CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.
npxskills add davila7/claude-code-templates--skill ggetLoading…
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.
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
Basic usage pattern for all modules:
# Command-line
gget <module> [arguments] [options]
# Python
gget.module(arguments, options)
Most modules return:
-csv flagCommon flags across modules:
-o/--out: Save results to file-q/--quiet: Suppress progress information-csv: Return CSV format (command-line only)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)
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 returnReturns: 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")
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)
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)
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:
-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)
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")
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)
Perform fast local protein or translated DNA alignment using DIAMOND.
Parameters:
--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 alignmentReturns: 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)
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 IDReturns: 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)
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 modelplot: 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)
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:
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")
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 IDReturns:
Examples:
# Get correlated genes
gget archs4 ACE2
# Get tissue expression
gget archs4 -w tissue ACE2
# Python
gget.archs4("ACE2", which="tissue")
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 onlyReturns: 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
# Python
adata = gget.cellxgene(gene=["ACE2", "ABCA1"], tissue="lung", cell_type="mucus secreting cell")
Perform ontology enrichment analysis on gene lists using Enrichr.
Parameters:
genes: Gene symbols or Ensembl IDs-db/--database: Reference database (supports shortcuts: 'pathway', 'transcription', 'ontology', 'diseases_drugs', 'celltypes')-s/--species: human (default), mouse, fly, yeast, worm, fish-bkg_l/--background_list: Background genes for comparison-ko/--kegg_out: Save KEGG pathway images with highlighted genesplot: Python-only; generate graphical resultsDatabase Shortcuts:
Examples:
# Enrichment analysis for ontology
gget enrichr -db ontology ACE2 AGT AGTR1
# Save KEGG pathways
gget enrichr -db pathway ACE2 AGT AGTR1 -ko ./kegg_images/
# Python with plot
gget.enrichr(["ACE2", "AGT", "AGTR1"], database="ontology", plot=True)
Retrieve orthology and gene expression data from Bgee database.
Parameters:
ens_id: Ensembl gene ID or NCBI gene ID (for non-Ensembl species). Multiple IDs supported when type=expression-t/--type: 'orthologs' (default) or 'expression'Returns:
Examples:
# Get orthologs
gget bgee ENSG00000169194
# Get expression data
gget bgee ENSG00000169194 -t expression
# Multiple genes
gget bgee ENSBTAG00000047356 ENSBTAG00000018317 -t expression
# Python
gget.bgee("ENSG00000169194", type="orthologs")
Retrieve disease and drug associations from OpenTargets.
Parameters:
-r/--resource: diseases (default), drugs, tractability, pharmacogenetics, expression, depmap, interactions-l/--limit: Cap results count--filter_disease--filter_drug--filter_tissue, --filter_anat_sys, --filter_organ--filter_protein_a, --filter_protein_b, --filter_gene_bExamples:
# Get associated diseases
gget opentargets ENSG00000169194 -r diseases -l 5
# Get associated drugs
gget opentargets ENSG00000169194 -r drugs -l 10
# Get tissue expression
gget opentargets ENSG00000169194 -r expression --filter_tissue brain
# Python
gget.opentargets("ENSG00000169194", resource="diseases", limit=5)
Plot cancer genomics heatmaps using cBioPortal data.
Two subcommands:
search - Find study IDs:
gget cbio search breast lung
plot - Generate heatmaps:
Parameters:
-s/--study_ids: Space-separated cBioPortal study IDs (required)-g/--genes: Space-separated gene names or Ensembl IDs (required)-st/--stratification: Column to organize data (tissue, cancer_type, cancer_type_detailed, study_id, sample)-vt/--variation_type: Data type (mutation_occurrences, cna_nonbinary, sv_occurrences, cna_occurrences, Consequence)-f/--filter: Filter by column value (e.g., 'study_id:msk_impact_2017')-dd/--data_dir: Cache directory (default: ./gget_cbio_cache)-fd/--figure_dir: Output directory (default: ./gget_cbio_figures)-dpi: Resolution (default: 100)-sh/--show: Display plot in windowExamples:
# Search for studies
gget cbio search esophag ovary
# Create heatmap
gget cbio plot -s msk_impact_2017 -g AKT1 ALK BRAF -st tissue -vt mutation_occurrences
# Python
gget.cbio_search(["esophag", "ovary"])
gget.cbio_plot(["msk_impact_2017"], ["AKT1", "ALK"], stratification="tissue")
Search COSMIC (Catalogue Of Somatic Mutations In Cancer) database.
Important: License fees apply for commercial use. Requires COSMIC account credentials.
Parameters:
searchterm: Gene name, Ensembl ID, mutation notation, or sample ID-ctp/--cosmic_tsv_path: Path to downloaded COSMIC TSV file (required for querying)-l/--limit: Maximum results (default: 100)Database download flags:
-d/--download_cosmic: Activate download mode-gm/--gget_mutate: Create version for gget mutate-cp/--cosmic_project: Database type (cancer, census, cell_line, resistance, genome_screen, targeted_screen)-cv/--cosmic_version: COSMIC version-gv/--grch_version: Human reference genome (37 or 38)--email, --password: COSMIC credentialsExamples:
# First download database
gget cosmic -d --email [email protected] --password xxx -cp cancer
# Then query
gget cosmic EGFR -ctp cosmic_data.tsv -l 10
# Python
gget.cosmic("EGFR", cosmic_tsv_path="cosmic_data.tsv", limit=10)
Generate mutated nucleotide sequences from mutation annotations.
Parameters:
sequences: FASTA file path or direct sequence input (string/list)-m/--mutations: CSV/TSV file or DataFrame with mutation data (required)-mc/--mut_column: Mutation column name (default: 'mutation')-sic/--seq_id_column: Sequence ID column (default: 'seq_ID')-mic/--mut_id_column: Mutation ID column-k/--k: Length of flanking sequences (default: 30 nucleotides)Returns: Mutated sequences in FASTA format
Examples:
# Single mutation
gget mutate ATCGCTAAGCT -m "c.4G>T"
# Multiple sequences with mutations from file
gget mutate sequences.fasta -m mutations.csv -o mutated.fasta
# Python
import pandas as pd
mutations_df = pd.DataFrame({"seq_ID": ["seq1"], "mutation": ["c.4G>T"]})
gget.mutate(["ATCGCTAAGCT"], mutations=mutations_df)
Generate natural language text using OpenAI's API.
Setup Required:
gget setup gpt
Important: Free tier limited to 3 months after account creation. Set monthly billing limits.
Parameters:
prompt: Text input for generation (required)api_key: OpenAI authentication (required)Examples:
gget gpt "Explain CRISPR" --api_key your_key_here
# Python
gget.gpt("Explain CRISPR", api_key="your_key_here")
Install/download third-party dependencies for specific modules.
Parameters:
module: Module name requiring dependency installation-o/--out: Output folder path (elm module only)Modules requiring setup:
alphafold - Downloads ~4GB of model parameterscellxgene - Installs cellxgene-census (may not support latest Python)elm - Downloads local ELM databasegpt - Configures OpenAI integrationExamples:
# Setup AlphaFold
gget setup alphafold
# Setup ELM with custom directory
gget setup elm -o /path/to/elm_data
# Python
gget.setup("alphafold")
Find and analyze genes of interest:
# 1. Search for genes
results = gget.search(["GABA", "receptor"], species="homo_sapiens")
# 2. Get detailed information
gene_ids = results["ensembl_id"].tolist()
info = gget.info(gene_ids[:5])
# 3. Retrieve sequences
sequences = gget.seq(gene_ids[:5], translate=True)
Align sequences and predict structures:
# 1. Align multiple sequences
alignment = gget.muscle("sequences.fasta")
# 2. Find similar sequences
blast_results = gget.blast(my_sequence, database="swissprot", limit=10)
# 3. Predict structure
structure = gget.alphafold(my_sequence, plot=True)
# 4. Find linear motifs
ortholog_df, regex_df = gget.elm(my_sequence)
Analyze expression patterns and functional enrichment:
# 1. Get tissue expression
tissue_expr = gget.archs4("ACE2", which="tissue")
# 2. Find correlated genes
correlated = gget.archs4("ACE2", which="correlation")
# 3. Get single-cell data
adata = gget.cellxgene(gene=["ACE2"], tissue="lung", cell_type="epithelial cell")
# 4. Perform enrichment analysis
gene_list = correlated["gene_symbol"].tolist()[:50]
enrichment = gget.enrichr(gene_list, database="ontology", plot=True)
Investigate disease associations and therapeutic targets:
# 1. Search for genes
genes = gget.search(["breast cancer"], species="homo_sapiens")
# 2. Get disease associations
diseases = gget.opentargets("ENSG00000169194", resource="diseases")
# 3. Get drug associations
drugs = gget.opentargets("ENSG00000169194", resource="drugs")
# 4. Query cancer genomics data
study_ids = gget.cbio_search(["breast"])
gget.cbio_plot(study_ids[:2], ["BRCA1", "BRCA2"], stratification="cancer_type")
# 5. Search COSMIC for mutations
cosmic_results = gget.cosmic("BRCA1", cosmic_tsv_path="cosmic.tsv")
Compare proteins across species:
# 1. Get orthologs
orthologs = gget.bgee("ENSG00000169194", type="orthologs")
# 2. Get sequences for comparison
human_seq = gget.seq("ENSG00000169194", translate=True)
mouse_seq = gget.seq("ENSMUSG00000026091", translate=True)
# 3. Align sequences
alignment = gget.muscle([human_seq, mouse_seq])
# 4. Compare structures
human_structure = gget.pdb("7S7U")
mouse_structure = gget.alphafold(mouse_seq)
Prepare reference data for downstream analysis (e.g., kallisto|bustools):
# 1. List available species
gget ref --list_species
# 2. Download reference files
gget ref -w gtf -w cdna -d homo_sapiens
# 3. Build kallisto index
kallisto index -i transcriptome.idx transcriptome.fasta
# 4. Download genome for alignment
gget ref -w dna -d homo_sapiens
--limit to control result sizes for large queries-o/--out for reproducibility--quiet in production scripts to reduce outputgget diamond with --threads for faster local alignment--diamond_db for repeated queries-s5/--super5 for large datasetsgget setup before first use of alphafold, cellxgene, elm, gpt-dd to avoid repeated downloads-mr 20 for higher accuracy-r flag for AMBER relaxation of final structuresplot=Trueuv pip install --upgrade gget-csv flagjson=True parametersave=True or specify out="filename"This skill includes reference documentation for detailed module information:
module_reference.md - Comprehensive parameter reference for all modulesdatabase_info.md - Information about queried databases and their update frequenciesworkflows.md - Extended workflow examples and use casesFor additional help:
-nc/--no_confirm: Skip download confirmations
Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Set up and use 1Password CLI (op). Use when installing the CLI, enabling desktop app integration, signing in (single or multi-account), or reading/injecting/running secrets via op.
CLI to manage emails via IMAP/SMTP. Use `himalaya` to list, read, write, reply, forward, search, and organize emails from the terminal. Supports multiple accounts and message composition with MML (MIME Meta Language).
Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Create or update AgentSkills. Use when designing, structuring, or packaging skills with scripts, references, and assets.
Set up and use 1Password CLI (op). Use when installing the CLI, enabling desktop app integration, signing in (single or multi-account), or reading/injecting/running secrets via op.
CLI to manage emails via IMAP/SMTP. Use `himalaya` to list, read, write, reply, forward, search, and organize emails from the terminal. Supports multiple accounts and message composition with MML (MIME Meta Language).