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filter: Fix support for numerical IDs with both metadata and sequences #1256

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merged 3 commits into from
Jul 10, 2023
Merged

filter: Fix support for numerical IDs with both metadata and sequences #1256

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253a8f0
Add test for numerical strain IDs
victorlin Jul 10, 2023
7eda4bb
Read sequence index ID column as a string
victorlin Jul 10, 2023
7ff6a84
Update changelog
victorlin Jul 10, 2023
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2 changes: 2 additions & 0 deletions CHANGES.md
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Expand Up @@ -11,11 +11,13 @@

* parse: Fix a bug where `--fix-dates` was always applied, with a default of `--fix-dates=monthfirst`. Now, running without `--fix-dates` will leave dates as-is. [#1247][] (@victorlin)
* `augur.io.open_file`: Previously, the docs described a type restriction on `path_or_buffer` but it was not enforced. It has been updated to allow all I/O classes, and is enforced at run-time. [#1250][] (@victorlin)
* filter: Fix a bug where data files consisting of only numerical strain names would not work when both `--metadata` and `--sequences` are passed. [#1256][] (@victorlin)

[#1146]: https://github.com/nextstrain/augur/pull/1146
[#1240]: https://github.com/nextstrain/augur/pull/1240
[#1247]: https://github.com/nextstrain/augur/issues/1247
[#1250]: https://github.com/nextstrain/augur/pull/1250
[#1256]: https://github.com/nextstrain/augur/pull/1256

## 22.0.3 (14 June 2023)

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1 change: 1 addition & 0 deletions augur/filter/_run.py
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Expand Up @@ -65,6 +65,7 @@ def run(args):
sequence_index_path,
sep=SEQUENCE_INDEX_DELIMITER,
index_col=SEQUENCE_INDEX_ID_COLUMN,
dtype={SEQUENCE_INDEX_ID_COLUMN: "string"},
)

# Remove temporary index file, if it exists.
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32 changes: 32 additions & 0 deletions tests/functional/filter/cram/filter-numerical-ids.t
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@@ -0,0 +1,32 @@
Setup

$ source "$TESTDIR"/_setup.sh

Create a pair of files with numerical strain IDs.

$ cat >metadata.tsv <<~~
> strain col1
> 1 A
> 2 B
> 3 C
> ~~
$ cat >sequences.fasta <<~~
> >1
> AAAA
> >2
> AAAA
> >3
> AAAA
> ~~

Test that nothing is filtered out due to missing sequence data.

$ ${AUGUR} filter \
> --metadata metadata.tsv \
> --sequences sequences.fasta \
> --output-strains filtered_strains.txt \
> > /dev/null 2>&1
$ sort filtered_strains.txt
1
2
3
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