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Add multi-tax-id support and --output-table flag#3

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feat/multi-tax-id-output-table
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Add multi-tax-id support and --output-table flag#3
audy wants to merge 1 commit into
masterfrom
feat/multi-tax-id-output-table

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@audy

@audy audy commented May 11, 2026

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Summary

  • --tax-id can now be specified multiple times to download assemblies from multiple taxa (OR logic)
  • New --output-table flag writes a TSV with tax_id, lineage, accession, asm_name, organism, assembly_level, refseq_category, and path (use - for stdout)
  • NCBIAssembly struct now includes assembly_accession, organism_name, and asm_name fields

Test plan

  • cargo test passes
  • gdl --tax-id 821 --tax-id 1350 --format fna --source refseq --dry-run returns assemblies from both taxa
  • gdl --tax-id 821 --output-table out.tsv writes expected TSV columns
  • gdl --tax-id 821 --output-table - streams TSV to stdout

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