Update kraken summary with etetoolkit #24
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Pull Request Overview
This PR refactors the Kraken2 report summarization script to use NCBI taxonomy lineage instead of parsing Kraken2 report format directly. The key changes include:
- Replacing custom lineage construction with ete3's NCBITaxa for taxonomy lookups
- Simplifying the parsing logic to extract only taxon IDs and fragment counts
- Removing old test functions that tested the deprecated implementation
- Adding the ete3 dependency to the conda environment
Reviewed Changes
Copilot reviewed 4 out of 5 changed files in this pull request and generated 6 comments.
Show a summary per file
| File | Description |
|---|---|
| scripts/summarize_kraken2_reports.py | Complete refactor to use NCBITaxa for lineage resolution; simplified parsing and output logic |
| scripts/test_summarize_kraken2_reports.py | Updated imports and removed deprecated test functions |
| envs/sbx_kraken_env.yml | Added ete3 dependency |
| envs/sbx_kraken_env.linux-64.pin.txt | Removed pinned dependencies (appears to be regenerated) |
| config.yml | Whitespace-only change |
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…ge-to-include-blank-family Handle missing taxonomy ranks when building consensus lineage
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