Add support for Nextclade GFFs to augur translate #1017
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Adds Cram tests for augur translate with GenBank- and GFF-based gene maps. Much of the data are copied from the Zika and TB builds. These tests capture the current behavior of augur translate in preparation for future improvements to this behavior. This commit adds support to `diff_jsons.py` for excluding paths in JSON files by regular expression, so we can ignore differences in temporary file names. Version DeepDiff 5.2.0 introduced a command line interface [1] that provides this same functionality and more, eliminating the need for custom scripts like `diff_jsons.py`. In the future, we may wish to update Augur's deepdiff dependency [2] and switch to this CLI. [1] https://zepworks.com/deepdiff/current/commandline.html [2] https://github.com/nextstrain/augur/blob/67027a6ae6a7a324c8eb646593cc5c0a89650ccf/setup.py#L72
Adds check for "gene_name" qualifier when loading features from a GFF file. This change allows us to read gene maps from Nextclade datasets. We check for "gene_name" immediately after looking for the "gene" qualifier, since these qualifiers are most commonly used with viral pathogen GFFs files we encounter. Note that there is still an inconsistency in treatment of GFF and GenBank files where we check for "locus_tag" in GenBank files first instead of "gene".
3 tasks
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #1017 +/- ##
==========================================
+ Coverage 59.36% 61.75% +2.38%
==========================================
Files 52 52
Lines 6271 6275 +4
Branches 1579 1581 +2
==========================================
+ Hits 3723 3875 +152
+ Misses 2285 2129 -156
- Partials 263 271 +8 ☔ View full report in Codecov by Sentry. |
victorlin
approved these changes
Aug 8, 2022
Comment on lines
+1
to
+2
| pushd "$TESTDIR/../../" > /dev/null | ||
| export AUGUR="${AUGUR:-../../bin/augur}" |
There was a problem hiding this comment.
(non-blocking)
It would be nice to have just one of these files (the same as tests/functional/filter/cram/_setup.sh), but this is fine for now.
|
Thanks for the quick check, @victorlin! Agreed that the functional tests could use some consolidation. Maybe we could brainstorm at the retreat a bit, if that's a topic you're down to discuss... :D |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
Nextclade's datasets provide gene maps for SARS-CoV-2 and influenza subtypes in GFF format. These files are easy to fetch with
nextclade dataset getmaking them especially useful for bootstrapping training environments and supporting any custom analysis a user might want to perform with these pathogens. Unfortunately, Nextclade's gene maps store gene names in a GFF qualifier namedgene_name, whileaugur translateonly looks for gene names in qualifiers namedgeneandlocus_tag. This PR adds support for Nextclade's GFFs toaugur translatethrough two steps:load_featuresfunction inutils.pythat gets called byaugur translateto support thegene_namequalifier (8cdca95).Related issues
Testing
augur translatebehavioraugur translatebehaviorChecklist