davila7/claude-code-templates/gget

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, expression data, and disease associations through a consistent interface. All 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. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary.

Installation

Install gget in a clean virtual environment to avoid conflicts:

# Using uv (recommended)
uv uv pip install gget
 
# Or using pip
uv pip install --upgrade gget
 
# 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)

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 (gtf, cdna, dna, cds, cdrna, pep). Default: all
• -r/--release: Ensembl release number (default: latest)
• -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)

Examples:

# List available species
gget ref --list_species
 
# Get all reference files for human
gget ref homo_sapiens
 
# Download only GTF annotation for mouse
gget ref -w gtf -d mouse

# Python
gget.ref("homo_sapiens")
gget.ref("mus_musculus", which="gtf", download=True)

gget search - Gene Search

Locate genes by name or description across species.

Parameters:

• searchwords: One or more search terms (case-insensitive)
• -s/--species: Target species (e.g., 'homo_sapiens', 'mouse')
• -r/--release: Ensembl release number
• -t/--id_type: Return 'gene' (default) or 'transcript'
• -ao/--andor: 'or' (default) finds ANY searchword; 'and' requires ALL
• -l/--limit: Maximum results to return

Returns: ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, URL

Examples:

# Search for GABA-related genes in human
gget search -s human gaba gamma-aminobutyric
 
# Find specific gene, require all terms
gget search -s mouse -ao and pax7 transcription

# Python
gget.search(["gaba", "gamma-aminobutyric"], species="homo_sapiens")

gget info - Gene/Transcript Information

Retrieve comprehensive gene and transcript metadata from Ensembl, UniProt, and NCBI.

Parameters:

• ens_ids: One or more Ensembl IDs (also supports WormBase, Flybase IDs). Limit: ~1000 IDs
• -n/--ncbi: Disable NCBI data retrieval
• -u/--uniprot: Disable UniProt data retrieval
• -pdb: Include PDB identifiers (increases runtime)

Returns: UniProt ID, NCBI gene ID, primary gene name, synonyms, protein names, descriptions, biotype, canonical transcript

Examples:

# Get info for multiple genes
gget info ENSG00000034713 ENSG00000104853 ENSG00000170296
 
# Include PDB IDs
gget info ENSG00000034713 -pdb

# Python
gget.info(["ENSG00000034713", "ENSG00000104853"], pdb=True)

gget seq - Sequence Retrieval

Fetch nucleotide or amino acid sequences for genes and transcripts.

Parameters:

• ens_ids: One or more Ensembl identifiers
• -t/--translate: Fetch amino acid sequences instead of nucleotide
• -iso/--isoforms: Return all transcript variants (gene IDs only)

Returns: FASTA format sequences

Examples:

# Get nucleotide sequences
gget seq ENSG00000034713 ENSG00000104853
 
# Get all protein isoforms
gget seq -t -iso ENSG00000034713

# Python
gget.seq(["ENSG00000034713"], translate=True, isoforms=True)

2. Sequence Analysis & Alignment

gget blast - BLAST Searches

BLAST nucleotide or amino acid sequences against standard databases.

Parameters:

• sequence: Sequence string or path to FASTA/.txt file
• -p/--program: blastn, blastp, blastx, tblastn, tblastx (auto-detected)
• -db/--database:
• Nucleotide: nt, refseq_rna, pdbnt
• Protein: nr, swissprot, pdbaa, refseq_protein
• -l/--limit: Max hits (default: 50)
• -e/--expect: E-value cutoff (default: 10.0)
• -lcf/--low_comp_filt: Enable low complexity filtering
• -mbo/--megablast_off: Disable MegaBLAST (blastn only)

Examples:

# BLAST protein sequence
gget blast MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR
 
# BLAST from file with specific database
gget blast sequence.fasta -db swissprot -l 10

# Python
gget.blast("MKWMFK...", database="swissprot", limit=10)

gget blat - BLAT Searches

Locate genomic positions of sequences using UCSC BLAT.

Parameters:

• sequence: Sequence string or path to FASTA/.txt file
• -st/--seqtype: 'DNA', 'protein', 'translated%20RNA', 'translated%20DNA' (auto-detected)
• -a/--assembly: Target assembly (default: 'human'/hg38; options: 'mouse'/mm39, 'zebrafinch'/taeGut2, etc.)

Returns: genome, query size, alignment positions, matches, mismatches, alignment percentage

Examples:

# Find genomic location in human
gget blat ATCGATCGATCGATCG
 
# Search in different assembly
gget blat -a mm39 ATCGATCGATCGATCG

# Python
gget.blat("ATCGATCGATCGATCG", assembly="mouse")

gget muscle - Multiple Sequence Alignment

Align multiple nucleotide or amino acid sequences using Muscle5.

Parameters:

• fasta: Sequences or path to FASTA/.txt file
• -s5/--super5: Use Super5 algorithm for faster processing (large datasets)

Returns: Aligned sequences in ClustalW format or aligned FASTA (.afa)

Examples:

# Align sequences from file
gget muscle sequences.fasta -o aligned.afa
 
# Use Super5 for large dataset
gget muscle large_dataset.fasta -s5

# Python
gget.muscle("sequences.fasta", save=True)

gget diamond - Local Sequence Alignment

Perform fast local protein or translated DNA alignment using DIAMOND.

Parameters:

• Query: Sequences (string/list) or FASTA file path
• --reference: Reference sequences (string/list) or FASTA file path (required)
• --sensitivity: fast, mid-sensitive, sensitive, more-sensitive, very-sensitive (default), ultra-sensitive
• --threads: CPU threads (default: 1)
• --diamond_db: Save database for reuse
• --translated: Enable nucleotide-to-amino acid alignment

Returns: Identity percentage, sequence lengths, match positions, gap openings, E-values, bit scores

Examples:

# Align against reference
gget diamond GGETISAWESQME -ref reference.fasta --threads 4
 
# Save database for reuse
gget diamond query.fasta -ref ref.fasta --diamond_db my_db.dmnd

# Python
gget.diamond("GGETISAWESQME", reference="reference.fasta", threads=4)

3. Structural & Protein Analysis

gget pdb - Protein Structures

Query RCSB Protein Data Bank for structure and metadata.

Parameters:

• pdb_id: PDB identifier (e.g., '7S7U')
• -r/--resource: Data type (pdb, entry, pubmed, assembly, entity types)
• -i/--identifier: Assembly, entity, or chain ID

Returns: PDB format (structures) or JSON (metadata)

Examples:

# Download PDB structure
gget pdb 7S7U -o 7S7U.pdb
 
# Get metadata
gget pdb 7S7U -r entry

# Python
gget.pdb("7S7U", save=True)

gget alphafold - Protein Structure Prediction

Predict 3D protein structures using simplified AlphaFold2.

Setup Required:

# Install OpenMM first
uv pip install openmm
 
# Then setup AlphaFold
gget setup alphafold

Parameters:

• sequence: Amino acid sequence (string), multiple sequences (list), or FASTA file. Multiple sequences trigger multimer modeling
• -mr/--multimer_recycles: Recycling iterations (default: 3; recommend 20 for accuracy)
• -mfm/--multimer_for_monomer: Apply multimer model to single proteins
• -r/--relax: AMBER relaxation for top-ranked model
• plot: Python-only; generate interactive 3D visualization (default: True)
• show_sidechains: Python-only; include side chains (default: True)

Returns: PDB structure file, JSON alignment error data, optional 3D visualization

Examples:

# Predict single protein structure
gget alphafold MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR
 
# Predict multimer with higher accuracy
gget alphafold sequence1.fasta -mr 20 -r

# Python with visualization
gget.alphafold("MKWMFK...", plot=True, show_sidechains=True)
# Multimer prediction
gget.alphafold(["sequence1", "sequence2"], multimer_recycles=20)

gget elm - Eukaryotic Linear Motifs

Predict Eukaryotic Linear Motifs in protein sequences.

Setup Required:

gget setup elm

Parameters:

• sequence: Amino acid sequence or UniProt Acc
• -u/--uniprot: Indicates sequence is UniProt Acc
• -e/--expand: Include protein names, organisms, references
• -s/--sensitivity: DIAMOND alignment sensitivity (default: "very-sensitive")
• -t/--threads: Number of threads (default: 1)

Returns: Two outputs:

1. ortholog_df: Linear motifs from orthologous proteins
2. regex_df: Motifs directly matched in input sequence

Examples:

# Predict motifs from sequence
gget elm LIAQSIGQASFV -o results
 
# Use UniProt accession with expanded info
gget elm --uniprot Q02410 -e

# Python
ortholog_df, regex_df = gget.elm("LIAQSIGQASFV")

4. Expression & Disease Data

gget archs4 - Gene Correlation & Tissue Expression

Query ARCHS4 database for correlated genes or tissue expression data.

Parameters:

• gene: Gene symbol or Ensembl ID (with --ensembl flag)
• -w/--which: 'correlation' (default, returns 100 most correlated genes) or 'tissue' (expression atlas)
• -s/--species: 'human' (default) or 'mouse' (tissue data only)
• -e/--ensembl: Input is Ensembl ID

Returns:

• Correlation mode: Gene symbols, Pearson correlation coefficients
• Tissue mode: Tissue identifiers, min/Q1/median/Q3/max expression values

Examples:

# Get correlated genes
gget archs4 ACE2
 
# Get tissue expression
gget archs4 -w tissue ACE2

# Python
gget.archs4("ACE2", which="tissue")

gget cellxgene - Single-Cell RNA-seq Data

Query CZ CELLxGENE Discover Census for single-cell data.

Setup Required:

gget setup cellxgene

Parameters:

• --gene (-g): Gene names or Ensembl IDs (case-sensitive! 'PAX7' for human, 'Pax7' for mouse)
• --tissue: Tissue type(s)
• --cell_type: Specific cell type(s)
• --species (-s): 'homo_sapiens' (default) or 'mus_musculus'
• --census_version (-cv): Version ("stable", "latest", or dated)
• --ensembl (-e): Use Ensembl IDs
• --meta_only (-mo): Return metadata only
• Additional filters: disease, development_stage, sex, assay, dataset_id, donor_id, ethnicity, suspension_type

Returns: AnnData object with count matrices and metadata (or metadata-only dataframes)

Examples:

# Get single-cell data for specific genes and cell types
gget cellxgene --gene ACE2 ABCA1 --tissue lung --cell_type "mucus secreting cell" -o lung_data.h5ad
 
# Metadata only
gget cellxgene --gene PAX7 --tissue muscle --meta_only -o metadata.csv