Pipeline components for real-time phylodynamic analysis

NEXT

5.4.1 (12 November 2019)

Bug fixes

  • export v1: Include --minify-json option that was mistakenly not included in PR 398. See PR 409

5.4.0 (7 November 2019)

Features

  • frequencies: Include --minimal-clade-size-to-estimate command line option. See PR 383
  • lbi: Include --no-normalization command line option. See PR 380

Compatibility fixes

  • export: Include v1 subcommand to allow forwards compatibiliy with Augur v6 builds. See PR 398

Bug fixes

  • export: Include warning if using a mismatched v6 translate file. See PR 392
  • frequencies: Fix determination of interval for clipping of non-informative pivots

5.3.0 (9 September 2019)

Features

  • export: Improve printing of error messages with missing or conflicting author data. See issue 274
  • filter: Improve printing of dropped strains to include reasons why strains were dropped. See PR 367
  • refine: Add support for command line flag --keep-polytomies to not resolve polytomies when producing a time tree. See PR 345

Bug fixes

  • Catch and throw error when there are duplicate strain names. See PR 356
  • Fix missing annotation of "parent" attribute for the root node
  • Run shell commands with more robust error checking. See PR 350
  • Better handling of rerooting options for trees without temporal information. See issue 348

Data

  • Small fixes in geographic coordinate file

5.2.1 (4 August 2019)

Bug fixes

  • Print more useful error message if Python recursion limit is reached. See issue 328
  • Print more useful error message if vcftools if missing. See PR 312

Development

  • Significantly relax version requirements specified in setup.py for biopython, pandas, etc... Additionally, move lesser used packages (cvxopt, matplotlib, seaborn) into an "extras_require" field. This should reduce conflicts with other pip installed packages. See PR 323

Data

  • Include additional country lat/longs in base data

5.2.0 (23 July 2019)

Features

  • ancestral: Adds a new flag --output-sequences and logic to support saving ancestral sequences and leaves from the given tree to a FASTA file. Also adds a redundant, more specific flag --output-node-data that will replace the current --output flag in the next major version release of augur. For now, we issue a deprecation warning when the --output flag is used. Note that FASTA output is only allowed for FASTA inputs and not for VCFs. We don't allow FASTA output for VCFs anywhere else and, if we did here, the output files would be very large. See PR 293

  • frequencies: Allow --method kde flag to compute frequencies via KDE kernels. This complements existing method of --method diffusion. Generally, KDE frequencies should be more robust and faster to run, but will not project as well when forecasting frequencies into the future. See PR 271

Bug fixes

  • ancestral, traits, translate: Print warning if supplied tree is missing internal node names (normally provided by running augur refine). See PR 283

  • Include pip in Conda enviroment file. See PR 309

Documentation

  • Document environment variables respected by Augur

Development

  • Remove matplotlib and seaborn from setup.py install. These are still called a few places in augur (like titers.validate()), but it was deemed rare enough that remove this from setup.py would ease general install for most users. Additionally, the ipdb debugger has been moved to dev dependencies. See PR 291

  • Refactor logic to read trees from multiple formats into a function. Adds a new function read_tree to the utils module that tries to safely handle reading trees in multiple input formats. See PR 310

5.1.1 (1 July 2019)

Features

  • tree: Add support for the GTR+R10 substitution model.
  • tree: Support parentheses in node names when using IQ-TREE.

Bug fixes

  • Use the center of the UK for its coordinates instead of London.
  • filter: Mark --output required, which it always was but wasn't marked.
  • filter: Avoid error when no excluded strains file is provided.
  • export: Fix for preliminary version 2 schema support.
  • refine: Correct error handling when the tree file is missing or empty.

Documentation

  • Add examples of Augur usage in the wild.
  • Rename and reorganize CLI and Python API pages a little bit to make "where do I start learning to use Augur?" clearer to non-devs.

Development

  • Relax version requirements of pandas and seaborn. The hope is this will make installation smoother (particularly alongside other packages which require newer pandas versions) while not encountering breaking changes in newer versions ourselves.

5.1.0 (29 May 2019)

Documentation

  • Documentation is now available online for the augur CLI and Python API via Read The Docs: https://nextstrain-augur.readthedocs.io. The latest version on RTD points to the git master branch, and the stable version to the most recent tagged release. Instructions for building the docs locally are in the README.

5.0.0 (26 May 2019)

Features

  • ancestral: New option to --keep-ambiguous, which will not infer nucleotides at ambiguous (N) sites on tip sequences and instead leave as 'N' See PR 280.
  • ancestral: New option to --keep-overhangs, which will not infer nucleotides for gaps on either side of the alignment and instead leave as '-'. See PR 286.
  • clades: This module has been reconfigured to identify clade defining mutations on top of a reference rather than identifying mutations along the tree. The command line arguments are the same except for the addition of --reference, which explicitly passes in a reference sequence. If --reference is not defined, then reference will be drawn from the root node of the phylogeny by looking for sequence attribute attached to root node of --tree. See PR 288.
  • refine: Revise rooting behavior. Previously --root took 'best', 'residual', 'rsq' and 'min_dev' as options. In this update --root takes 'best', least-squares', 'min_dev' and 'oldest' as rooting options. This eliminates 'residual' and 'rsq' as options. This is a backwards-incompatible change. This requires updating TreeTime to version 0.5.4 or above. See PR 263.
  • refine: Add --keep-root option that overrides --root specification to preserve tree rooting. See PR 263.
  • refine: Add --covariance and --no-covariance options that specify TreeTime behavior. See PR 263.
  • titers: This command now throws an InsufficientDataException if there are not sufficient titers to infer a model. This is paired with a new --allow-empty-model flag that proceeds past the InsufficientDataException and writes out a model JSON corresponding to an 'empty' model. See PR 281.
  • By default JSONs are written with index=1 to give a pretty-printed JSON. However, this adds significant file size to large tree JSONs. If the environment variable AUGUR_MINIFY_JSON is set then minified JSONs are printed instead. This mirror the explicit --minify-json argument available to augur export. See PR 278.

Bug fixes

  • export: Cast numeric values to strings for export. See issue 287.
  • export: Legend order preserves ordering passed in by user for traits that have default colorings ('country' and 'region'). See PR 284.
  • refine: Previously, the --root argument was silently ignored when no timetree was inferred. Re-rooting with an outgroup is sensible even without a timetree. See PR 282.

4.0.0 (24 April 2019)

Features

  • distance: New interface for specifying distances between sequences. This is a backwards-incompatible change. Refer to augur distance --help for all the details.

  • export: Add a --minify-json flag to omit indentation in Auspice JSONs.

Bug fixes

  • frequencies: Emit one-based coordinates (instead of zero-based) for KDE-based mutation frequencies

Data

  • Include additional country lat/longs in base data

3.1.8 (13 February 2019)

Bug fixes

  • titers: fix calculation of mean_potentency for model export

3.1.7 (5 February 2019)

Bug fixes

  • Update to TreeTime 0.5.3
  • tree: Fix bug in printing causing errors in Python versions <3.6
  • tree: Alter site masking to not be so memory intensive

3.1.6 (29 January 2019)

Features

  • filter: Allow negative matches to --exclude-where. For example, --exclude-where country!=usa would exclude all samples where metadata country does not equal usa.
  • tree: Allow --exclude-sites to work with FASTA input. Ensure that indexing of input sites is one-based.

Bug fixes

  • fix loading of strains when loading titers from file, previously strains had not been filtered to match the tree appropriately

3.1.5 (13 January 2019)

Features

  • frequencies: Add --ignore-char and --minimal-clade-size as options.
  • frequencies: Include --stiffness and --inertia as options.
  • titers: Allow multiple titer date files in --titers import.

Bug fixes

  • filter: Fix --non-nucleotide call to include ? as allowed character.
  • tree: Fix --method raxml to properly delimit interim RAxML output so that simultaneous builds don't conflict.

Data

  • Include additional country lat/longs in base data

3.1.4 (1 January 2019)

Bug fixes

  • frequencies: Include counts in augur frequencies output JSON to support downstream plotting.

Data

  • Include additional country lat/longs in base data

3.1.3 (29 December 2018)

Features

  • filter: Add --non-nucleotide option to remove sequences with non-conforming nucleotide characters.

Bug fixes

  • Revise treatment of -, in augur parse to leave - as is and remove white space. Also delimit [ and ] to _.
  • Fix bug in naming of temp IQTREE fixes to prevent conflicts from simultaneous builds.

Data

  • Include additional country lat/longs in base data

Development

3.1.2 (21 December 2018)

Bug fixes

  • Update dependencies

3.1.1 (21 December 2018)

Bug fixes

  • filter: Fix --include-where. Adds an all_seq variable needed by the logic to include records by value. This was previously working for VCF but threw an exception for sequences in FASTA format.
  • Update flu reference viruses and lat longs.
  • Update dependencies

3.1.0 (18 December 2018)

Features

  • reconstruct-sequences: Include augur reconstruct-sequences module that reconstructs alignments from mutations inferred on the tree
  • distance: Include augur distance module that calculates the distance between amino acid sequences across entire genes or at a predefined subset of sites
  • lbi: Include augur lbi module that calculates local branching index (LBI) for a given tree and one or more sets of parameters.
  • frequencies: Include --method kde as option to augur frequencies, separate from the existing --method diffusion logic. KDE frequencies are faster and better for smaller clades but don't extrapolate as well as diffusion frequencies.
  • titers: Enable annotation of nodes in a tree from the substitution model

3.0.5.dev1 (26 November 2018)

Bug fixes

  • translate: Nucleotide ("nuc") annotation for non-bacterial builds starts at 0 again, not 1, fixing a regression.

Documentation

  • Schemas: Correct coordinate system description for genome start/end annotations.

3.0.4.dev1 (26 November 2018)

Bug fixes

  • validate: Fix regression for gene names containing an asterisk.

Development

  • Fix Travis CI tests which were silently not running.

3.0.3.dev1 (26 November 2018)

Features

  • refine: Add a --clock-std-dev option

  • traits: Add a --sampling-bias-correction option for mugration model

  • validate: Gene names in tree annotations may now contain hyphens. Compatible with Auspice version 1.33.0 and later.

  • All JSON is now emitted with sorted keys, making it easier to diff and run other textual comparisons against output.

Bug fixes

  • filter: Only consider A, T, C, and G when calculating sequence length for the --min-length option.

  • filter: Allow comments in files passed to --exclude.

  • filter: Ignore case when matching trait values against excluded values.

  • Normalize custom geographic names to lower case for consistent matching.

Data

  • Fix typo in geographic entry for netherlands.

  • Schemas: Reconcile naming patterns used in gene definitions and tree annotations.

Development

  • Upgrade TreeTime dependency to 0.5.x and at least 0.5.1.

  • Add an environment.yml file for use with conda env create.

  • Stop testing under Python 2.7 on Travis CI.

3.0.2.dev1 (27 September 2018)

Bug fixes

  • translate: Fix broken --help message

3.0.1.dev1 (27 September 2018)

Features

  • align and tree: The --nthreads option now accepts the special value "auto" to automatically set the number of threads to the number of CPU cores available.

  • Alias augur --version to augur version

Bug fixes

  • tree: The --nthreads option is now respected. Previously all tree builders were ignoring the value and using either 2 threads (RAxML, IQ-TREE) or as many threads as cores (FastTree, if the OpenMP version).

  • translate: Check for and, if necessary pad, nucleotide sequences which aren't a multiple of 3 earlier to avoid errors later.

  • export: Optionally write inferred nucleotide and amino acid sequences (or mutations) to a separate file.

  • export: Omit genes with no amino acid mutations.

  • validate: Allow underscores in gene names.

  • refine: Remove unused --nthreads argument.

  • ancestral, filter, tree, refine: Exit 1 instead of -1 on error.

  • Print the help message, instead of throwing an exception, when augur is run without arguments.

Documentation

  • Briefly describe each command in its --help output and in the global augur --help output.

  • Revamp README to emphasize new, modular augur and make it suitable for inclusion on PyPi.

  • Reconciled conflicting license declarations; augur is AGPLv3 (not MIT) licensed like the rest of Nextstrain.

  • Include URLs for bug reports, the change log, and the source on PyPi.

Data

  • Geographic coordinates added for the Netherlands and the Philippines.

Development

  • Reset the release branch when rewinding a failed local release process.

  • Refactor the augur program and command architecture for improved maintainability.

3.0.0.dev3 (4 September 2018)

Development

  • Use an allowed Topic classifier so we can upload to PyPi

  • Ignore distribution egg-info build files

3.0.0.dev2 (4 September 2018)

Features

  • Export: Add safety checks for optional annotations and geo data

  • Include more lat/longs in the default geo data

Development

  • Add release tooling

  • Document the release process and a few development practices

  • Travis CI: Switch to rebuilding the Docker image only for new releases

  • Remove ebola, lassa, tb, WNV, and zika builds now in their own repos. These builds are now available at URLs like https://github.com/nextstrain/ebola, for example.

3.0.0.dev1 (unreleased)

Development

  • Start versioning augur beginning with 3.0.0. A new augur version command reports the running version.