# Get Species Taxids Sh

> Use when resolving taxonomy names or taxids into BLAST-filterable NCBI taxonomy IDs with the NCBI helper script.

- Skill: `vimalinx/get-species-taxids-sh` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds add vimalinx/get-species-taxids-sh`
- Raw SKILL.md: https://api.skillmd.com/api/skills/vimalinx/get-species-taxids-sh/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: vimalinx (https://skillmd.com/u/vimalinx)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/vimalinx/get-species-taxids-sh

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# get-species-taxids-sh

## Quick Start

- **Command:** `get_species_taxids.sh`
- **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/get_species_taxids.sh`
- **Full reference:** [references/help.md](references/help.md)

## When To Use This Tool

- Retrieving taxonomy IDs at or below a specified taxonomy rank using `-t <taxonomy ID>`
- Looking up taxonomy information for an organism using `-n <Scientific Name, Common Name or Keyword>`

## Common Patterns

```bash
# 1) Expand a taxid to all taxids at or below that taxonomy level
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/get_species_taxids.sh -t 9606
```

```bash
# 2) Search taxonomy by scientific or common name
PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH \
  /home/vimalinx/miniforge3/envs/bio/bin/get_species_taxids.sh -n "human"
```

## Recommended Workflow

1. Identify the target organism or taxonomic group by scientific name, common name, or keyword.
2. Use `-n` to search and confirm the correct taxonomy entry.
3. Use `-t` with the confirmed taxonomy ID to retrieve all taxids at or below that level.
4. Use the resulting taxid list to filter downstream BLAST database queries.

## Guardrails

- The real executable uses underscores: `get_species_taxids.sh`.
- Dependency checks run before normal usage output. In a shell where `esearch`, `efetch`, and `esummary` are not on `PATH`, even a no-argument run fails before showing help.
- `-t` and `-n` are mutually exclusive.
- `-t` returns sorted taxids, while `-n` emits a formatted taxonomy summary rather than a bare taxid list.