John Huddleston
John Huddleston
Document case studies to guide interpretation of SARS-CoV-2 evolution based on Nextstrain analyses
**Context** [Our current ncov tutorial lists an unlinked item for "case studies"](https://github.com/nextstrain/ncov/blob/40ae575/docs/index.md#getting-started-with-visualization--interpretation) and states that these are "coming soon!". These docs were written nearly a year ago and the case...
## Description of proposed changes If the workflow errors out and the user isn't using the `--use-conda` Snakemake flag, let the user know what Augur version they have installed and...
### Description of proposed changes Adds a Snakemake profile with a single build that subsamples an existing filtered alignment of GISAID data to one sample per Pangolin lineage. The resulting...
**Context** In the refine step of the ncov workflow, the `--clock-filter-iqd` argument is hardcoded such that TreeTime will always apply its clock filter to strains that fall beyond the given...
## Current Behavior The `get_numerical_dates` function in `augur.dates` expects the metadata argument to be a pandas DataFrame. [When the metadata is not a DataFrame, the function returns an empty dictionary](https://github.com/nextstrain/augur/blob/e8392b320123b1422f86a8d61db1711681d9862f/augur/dates.py#L124-L125)....
## Context Augur supports [a "full" installation](https://github.com/nextstrain/augur/blob/8d69df645b2bfce8778861402ad5cf3a104d8fb3/setup.py#L59-L63) that installs optional dependencies including cvxopt, matplotlib, and seaborn. Although cvxopt is required for titer models to work (arguably a dependency that should...
## Description of proposed changes Fixes a confusing error message produced by augur index when the output directory for the sequence index does not exist but the error message says...
## Description of proposed changes Adds functional tests for the expected behavior of the `augur translate` command and then updates related translate logic to make tests pass. The main changes...
## Context Augur's functional tests rely on a lightweight wrapper script around DeepDiff, `scripts/diff_jsons.py`, to support comparisons between JSONs. [Augur's dev requirements specify DeepDiff >=4.3.2](https://github.com/nextstrain/augur/blob/67027a6ae6a7a324c8eb646593cc5c0a89650ccf/setup.py#L72). However, [version 5.2.0 of DeepDiff...
## Current Behavior Nextclade provides gene map GFFs for [its many datasets](https://github.com/nextstrain/nextclade_data/). These gene maps use the `gene_name` qualifier key to define the name of each gene (e.g., [the SARS-CoV-2...