gget

gget is a skill for Claude Code from dralkh/iktinah. It costs 93 tokens per session (8,721 once invoked), scanned A, original, MIT.

A command-line tool and Python package that provides one interface for querying more than 20 bioinformatics databases. These databases contain information about genes, sequences, proteins, diseases, expression, and related biology.

In plain words
What is it for?
It is for looking up gene information, downloading sequences, checking protein structures, running sequence searches, and exploring expression or disease data.
Why use it?
It removes the need to learn separate query methods for many biological data sources during exploratory work.

Skill for Claude Code

Written for Claude Code: allowed-tools in frontmatter.

Needs its repository: it runs a file that does not travel with it, so clone the repository first. The line is gget enrichr -db pathway ACE2 AGT AGTR1 -ko ./kegg_images/.

Good fit It is for looking up gene information, downloading sequences, checking protein structures, running sequence searches, and exploring expression or disease data.

Compare 6 skills from other repositories ↓
Install

Getting it into your agent

It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.

Clone the repo
git clone --depth 1 https://github.com/dralkh/iktinah
agentmods
npx agentmods add skills/dralkh/iktinah/gget

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for gget

README.md
[![agentmods](https://agentmods.dev/badge/skills/dralkh/iktinah/gget/github.svg)](https://agentmods.dev/skills/dralkh/iktinah/gget)
Your own site
<a href="https://agentmods.dev/skills/dralkh/iktinah/gget"><img src="https://agentmods.dev/badge/skills/dralkh/iktinah/gget/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for gget

Your own site · 80×15
<a href="https://agentmods.dev/skills/dralkh/iktinah/gget"><img src="https://agentmods.dev/badge/skills/dralkh/iktinah/gget.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 93 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 8,721 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00093 $0.08721
Opus 5 $0.00046 $0.04360
Sonnet 5 $0.00019 $0.01744
Haiku 4.5 $0.00009 $0.00872

Measured 6d ago against content hash 8b799626b864, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

gget scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 6d ago.

The scan reads SKILL.md. This mod also ships 3 executable files (scripts/batch_sequence_analysis.py, scripts/enrichment_pipeline.py, scripts/gene_analysis.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

- `-d/--download`: Download files (requires curl)
Origin

Copies of this mod

2 near-identical copies found in the catalogue:

  • gget — 100% identical, 0 lines differ
  • gget — 100% identical, 0 lines differ
skills/gget/SKILL.md · 973 lines

How it starts

The opening of the file, as written. The whole thing — 973 lines — stays where its author put it; the contents beside it link to each section on GitHub.

gget

Overview

gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, viral sequences, expression data, disease associations, and mouse tissue/cell specificity metrics through a consistent interface. Most gget modules work both as command-line tools and as Python functions.

Important: The databases queried by gget are continuously updated, which sometimes changes their structure. Guidance here targets gget 0.30.5 (PyPI current as of 2026-06-07). For reproducible work, pin gget==0.30.5; for broken upstream database adapters, update gget after checking release notes.

Installation

Install gget in a clean virtual environment to avoid conflicts:

# Reproducible install targeting this skill
uv venv .venv
source .venv/bin/activate
uv pip install "gget==0.30.5"

# In Python/Jupyter
import gget

Quick Start

Basic usage pattern for all modules:

# Command-line
gget <module> [arguments] [options]

# Python
gget.module(arguments, options)

Most modules return:

  • Command-line: JSON (default) or CSV with -csv flag
  • Python: DataFrame or dictionary

Common flags across modules:

  • -o/--out: Save results to file
  • -q/--quiet: Suppress progress information
  • -csv: Return CSV format (command-line only)

Python argument names generally match long CLI options without leading dashes. For example, --census_version becomes census_version=.... Use gget <module> --help for the exact current signature.

Module Categories

1. Reference & Gene Information

gget ref - Reference Genome Downloads

Retrieve download links and metadata for Ensembl reference genomes.

Parameters:

  • species: Genus_species format (e.g., 'homo_sapiens', 'mus_musculus'). Shortcuts: 'human', 'mouse'
  • -w/--which: Specify return types as comma-separated CLI values or Python list (gtf, cdna, dna, cds, cdrna, pep). Default: all
  • -r/--release: Ensembl release number (default: latest)
  • -od/--out_dir: Directory for downloaded files
  • -l/--list_species: List available vertebrate species
  • -liv/--list_iv_species: List available invertebrate species
  • -ftp: Return only FTP links
  • -d/--download: Download files (requires curl)

Read the full file on GitHub · 973 lines

Files

What ships with it

6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 6d ago First seen · 973 lines · 93 tokens per session scan A 8b799626b864

Subscribe to this mod's changes

gget is a skill published in the GitHub repository dralkh/iktinah (77 stars, last pushed 2mo ago), licensed MIT. It adds 93 tokens to every session and 8,721 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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