gget Module Reference
Comprehensive parameter reference for all gget modules.
Reference & Gene Information Modules
gget ref
Retrieve Ensembl reference genome FTPs and metadata.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| species | str | Species in Genus_species format or shortcuts ('human', 'mouse') | Required |
| -w/--which | str | File types to return: gtf, cdna, dna, cds, cdrna, pep | All |
| -r/--release | int | Ensembl release number | Latest |
| -od/--out_dir | str | Output directory path | None |
| -o/--out | str | JSON file path for results | None |
| -l/--list_species | flag | List available vertebrate species | False |
| -liv/--list_iv_species | flag | List available invertebrate species | False |
| -ftp | flag | Return only FTP links | False |
| -d/--download | flag | Download files (requires curl) | False |
| -q/--quiet | flag | Suppress progress information | False |
Returns: JSON containing FTP links, Ensembl release numbers, release dates, file sizes
gget search
Search for genes by name or description in Ensembl.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| searchwords | str/list | Search terms (case-insensitive) | Required |
| -s/--species | str | Target species or core database name | Required |
| -r/--release | int | Ensembl release number | Latest |
| -t/--id_type | str | Return 'gene' or 'transcript' | 'gene' |
| -ao/--andor | str | 'or' (ANY term) or 'and' (ALL terms) | 'or' |
| -l/--limit | int | Maximum results to return | None |
| -o/--out | str | Output file path (CSV/JSON) | None |
Returns: ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, URL
gget info
Get comprehensive gene/transcript metadata from Ensembl, UniProt, and NCBI.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| ens_ids | str/list | Ensembl IDs (WormBase, Flybase also supported) | Required |
| -o/--out | str | Output file path (CSV/JSON) | None |
| -n/--ncbi | bool | Disable NCBI data retrieval | False |
| -u/--uniprot | bool | Disable UniProt data retrieval | False |
| -pdb | bool | Include PDB identifiers | False |
| -csv | flag | Return CSV format (CLI) | False |
| -q/--quiet | flag | Suppress progress display | False |
Python-specific:
- save=True: Save output to current directory
- wrap_text=True: Format dataframe with wrapped text
Note: Processing >1000 IDs simultaneously may cause server errors.
Returns: UniProt ID, NCBI gene ID, gene name, synonyms, protein names, descriptions, biotype, canonical transcript
gget seq
Retrieve nucleotide or amino acid sequences in FASTA format.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| ens_ids | str/list | Ensembl identifiers | Required |
| -o/--out | str | Output file path | stdout |
| -t/--translate | flag | Fetch amino acid sequences | False |
| -iso/--isoforms | flag | Return all transcript variants | False |
| -q/--quiet | flag | Suppress progress information | False |
Data sources: Ensembl (nucleotide), UniProt (amino acid)
Returns: FASTA format sequences
Sequence Analysis & Alignment Modules
gget blast
BLAST sequences against standard databases.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| sequence | str | Sequence or path to FASTA/.txt | Required |
| -p/--program | str | blastn, blastp, blastx, tblastn, tblastx | Auto-detect |
| -db/--database | str | nt, refseq_rna, pdbnt, nr, swissprot, pdbaa, refseq_protein | nt or nr |
| -l/--limit | int | Max hits returned | 50 |
| -e/--expect | float | E-value cutoff | 10.0 |
| -lcf/--low_comp_filt | flag | Enable low complexity filtering | False |
| -mbo/--megablast_off | flag | Disable MegaBLAST (blastn only) | False |
| -o/--out | str | Output file path | None |
| -q/--quiet | flag | Suppress progress | False |
Returns: Description, Scientific Name, Common Name, Taxid, Max Score, Total Score, Query Coverage
gget blat
Find genomic positions using UCSC BLAT.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| sequence | str | Sequence or path to FASTA/.txt | Required |
| -st/--seqtype | str | 'DNA', 'protein', 'translated%20RNA', 'translated%20DNA' | Auto-detect |
| -a/--assembly | str | Target assembly (hg38, mm39, taeGut2, etc.) | 'human'/hg38 |
| -o/--out | str | Output file path | None |
| -csv | flag | Return CSV format (CLI) | False |
| -q/--quiet | flag | Suppress progress | False |
Returns: genome, query size, alignment start/end, matches, mismatches, alignment percentage
gget muscle
Align multiple sequences using Muscle5.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| fasta | str/list | Sequences or FASTA file path | Required |
| -o/--out | str | Output file path | stdout |
| -s5/--super5 | flag | Use Super5 algorithm (faster, large datasets) | False |
| -q/--quiet | flag | Suppress progress | False |
Returns: ClustalW format alignment or aligned FASTA (.afa)
gget diamond
Fast local protein/translated DNA alignment.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| query | str/list | Query sequences or FASTA file | Required |
| --reference | str/list | Reference sequences or FASTA file | Required |
| --sensitivity | str | fast, mid-sensitive, sensitive, more-sensitive, very-sensitive, ultra-sensitive | very-sensitive |
| --threads | int | CPU threads | 1 |
| --diamond_binary | str | Path to DIAMOND installation | Auto-detect |
| --diamond_db | str | Save database for reuse | None |
| --translated | flag | Enable nucleotide-to-amino acid alignment | False |
| -o/--out | str | Output file path | None |
| -csv | flag | CSV format (CLI) | False |
| -q/--quiet | flag | Suppress progress | False |
Returns: Identity %, sequence lengths, match positions, gap openings, E-values, bit scores
Structural & Protein Analysis Modules
gget pdb
Query RCSB Protein Data Bank.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| pdb_id | str | PDB identifier (e.g., '7S7U') | Required |
| -r/--resource | str | pdb, entry, pubmed, assembly, entity types | 'pdb' |
| -i/--identifier | str | Assembly, entity, or chain ID | None |
| -o/--out | str | Output file path | stdout |
Returns: PDB format (structures) or JSON (metadata)
gget alphafold
Predict 3D protein structures using AlphaFold2.
Setup: Requires OpenMM and gget setup alphafold (~4GB download)
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| sequence | str/list | Amino acid sequence(s) or FASTA file | Required |
| -mr/--multimer_recycles | int | Recycling iterations for multimers | 3 |
| -o/--out | str | Output folder path | timestamped |
| -mfm/--multimer_for_monomer | flag | Apply multimer model to monomers | False |
| -r/--relax | flag | AMBER relaxation for top model | False |
| -q/--quiet | flag | Suppress progress | False |
Python-only:
- plot (bool): Generate 3D visualization (default: True)
- show_sidechains (bool): Include side chains (default: True)
Note: Multiple sequences automatically trigger multimer modeling
Returns: PDB structure file, JSON alignment error data, optional 3D plot
gget elm
Predict Eukaryotic Linear Motifs.
Setup: Requires gget setup elm
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| sequence | str | Amino acid sequence or UniProt Acc | Required |
| -s/--sensitivity | str | DIAMOND alignment sensitivity | very-sensitive |
| -t/--threads | int | Number of threads | 1 |
| -bin/--diamond_binary | str | Path to DIAMOND binary | Auto-detect |
| -o/--out | str | Output directory path | None |
| -u/--uniprot | flag | Input is UniProt Acc | False |
| -e/--expand | flag | Include protein names, organisms, references | False |
| -csv | flag | CSV format (CLI) | False |
| -q/--quiet | flag | Suppress progress | False |
Returns: Two outputs: 1. ortholog_df: Motifs from orthologous proteins 2. regex_df: Motifs matched in input sequence
Expression & Disease Data Modules
gget archs4
Query ARCHS4 for gene correlation or tissue expression.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| gene | str | Gene symbol or Ensembl ID | Required |
| -w/--which | str | 'correlation' or 'tissue' | 'correlation' |
| -s/--species | str | 'human' or 'mouse' (tissue only) | 'human' |
| -o/--out | str | Output file path | None |
| -e/--ensembl | flag | Input is Ensembl ID | False |
| -csv | flag | CSV format (CLI) | False |
| -q/--quiet | flag | Suppress progress | False |
Returns: - correlation: Gene symbols, Pearson correlation coefficients (top 100) - tissue: Tissue IDs, min/Q1/median/Q3/max expression
gget cellxgene
Query CZ CELLxGENE Discover Census for single-cell data.
Setup: Requires gget setup cellxgene
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| --gene (-g) | list | Gene names or Ensembl IDs (case-sensitive!) | Required |
| --tissue | list | Tissue type(s) | None |
| --cell_type | list | Cell type(s) | None |
| --species (-s) | str | 'homo_sapiens' or 'mus_musculus' | 'homo_sapiens' |
| --census_version (-cv) | str | "stable", "latest", or dated version | "stable" |
| -o/--out | str | Output file path (required for CLI) | Required |
| --ensembl (-e) | flag | Use Ensembl IDs | False |
| --meta_only (-mo) | flag | Return metadata only | False |
| -q/--quiet | flag | Suppress progress | False |
Additional filters: disease, development_stage, sex, assay, dataset_id, donor_id, ethnicity, suspension_type
Important: Gene symbols are case-sensitive ('PAX7' for human, 'Pax7' for mouse)
Returns: AnnData object with count matrices and metadata
gget enrichr
Perform enrichment analysis using Enrichr/modEnrichr.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| genes | list | Gene symbols or Ensembl IDs | Required |
| -db/--database | str | Reference database or shortcut | Required |
| -s/--species | str | human, mouse, fly, yeast, worm, fish | 'human' |
| -bkg_l/--background_list | list | Background genes | None |
| -o/--out | str | Output file path | None |
| -ko/--kegg_out | str | KEGG pathway images directory | None |
Python-only:
- plot (bool): Generate graphical results
Database shortcuts: - 'pathway' → KEGG_2021_Human - 'transcription' → ChEA_2016 - 'ontology' → GO_Biological_Process_2021 - 'diseases_drugs' → GWAS_Catalog_2019 - 'celltypes' → PanglaoDB_Augmented_2021
Returns: Pathway/function associations with adjusted p-values, overlapping gene counts
gget bgee
Retrieve orthology and expression from Bgee.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| ens_id | str/list | Ensembl or NCBI gene ID | Required |
| -t/--type | str | 'orthologs' or 'expression' | 'orthologs' |
| -o/--out | str | Output file path | None |
| -csv | flag | CSV format (CLI) | False |
| -q/--quiet | flag | Suppress progress | False |
Note: Multiple IDs supported when type='expression'
Returns: - orthologs: Genes across species with IDs, names, taxonomic info - expression: Anatomical entities, confidence scores, expression status
gget opentargets
Retrieve disease/drug associations from OpenTargets.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| ens_id | str | Ensembl gene ID | Required |
| -r/--resource | str | diseases, drugs, tractability, pharmacogenetics, expression, depmap, interactions | 'diseases' |
| -l/--limit | int | Maximum results | None |
| -o/--out | str | Output file path | None |
| -csv | flag | CSV format (CLI) | False |
| -q/--quiet | flag | Suppress progress | False |
Resource-specific filters:
- drugs: --filter_disease
- pharmacogenetics: --filter_drug
- expression/depmap: --filter_tissue, --filter_anat_sys, --filter_organ
- interactions: --filter_protein_a, --filter_protein_b, --filter_gene_b
Returns: Disease/drug associations, tractability, pharmacogenetics, expression, DepMap, interactions
gget cbio
Plot cancer genomics heatmaps from cBioPortal.
Subcommands: search, plot
search parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| keywords | list | Search terms | Required |
plot parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| -s/--study_ids | list | cBioPortal study IDs | Required |
| -g/--genes | list | Gene names or Ensembl IDs | Required |
| -st/--stratification | str | tissue, cancer_type, cancer_type_detailed, study_id, sample | None |
| -vt/--variation_type | str | mutation_occurrences, cna_nonbinary, sv_occurrences, cna_occurrences, Consequence | None |
| -f/--filter | str | Filter by column value (e.g., 'study_id:msk_impact_2017') | None |
| -dd/--data_dir | str | Cache directory | ./gget_cbio_cache |
| -fd/--figure_dir | str | Output directory | ./gget_cbio_figures |
| -t/--title | str | Custom figure title | None |
| -dpi | int | Resolution | 100 |
| -q/--quiet | flag | Suppress progress | False |
| -nc/--no_confirm | flag | Skip download confirmations | False |
| -sh/--show | flag | Display plot in window | False |
Returns: PNG heatmap figure
gget cosmic
Search COSMIC database for cancer mutations.
Important: License fees for commercial use. Requires COSMIC account.
Query parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| searchterm | str | Gene name, Ensembl ID, mutation, sample ID | Required |
| -ctp/--cosmic_tsv_path | str | Path to COSMIC TSV file | Required |
| -l/--limit | int | Maximum results | 100 |
| -csv | flag | CSV format (CLI) | False |
Download parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| -d/--download_cosmic | flag | Activate download mode | False |
| -gm/--gget_mutate | flag | Create version for gget mutate | False |
| -cp/--cosmic_project | str | cancer, census, cell_line, resistance, genome_screen, targeted_screen | None |
| -cv/--cosmic_version | str | COSMIC version | Latest |
| -gv/--grch_version | int | Human reference genome (37 or 38) | None |
| --email | str | COSMIC account email | Required |
| --password | str | COSMIC account password | Required |
Note: First-time users must download database
Returns: Mutation data from COSMIC
Additional Tools
gget mutate
Generate mutated nucleotide sequences.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| sequences | str/list | FASTA file or sequences | Required |
| -m/--mutations | str/df | CSV/TSV file or DataFrame | Required |
| -mc/--mut_column | str | Mutation column name | 'mutation' |
| -sic/--seq_id_column | str | Sequence ID column | 'seq_ID' |
| -mic/--mut_id_column | str | Mutation ID column | None |
| -k/--k | int | Length of flanking sequences | 30 |
| -o/--out | str | Output FASTA file path | stdout |
| -q/--quiet | flag | Suppress progress | False |
Returns: Mutated sequences in FASTA format
gget gpt
Generate text using OpenAI's API.
Setup: Requires gget setup gpt and OpenAI API key
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| prompt | str | Text input for generation | Required |
| api_key | str | OpenAI API key | Required |
| model | str | OpenAI model name | gpt-3.5-turbo |
| temperature | float | Sampling temperature (0-2) | 1.0 |
| top_p | float | Nucleus sampling | 1.0 |
| max_tokens | int | Maximum tokens to generate | None |
| frequency_penalty | float | Frequency penalty (0-2) | 0 |
| presence_penalty | float | Presence penalty (0-2) | 0 |
Important: Free tier limited to 3 months. Set billing limits.
Returns: Generated text string
gget setup
Install/download dependencies for modules.
Parameters:
| Parameter | Type | Description | Default |
|-----------|------|-------------|---------|
| module | str | Module name | Required |
| -o/--out | str | Output folder (elm only) | Package install folder |
| -q/--quiet | flag | Suppress progress | False |
Modules requiring setup:
- alphafold - Downloads ~4GB model parameters
- cellxgene - Installs cellxgene-census
- elm - Downloads local ELM database
- gpt - Configures OpenAI integration
Returns: None (installs dependencies)