Nextstrain-augur

Latest version: v24.4.0

Safety actively analyzes 629855 Python packages for vulnerabilities to keep your Python projects secure.

Scan your dependencies

Page 3 of 19

22.3.0

Features

* ancestral: add functionality to reconstruct ancestral amino acid sequences and add inferred mutations to the `node_data_json` with output equivalent to `augur translate`. `ancestral` now takes an annotation (`--annotation`), a list of genes (`--genes`), and a file name pattern for amino acid alignments (`--translations`). Mutations for each of these genes will be inferred and added to the output JSON to each node as a list at `['aa_muts'][gene]`. The annotations will be added to the `annotation` field in the output JSON. Inferred amino acids sequences can be saved with the new `--output-translations` argument. [1258][] (rneher, huddlej)
* ancestral: add the ability to report mutations relative to a sequence other than the inferred root of the tree. This sequence can be specified via `--root-sequence` and difference between this sequence and the inferred root of the tree will be added as mutations to the root node for nucleotides and amino acids. All differences between the specified `root-sequence` and the inferred sequence of the root node of the tree will be added as mutations to the root node. This was previously already possible for `vcf` input via `--vcf-reference`. [1258][] (rneher)
* refine: add `mid_point` as rooting option to `refine`. [1257][] (rneher)

Bug fixes

* filter: In version 22.2.0, `--query` would fail when the `.str` accessor was used on a column. This has been fixed. [1277][] (victorlin)

[1257]: https://github.com/nextstrain/augur/pull/1257
[1258]: https://github.com/nextstrain/augur/pull/1258
[1277]: https://github.com/nextstrain/augur/issues/1277

22.2.0

Features

* Adds a new sub-command augur curate titlecase. The titlecase command is intended to apply titlecase to string fields in a metadata record (e.g. BRAINE-LE-COMTE, FRANCE -> Braine-le-Comte, France). Previously, this was available in the transform-string-fields script within the monkeypox repo.
[1197][] (j23414 and joverlee521)

[1197]: https://github.com/nextstrain/augur/pull/1197

Bug fixes

* export v2: Previously, when `strain` was not used as the metadata ID column, node attributes might have gone missing from the final Auspice JSON. This has been fixed. [1260][], [1262][] (victorlin, joverlee521)
* export v1: Added a deprecation warning for this command. [1265][] (victorlin)
* export v1: The recently introduced flag `--metadata-id-columns` did not work properly due to the same `export v2` bug that was fixed in this release. Instead of fixing it in `export v1`, drop the broken feature since this command is no longer being maintained. [1265][] (victorlin)
* filter: Expose internal Pandas errors from `--query` which may be useful to users. [1267][] (victorlin)
* filter: Previously, `--query` would fail when numerical comparisons were used on columns with missing values. This has been fixed. [1269][] (victorlin)

[1260]: https://github.com/nextstrain/augur/issues/1260
[1262]: https://github.com/nextstrain/augur/issues/1262
[1265]: https://github.com/nextstrain/augur/pull/1265
[1267]: https://github.com/nextstrain/augur/pull/1267
[1269]: https://github.com/nextstrain/augur/issues/1269

22.1.0

Features

* export, frequencies, refine, traits: Add a new flag `--metadata-id-columns` to customize the possible metadata ID columns. Previously, this was only available in `augur filter`. [1240][] (victorlin)
* Add new sub-subcommand augur curate format-dates. The format-dates command is intended to be used to format date fields to ISO 8601 date format (YYYY-MM-DD), where incomplete dates are masked with `XX` (e.g. 2023 -> 2023-XX-XX). [1146][] (joverlee521)

Bug fixes

* 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

Bug fixes

* utils: Serialize pandas Series in `write_json`. [1213][] (victorlin)

[1213]: https://github.com/nextstrain/augur/pull/1213

22.0.2

Bug fixes

* CI: Add a Github action to test augur on 8 Nextstrain pathogen workflows using example data. [1217][] (corneliusroemer)
* parse: Denote required arguments including `--fields`, `--output-sequences`, and `--output-metadata`. [1228][] (huddlej)
* Fix export of the `strand` attribute of gene annotations. Previously, features on the negative strand were not annotated as such since the code assumed that the `strand` attribute was boolean instead of `[-1, +1]`. [1211] rneher and j23414.
* augur.io.read_metadata: explicitly set `date` column as `string` type to prevent year only dates from being inferred as integers. [1235][] (joverlee521)

[1211]: https://github.com/nextstrain/augur/pull/1211
[1217]: https://github.com/nextstrain/augur/pull/1217
[1228]: https://github.com/nextstrain/augur/pull/1228
[1235]: https://github.com/nextstrain/augur/pull/1235

22.0.1

Bug fixes

* export: No longer export duplicate entries in the colorings array, a bug which has been present in Augur since at least v12 [719][]. [1218][] (jameshadfield)
* export: In version 22.0.0, some configurations of export may have resulted in the clade coloring appearing last in the Auspice dropdown rather than first. This is now fixed. [1218] (jameshadfield)
* export: In version 22.0.0, validation of `augur.utils.read_node_data` was changed to error when a node data JSON did not contain any actual data. This causes export to error when an empty node data JSON is passed, as for example in ncov's pathogen-ci. This is now fixed by warning instead. The bug was originally introduced in PR [728][]. [1214][] (corneliusroemer)

[719]: https://github.com/nextstrain/augur/issues/719
[1214]: https://github.com/nextstrain/augur/pull/1214
[1218]: https://github.com/nextstrain/augur/pull/1218

Page 3 of 19

© 2024 Safety CLI Cybersecurity Inc. All Rights Reserved.