Basic Patterns

CLI shape:

gget <module> [arguments] [options]

Python shape:

import gget

result = gget.search(["BRCA1"], species="human")
print(result)

Common workflow:

1. Identify the species, assembly, gene ID type, and database needed.
2. Check the current module documentation for arguments.
3. Run a small query first.
4. Save output with an explicit filename and date.
5. Record module name, version, arguments, and database assumptions.

Common Modules

Use current upstream docs for exact arguments. These modules are common first choices:

• gget search: find Ensembl IDs from search terms.
• gget info: retrieve metadata for Ensembl, UniProt, or related IDs.
• gget seq: fetch nucleotide or amino-acid sequences.
• gget ref: retrieve reference genome download links.
• gget blast: run a quick BLAST query.
• gget blat: locate a sequence against supported genome assemblies.
• gget muscle: run multiple sequence alignment.
• gget diamond: run local sequence alignment against reference sequences.
• gget alphafold and gget pdb: inspect protein-structure references.
• gget enrichr, gget opentargets, gget archs4, gget bgee, gget cbio, and gget cosmic: explore enrichment, target, expression, cancer, and disease association data.

Do not assume every module supports every Python version or dependency set. Some optional scientific dependencies have narrower version support than the core package.

Quick Examples

Find genes:

gget search -s human brca1 dna repair -o brca1-search.json

Fetch gene metadata:

gget info ENSG00000012048 -o brca1-info.json

Fetch a sequence:

gget seq ENSG00000012048 -o brca1-seq.fa

Run a small BLAST query:

gget blast "MEEPQSDPSVEPPLSQETFSDLWKLLPEN" -l 10 -o blast-results.json

Python example:

import gget

genes = gget.search(["BRCA1", "DNA repair"], species="human")
info = gget.info(["ENSG00000012048"])
sequence = gget.seq("ENSG00000012048")

Reproducibility Log

For scientific outputs, include enough metadata to replay the query.

| Date | gget version | Module | Query | Species/assembly | Output | Notes |
| --- | --- | --- | --- | --- | --- | --- |
| 2026-05-11 | `gget --version` | search | `BRCA1 DNA repair` | human | `brca1-search.json` | Docs checked before run |

Also record:

• Python version and environment manager.
• Any optional dependency installed through gget setup.
• Database-specific identifiers returned by the query.
• Whether output is JSON, CSV, FASTA, or a DataFrame export.
• Any failures that were resolved by upgrading gget.

Review Checklist

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