MRG: handle (ignore) empty taxids for bioboxes format#3748
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## latest #3748 +/- ##
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- Coverage 88.19% 88.18% -0.01%
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Files 137 137
Lines 22553 22555 +2
Branches 2298 2299 +1
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- Misses 2348 2349 +1
- Partials 315 316 +1
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bluegenes
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bluegenes
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bioboxes format
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@ctb ready for review |
ctb
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Major new features: * start writing v4->v5 migration docs (#3721) * adjust warnings around tax abund and provide v5 upgrades to `tax metagenome` (#3711) Minor new features: * try setting up --v4 and --v5 behavior differences for `sig check` (#3072) * update `sig manifest` default rebuilding behavior for v5. (#3074) * handle (ignore) empty taxids for `bioboxes` format (#3748) * improve summary_csv for lingroups (#3758) Cleanup and documentation updates: * use auto-generated database list (#3754) Developer updates: * CI: fix dependabot config syntax, and clippy beta lints (#3762) * CI: update to cibuildwheel 3.1.1 (#3738) * ci: group dependabot updates by language (#3749) * Remove docutils dep (#3769) * bump version to 4.9.4-dev (#3715) * disable WebAssembly builds, for now (#3724) Dependabot updates: * Build(ci): Bump actions/download-artifact from 4 to 5 (#3766) * Build(deps): Bump DeterminateSystems/nix-installer-action from 17 to 18 (#3727) * Build(deps): Bump DeterminateSystems/nix-installer-action from 18 to 19 (#3746) * Build(deps): Bump criterion from 0.6.0 to 0.7.0 (#3741) * Build(deps): Bump md5 from 0.7.0 to 0.8.0 (#3719) * Build(deps): Bump memmap2 from 0.9.5 to 0.9.7 (#3732) * Build(deps): Bump prefix-dev/setup-pixi from 0.8.10 to 0.8.11 (#3733) * Build(deps): Bump prefix-dev/setup-pixi from 0.8.11 to 0.8.14 (#3747) * Build(deps): Bump rand from 0.9.1 to 0.9.2 (#3743) * Build(deps): Bump serde_json from 1.0.140 to 1.0.141 (#3742) * [pre-commit.ci] pre-commit autoupdate (#3718) * [pre-commit.ci] pre-commit autoupdate (#3725) * [pre-commit.ci] pre-commit autoupdate (#3731) * [pre-commit.ci] pre-commit autoupdate (#3737) * [pre-commit.ci] pre-commit autoupdate (#3740) * [pre-commit.ci] pre-commit autoupdate (#3756)
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taxid, so it fails with empty/missingtaxids. Some NCBI lineages have missing/empty internal tax ranks, e.g. order, genus, etc. Here we ignore (do not print) results from empty taxids, which allows us to bypass these problematic ranks and still get output from the classifiable ranks.example taxonomy with missing ranks (lineage from an older CAMI db):