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module_reference.md

550 lines · skills/gget/references/module_reference.md at 5f2bc03

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1# gget Module Reference

3Selected CLI parameters and Python differences for gget 0.30.8. Source-checked against the [released implementation](https://github.com/scverse/gget/tree/v0.30.8/gget); use `gget <module> --help` and `inspect.signature(gget.<module>)` for the full surface. [Database contracts](database_info.md) document return fields and completeness limits.

gget Module Reference

Selected CLI parameters and Python differences for gget 0.30.8. Source-checked against the released implementation; use gget <module> --help and inspect.signature(gget.<module>) for the full surface. Database contracts document return fields and completeness limits.

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5## Reference & Gene Information Modules

Reference & Gene Information Modules

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7### gget ref

8Retrieve Ensembl reference genome FTPs and metadata.

10**Parameters:**

12|-----------|------|-------------|---------|

24**Returns:** JSON containing FTP links, Ensembl release numbers, release dates, file sizes

26---

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/list	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	CLI-only download (requires curl; Python returns links)	False
`-q/--quiet`	flag	Suppress progress information	False

Returns: JSON containing FTP links, Ensembl release numbers, release dates, file sizes

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28### gget search

29Search for genes by name or description in Ensembl.

30Search includes Ensembl synonyms in current gget versions.

32**Parameters:**

34|-----------|------|-------------|---------|

39| `-ao/--andor` | str | 'or' (ANY term) or 'and' (ALL terms) | 'or' |

44**Returns:** ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, synonym, url

46---

gget search

Search for genes by name or description in Ensembl. Search includes Ensembl synonyms in current gget versions.

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
`wrap_text`	bool	Python-only wrapped text display for wide results	False

Returns: ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, synonym, url

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48### gget info

49Get comprehensive gene/transcript metadata from Ensembl, UniProt, and NCBI.

51**Parameters:**

53|-----------|------|-------------|---------|

62**Python-specific:**

63- `save=True`: Save output to current directory

64- `wrap_text=True`: Format dataframe with wrapped text

66**Note:** Processing >1000 IDs simultaneously may cause server errors.

68**Returns:** DataFrame indexed by query Ensembl ID, with `uniprot_id`, `ncbi_gene_id`, `primary_gene_name`, `ensembl_gene_name`, annotations and transcript metadata. Preserve the index on export.

70---

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: DataFrame indexed by query Ensembl ID, with uniprot_id, ncbi_gene_id, primary_gene_name, ensembl_gene_name, annotations and transcript metadata. Preserve the index on export.

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72### gget seq

73Retrieve nucleotide or amino acid sequences in FASTA format.

75**Parameters:**

77|-----------|------|-------------|---------|

84**Data sources:** Ensembl (nucleotide), UniProt (amino acid)

86**Returns:** Python list of FASTA lines (header, sequence, ...), or None on failure; CLI prints FASTA

88---

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 (gene IDs only)	False
`-q/--quiet`	flag	Suppress progress information	False

Data sources: Ensembl (nucleotide), UniProt (amino acid)

Returns: Python list of FASTA lines (header, sequence, ...), or None on failure; CLI prints FASTA

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90## Sequence Analysis & Alignment Modules

Sequence Analysis & Alignment Modules

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92### gget blast

93BLAST sequences against standard databases.

95**Parameters:**

97|-----------|------|-------------|---------|

101| `-l/--limit` | int | Max hits returned | 50 |

107

108**Returns:** Description, Scientific Name, Common Name, Taxid, Max Score, Total Score, Query Coverage

109

110---

111

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

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112### gget blat

113Find genomic positions using UCSC BLAT.

114

115**Parameters:**

117|-----------|------|-------------|---------|

124

125**Returns:** genome, query size, alignment start/end, matches, mismatches, alignment percentage

126

127---

128

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

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129### gget muscle

130Align multiple sequences using Muscle5.

131

132**Parameters:**

134|-----------|------|-------------|---------|

139

140**Returns:** Python returns None; prints ClustalW alignment or writes aligned FASTA using `out="alignment.afa"`

141

142---

143

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: Python returns None; prints ClustalW alignment or writes aligned FASTA using out="alignment.afa"

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144### gget diamond

145Fast local protein alignment and translated nucleotide-to-protein alignment.

146

147**Parameters:**

149|-----------|------|-------------|---------|

153| `-t/--threads` | int | CPU threads | 1 |

160

161**Returns:** Identity %, sequence lengths, match positions, gap openings, E-values, bit scores

162

163---

164

gget diamond

Fast local protein alignment and translated nucleotide-to-protein alignment.

Parameters:

Parameter	Type	Description	Default
`query`	str/list	Query sequences or FASTA file	Required
`-ref/--reference`	str/list	Reference sequences or FASTA file	Required
`-s/--sensitivity`	str	fast, mid-sensitive, sensitive, more-sensitive, very-sensitive, ultra-sensitive	very-sensitive
`-t/--threads`	int	CPU threads	1
`--diamond_binary`	str	Path to DIAMOND installation	Auto-detect
`-db/--diamond_db`	str	Database output path (reference still required)	None
`-x/--translated`	flag	Enable nucleotide query to amino acid reference 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

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165## Structural & Protein Analysis Modules

166

Structural & Protein Analysis Modules

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167### gget pdb

168Query RCSB Protein Data Bank.

169

170**Parameters:**

172|-----------|------|-------------|---------|

174| `-r/--resource` | str | pdb, mmcif, entry, pubmed, assembly, entity types | 'pdb' |

177

178**Returns:** PDB/mmCIF text (structures) or dictionary (metadata); `resource="pdb"` falls back to mmCIF if PDB is unavailable

179

180---

181

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, mmcif, entry, pubmed, assembly, entity types	'pdb'
`-i/--identifier`	str	Assembly, entity, or chain ID	None
`-o/--out`	str	Output file path	stdout

Returns: PDB/mmCIF text (structures) or dictionary (metadata); resource="pdb" falls back to mmCIF if PDB is unavailable

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182### gget g2p

183

184| Python parameter | Contract |

185| --- | --- |

186| `gene`, `uniprot_id` | At least one required; exact pair avoids approximate gene-only human lookup |

187| `resource` | features (default), map, alignment |

188| `isoform` | Required alternative isoform for alignment; canonical uniprot_id also explicit |

189| `residues` | Integer/list/range/set positions, filtered locally; unavailable for map |

190| `save`, `out` | CSV output; out takes precedence. No Python json parameter |

191

192Returns DataFrame or None on request failure; invalid arguments may raise.

193See [catalog examples](module_catalog.md) and [official manual](https://scverse.org/gget/en/g2p.html).

194

195---

196

gget g2p

Python parameter	Contract
`gene`, `uniprot_id`	At least one required; exact pair avoids approximate gene-only human lookup
`resource`	features (default), map, alignment
`isoform`	Required alternative isoform for alignment; canonical uniprot_id also explicit
`residues`	Integer/list/range/set positions, filtered locally; unavailable for map
`save`, `out`	CSV output; out takes precedence. No Python json parameter

Returns DataFrame or None on request failure; invalid arguments may raise. See catalog examples and official manual.

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197### gget alphafold

198Legacy AlphaFold2 wrapper; deprecated and no longer actively maintained since 0.30.7.

199

200**Legacy setup (not executed):** Requires OpenMM and `gget setup alphafold`; model assets are multi-gigabyte downloads. No current compatibility claim.

201

202**Parameters:**

204|-----------|------|-------------|---------|

206| `-mr/--multimer_recycles` | int | Recycling iterations for multimers | 3 |

212

213**Python-only:**

214- `plot` (bool): Generate 3D visualization (default: True)

215- `show_sidechains` (bool): Include side chains (default: True)

216

217**Note:** Multiple sequences automatically trigger multimer modeling

218

219**Returns:** PDB structure file, JSON alignment error data, optional 3D plot

220

221---

222

gget alphafold

Legacy AlphaFold2 wrapper; deprecated and no longer actively maintained since 0.30.7.

Legacy setup (not executed): Requires OpenMM and gget setup alphafold; model assets are multi-gigabyte downloads. No current compatibility claim.

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
`-jhd/--jackhmmer_savedir`	str	Temporary jackhmmer directory	~/tmp/jackhmmer
`-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

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223### gget elm

224Predict Eukaryotic Linear Motifs.

225

226**Setup:** Requires `gget setup elm`

227

228**Parameters:**

230|-----------|------|-------------|---------|

233| `-t/--threads` | int | Number of threads | 1 |

240

241**Returns:** Two outputs:

2421. **ortholog_df**: Motifs from orthologous proteins

2432. **regex_df**: Motifs matched in input sequence

244

245---

246

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:

ortholog_df: Motifs from orthologous proteins
regex_df: Motifs matched in input sequence

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Runs code bin/--diamond_binary :234

247## Expression & Disease Data Modules

248

Expression & Disease Data Modules

Raw lines 247 to 248

249### gget archs4

250Query ARCHS4 for gene correlation or tissue expression.

251

252**Parameters:**

254|-----------|------|-------------|---------|

262

263**Returns:**

264- **correlation**: `gene_symbol`, `pearson_correlation` (default 100 human genes; `gene_count` controls count)

265- **tissue**: `id`, `min`, `q1`, `median`, `q3`, `max`

266

267---

268

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_symbol, pearson_correlation (default 100 human genes; gene_count controls count)
tissue: id, min, q1, median, q3, max

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269### gget cellxgene

270Query CZ CELLxGENE Discover Census for single-cell data.

271

272**Setup:** Requires `gget setup cellxgene`

273

274**Parameters:**

276|-----------|------|-------------|---------|

286

287**Additional filters:** disease, development_stage, sex, assay, dataset_id, donor_id, self_reported_ethnicity, suspension_type

288

289**Important:** Gene symbols are case-sensitive ('PAX7' for human, 'Pax7' for mouse)

290

291**Returns:** AnnData with raw counts; `meta_only=True` instead returns a DataFrame of cells and ignores gene filters. Pin a dated Census version and constrain observation filters.

292

293---

294

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; not applied in metadata-only mode)	None (all genes)
`--tissue`	list	Tissue type(s)	None
`--cell_type`	list	Cell type(s)	None
`--species` (-s)	str	homo_sapiens, mus_musculus, macaca_mulatta, callithrix_jacchus, pan_troglodytes	'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, self_reported_ethnicity, suspension_type

Important: Gene symbols are case-sensitive ('PAX7' for human, 'Pax7' for mouse)

Returns: AnnData with raw counts; meta_only=True instead returns a DataFrame of cells and ignores gene filters. Pin a dated Census version and constrain observation filters.

Raw lines 269 to 294

295### gget enrichr

296Perform enrichment analysis using Enrichr/modEnrichr.

297

298**Parameters:**

300|-----------|------|-------------|---------|

307

308**Python-only:**

309- `plot` (bool): Generate graphical results

310

311**Database shortcuts:**

312- 'pathway' → KEGG_2021_Human

313- 'transcription' → ChEA_2016

314- 'ontology' → GO_Biological_Process_2021

315- 'diseases_drugs' → GWAS_Catalog_2019

316- 'celltypes' → PanglaoDB_Augmented_2021

317- 'kinase_interactions' → KEA_2015

318

319Shortcuts apply to human/mouse only. Other species need their full library names; custom backgrounds are human/mouse only. Ensembl background IDs also require `ensembl_bkg=True`.

320

321**Returns:** DataFrame with `path_name`, `p_val`, `adj_p_val`, `overlapping_genes` (gene lists), `database`, and scores; no automatic significance threshold.

322

323---

324

gget enrichr

Perform enrichment analysis using Enrichr/modEnrichr.

Parameters:

Parameter	Type	Description	Default
`genes`	list	Gene symbols, or Ensembl IDs with `ensembl=True`	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
'kinase_interactions' → KEA_2015

Shortcuts apply to human/mouse only. Other species need their full library names; custom backgrounds are human/mouse only. Ensembl background IDs also require ensembl_bkg=True.

Returns: DataFrame with path_name, p_val, adj_p_val, overlapping_genes (gene lists), database, and scores; no automatic significance threshold.

Raw lines 295 to 324

325### gget bgee

326Retrieve orthology and expression from Bgee.

327

328**Parameters:**

330|-----------|------|-------------|---------|

336

337**Note:** Multiple IDs supported when `type='expression'`

338

339**Returns:**

340- **orthologs**: Genes across species with IDs, names, taxonomic info

341- **expression**: Anatomical entities, confidence scores, expression status

342

343---

344

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

Raw lines 325 to 344

345### gget opentargets

346Retrieve disease/drug associations from OpenTargets.

347

348**Parameters:**

350|-----------|------|-------------|---------|

356| Filter combination | AND | Python dict / repeated CLI --filter | AND |

359

360**Current notes:**

361- gget 0.30.8 returns dot-separated columns, including `disease.name`, `score`, `drug.name`, and `drug.maximumClinicalStage`.

362- Expression is `baselineExpression`: `median/min/q1/q3/max/unit` and `tissueBiosample.*`/`celltypeBiosample.*`.

363- Filters apply locally after limit. Expression fetches one page (max 3000); diseases/drugs/interactions use server default pages. `limit=None` does not make a complete export.

364- The older `--filter_mode` argument was removed upstream. The released CLI also has no `--or`; implement an explicit pandas OR mask after retrieval if needed.

365- Prefer inspecting returned column names before writing filters, then filter with exact column names such as `intA` or `targetB.id`.

366

367**Returns:** Disease/drug associations, tractability, pharmacogenetics, expression, DepMap, interactions

368

369---

370

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
`--filter`	repeated key=value / dict	Exact-match filters using returned column names	None
Filter combination	AND	Python dict / repeated CLI --filter	AND
`-csv`	flag	CSV format (CLI)	False
`-q/--quiet`	flag	Suppress progress	False

Current notes:

gget 0.30.8 returns dot-separated columns, including disease.name, score, drug.name, and drug.maximumClinicalStage.
Expression is baselineExpression: median/min/q1/q3/max/unit and tissueBiosample.*/celltypeBiosample.*.
Filters apply locally after limit. Expression fetches one page (max 3000); diseases/drugs/interactions use server default pages. limit=None does not make a complete export.
The older --filter_mode argument was removed upstream. The released CLI also has no --or; implement an explicit pandas OR mask after retrieval if needed.
Prefer inspecting returned column names before writing filters, then filter with exact column names such as intA or targetB.id.

Returns: Disease/drug associations, tractability, pharmacogenetics, expression, DepMap, interactions

Raw lines 345 to 370

371### gget cbio

372Plot cancer genomics heatmaps from cBioPortal.

373

374**Setup:** `gget setup cbio` installs optional dependencies.

375

376**Subcommands:** search, plot

377

378**search parameters:**

380|-----------|------|-------------|---------|

382

383**plot parameters:**

385|-----------|------|-------------|---------|

394| `-dpi` | int | Resolution | 100 |

398

399**Returns:** PNG heatmap figure

400

401---

402

gget cbio

Plot cancer genomics heatmaps from cBioPortal.

Setup: gget setup cbio installs optional dependencies.

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	tissue
`-vt/--variation_type`	str	mutation_occurrences, cna_nonbinary, sv_occurrences, cna_occurrences, Consequence	mutation_occurrences
`-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

Raw lines 371 to 402

403### gget cosmic

404Search COSMIC database for cancer mutations.

405

406**Important:** License fees for commercial use. Requires COSMIC account. Avoid passing credentials directly on the command line on shared systems; prefer the interactive prompt or Python code that reads named environment variables.

407

408**Query parameters:**

410|-----------|------|-------------|---------|

413| `-l/--limit` | int | Maximum results | 100 |

415

416**Download parameters:**

418|-----------|------|-------------|---------|

423| `-gv/--grch_version` | int | Human reference genome (37 or 38) | 37 |

426

427**Note:** First-time users must download database

428

429**Returns:** Mutation data from COSMIC

430

431---

432

gget cosmic

Search COSMIC database for cancer mutations.

Important: License fees for commercial use. Requires COSMIC account. Avoid passing credentials directly on the command line on shared systems; prefer the interactive prompt or Python code that reads named environment variables.

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, cancer_example, census, cell_line, resistance, genome_screen, targeted_screen	cancer
`-cv/--cosmic_version`	str	COSMIC version	Latest
`-gv/--grch_version`	int	Human reference genome (37 or 38)	37
`--email`	str	COSMIC account email for non-interactive download	Prompt/env preferred
`--password`	str	COSMIC account password for non-interactive download	Prompt/env preferred

Note: First-time users must download database

Returns: Mutation data from COSMIC

Raw lines 403 to 432

433### gget virus

434Download viral nucleotide sequences and metadata from INSDC sources via NCBI Virus.

435

436**Parameters:**

438|-----------|------|-------------|---------|

454

455**Warning:** `--download_all_accessions` without restrictive filters can request the entire Viruses taxonomy and require many hours and substantial disk.

456

457**Returns:** FASTA, CSV, JSONL, optional GenBank metadata, and `command_summary.txt` in an output folder.

458

459---

460

gget virus

Download viral nucleotide sequences and metadata from INSDC sources via NCBI Virus.

Parameters:

Parameter	Type	Description	Default
`virus`	str	Virus taxon name, taxon ID, accession(s), or accession text file	Required unless `--download_all_accessions`
`-a/--is_accession`	flag	Treat `virus` as accession input	False
`--is_sars_cov2`	flag	Use optimized SARS-CoV-2 cached data path	False
`--is_alphainfluenza`	flag	Use optimized Influenza A cached data path	False
`--host`	str	Host organism name or NCBI Taxonomy ID	None
`--nuc_completeness`	str	complete or partial	None
`--min_seq_length` / `--max_seq_length`	int	Sequence length filters	None
`--segment`	str	Segment filter for segmented viruses	None
`--source_database`	str	genbank or refseq	None
`--annotated`	bool	Include/exclude annotated sequences	None
`--vaccine_strain`	bool	Include/exclude vaccine strain sequences	None
`-g/--genbank_metadata`	flag	Fetch detailed GenBank metadata	False
`--download_all_accessions`	flag	Apply filters across all viral accessions	False
`--baseline` / `--merge-results`	path/flag	Resume or merge with previous metadata; Python baseline_metadata/merge_results	None/True
`-q/--quiet`	flag	Suppress progress	False

Warning: --download_all_accessions without restrictive filters can request the entire Viruses taxonomy and require many hours and substantial disk.

Returns: FASTA, CSV, JSONL, optional GenBank metadata, and command_summary.txt in an output folder.

Raw lines 433 to 460

461### gget 8cube

462Query 8cubeDB mouse snRNA-seq specificity and expression metrics.

463

464**Subcommands:**

465| Subcommand | Description | Required arguments |

466|------------|-------------|--------------------|

467| `specificity` | Gene-level psi/zeta specificity values | `genes` |

468| `psi_block` | Block-level specificity values | `genes`, `--analysis_level`, `--analysis_type` |

469| `expression` | Mean/variance normalized expression values | `genes`, `--analysis_level`, `--analysis_type` |

470

471**Common parameters:**

473|-----------|------|-------------|---------|

480

481**Returns:** JSON/CSV on the CLI or DataFrame/JSON in Python.

482

483---

484

gget 8cube

Query 8cubeDB mouse snRNA-seq specificity and expression metrics.

Subcommands:

Subcommand	Description	Required arguments
`specificity`	Gene-level psi/zeta specificity values	`genes`
`psi_block`	Block-level specificity values	`genes`, `--analysis_level`, `--analysis_type`
`expression`	Mean/variance normalized expression values	`genes`, `--analysis_level`, `--analysis_type`

Common parameters:

Parameter	Type	Description	Default
`genes`	str/list	Gene symbols or Ensembl gene IDs	Required
`-al/--analysis_level`	str	Biological grouping such as Kidney or Across_tissues	Required for psi_block/expression
`-at/--analysis_type`	str	Partition type such as Sex:Celltype or Strain	Required for psi_block/expression
`-csv/--csv`	flag	Return CSV instead of JSON (CLI)	False
`-o/--out`	str	Output file path	None
`-q/--quiet`	flag	Suppress progress	False

Returns: JSON/CSV on the CLI or DataFrame/JSON in Python.

Raw lines 461 to 484

485## Additional Tools

486

Additional Tools

Raw lines 485 to 486

487### gget mutate

488Generate mutated nucleotide sequences.

489

490**Parameters:**

492|-----------|------|-------------|---------|

498| `-k/--k` | int | Length of flanking sequences | 30 |

501

502**Returns:** List of mutated sequence strings in Python; `out` writes FASTA

503

504**Note:** More complex variant-screening functionality moved upstream to the `kvar` project.

505

506---

507

gget mutate

Generate mutated nucleotide sequences.

Parameters:

Parameter	Type	Description	Default
`sequences`	str/list	FASTA file or nucleotide sequence(s)	Required
`-m/--mutations`	str/list/df	Mutation string/list, 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	Same as mut_column
`-k/--k`	int	Length of flanking sequences	30
`-o/--out`	str	Output FASTA file path	None (return list/stdout)
`-q/--quiet`	flag	Suppress progress	False

Returns: List of mutated sequence strings in Python; out writes FASTA

Note: More complex variant-screening functionality moved upstream to the kvar project.

Raw lines 487 to 507

508### gget gpt

509Legacy OpenAI wrapper; deprecated and no longer actively maintained since 0.30.7.

510

511**Setup:** Requires `gget setup gpt` and OpenAI API key

512

513**Parameters:**

515|-----------|------|-------------|---------|

521| `max_tokens` | int | Maximum tokens to generate | 200 |

526

527**Important:** This wrapper calls legacy `openai.ChatCompletion.create` and is incompatible with the modern OpenAI Python interface. Do not hard-code API keys or pass real keys in examples. The upstream CLI accepts a key argument; Python code that reads `OPENAI_API_KEY` is safer for notebooks and scripts.

528

529**Returns:** Generated text string

530

531---

532

gget gpt

Legacy OpenAI wrapper; deprecated and no longer actively maintained since 0.30.7.

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; prefer reading from `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	200
`frequency_penalty`	float	Frequency penalty (-2 to 2)	0
`presence_penalty`	float	Presence penalty (-2 to 2)	0
`stop`	str	Stop sequence	None
`logit_bias`	dict	Token bias map	None

Important: This wrapper calls legacy openai.ChatCompletion.create and is incompatible with the modern OpenAI Python interface. Do not hard-code API keys or pass real keys in examples. The upstream CLI accepts a key argument; Python code that reads OPENAI_API_KEY is safer for notebooks and scripts.

Returns: Generated text string

Raw lines 508 to 532

533### gget setup

534Install/download dependencies for modules.

535

536**Parameters:**

538|-----------|------|-------------|---------|

542

543**Modules requiring setup:**

544- `alphafold` - Downloads ~4GB model parameters

545- `cbio` - Installs optional cBioPortal dependencies (bravado)

546- `cellxgene` - Installs cellxgene-census