_libs/parsers.pyx:554: EmptyDataError

The downstream code should be updated to support empty mask files.

print(f"WARN: The mask file {args.mask_file} is an empty file.")
if not any((args.mask_file, args.mask_gaps, args.mask_from_beginning, args.mask_from_end, args.mask_sites, args.mask_invalid)):
print("No masking sites provided. Must include one of --mask, --mask-gaps, --mask-from-beginning, --mask-from-end, --mask-invalid, or --mask-sites")
sys.exit(1)
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