get-species-taxids-sh

name	get-species-taxids-sh
description	Use when resolving taxonomy names or taxids into BLAST-filterable NCBI taxonomy IDs with the NCBI helper script.
disable-model-invocation	true
user-invocable	true

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

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

# 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

# 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.