@pikaa-ai/pikaa 0.3.1 → 0.3.4

package/skills/gget/references/module_catalog.md

@@ -1,733 +0,0 @@
-# gget Module Catalog
-
-Every module by category, with its parameters and both command-line and Python examples.
-This is the usage-oriented cut; see `module_reference.md` for the fuller per-parameter
-reference and `database_info.md` for the underlying data sources.
-
-## 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 as comma-separated CLI values or Python list (gtf, cdna, dna, cds, cdrna, pep). Default: all
-- `-r/--release`: Ensembl release number (default: latest)
-- `-od/--out_dir`: Directory for downloaded files
-- `-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**:
-```bash
-# List available species
-gget ref --list_species
-
-# Get all reference files for human
-gget ref homo_sapiens
-
-# Download GTF and cDNA files for mouse
-gget ref -w gtf,cdna -d mouse
-```
-
-```python
-# Python
-gget.ref("homo_sapiens")
-gget.ref("mus_musculus", which=["gtf", "cdna"], download=True)
-```
-
-#### gget search - Gene Search
-
-Locate genes by name, description, and Ensembl synonyms 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
-- `wrap_text`: Python-only display helper for wide DataFrames
-
-**Returns**: ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, URL
-
-**Examples**:
-```bash
-# 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
-# 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**:
-```bash
-# Get info for multiple genes
-gget info ENSG00000034713 ENSG00000104853 ENSG00000170296
-
-# Include PDB IDs
-gget info ENSG00000034713 -pdb
-```
-
-```python
-# 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**:
-```bash
-# Get nucleotide sequences
-gget seq ENSG00000034713 ENSG00000104853
-
-# Get all protein isoforms
-gget seq -t -iso ENSG00000034713
-```
-
-```python
-# 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**:
-```bash
-# BLAST protein sequence
-gget blast MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR
-
-# BLAST from file with specific database
-gget blast sequence.fasta -db swissprot -l 10
-```
-
-```python
-# 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**:
-```bash
-# Find genomic location in human
-gget blat ATCGATCGATCGATCG
-
-# Search in different assembly
-gget blat -a mm39 ATCGATCGATCGATCG
-```
-
-```python
-# 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**:
-```bash
-# Align sequences from file
-gget muscle sequences.fasta -o aligned.afa
-
-# Use Super5 for large dataset
-gget muscle large_dataset.fasta -s5
-```
-
-```python
-# Python
-gget.muscle("sequences.fasta", save=True)
-```
-
-#### gget diamond - Local Sequence Alignment
-
-Perform fast local protein alignment or translated nucleotide-to-protein alignment using DIAMOND.
-
-**Parameters**:
-- Query: Sequences (string/list) or FASTA file path
-- `-ref/--reference`: Reference sequences (string/list) or FASTA file path (required)
-- `-s/--sensitivity`: fast, mid-sensitive, sensitive, more-sensitive, very-sensitive (default), ultra-sensitive
-- `-t/--threads`: CPU threads (default: 1)
-- `-db/--diamond_db`: Save database for reuse
-- `-x/--translated`: Enable nucleotide query to amino acid reference alignment
-
-**Returns**: Identity percentage, sequence lengths, match positions, gap openings, E-values, bit scores
-
-**Examples**:
-```bash
-# Align against reference
-gget diamond GGETISAWESQME -ref reference.fasta -t 4
-
-# Translate nucleotide query against amino acid reference
-gget diamond query_nt.fasta -ref proteins.fasta --translated
-```
-
-```python
-# Python
-gget.diamond("GGETISAWESQME", reference="reference.fasta", threads=4)
-gget.diamond("ATGGGC...", reference="proteins.fasta", translated=True)
-```
-
-### 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**:
-```bash
-# Download PDB structure
-gget pdb 7S7U -o 7S7U.pdb
-
-# Get metadata
-gget pdb 7S7U -r entry
-```
-
-```python
-# Python
-gget.pdb("7S7U", save=True)
-```
-
-#### gget alphafold - Protein Structure Prediction
-
-Predict 3D protein structures using simplified AlphaFold2.
-
-**Setup Required**:
-```bash
-# Installs modified third-party dependencies and downloads model parameters
-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**:
-```bash
-# Predict single protein structure
-gget alphafold MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR
-
-# Predict multimer with higher accuracy
-gget alphafold sequence1.fasta -mr 20 -r
-```
-
-```python
-# 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**:
-```bash
-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**:
-```bash
-# Predict motifs from sequence
-gget elm LIAQSIGQASFV -o results
-
-# Use UniProt accession with expanded info
-gget elm --uniprot Q02410 -e
-```
-
-```python
-# 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**:
-```bash
-# Get correlated genes
-gget archs4 ACE2
-
-# Get tissue expression
-gget archs4 -w tissue ACE2
-```
-
-```python
-# Python
-gget.archs4("ACE2", which="tissue")
-```
-
-#### gget cellxgene - Single-Cell RNA-seq Data
-
-Query CZ CELLxGENE Discover Census for single-cell data.
-
-**Setup Required**:
-```bash
-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**:
-```bash
-# 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
-# Python
-adata = gget.cellxgene(gene=["ACE2", "ABCA1"], tissue="lung", cell_type="mucus secreting cell")
-```
-
-#### gget enrichr - Enrichment Analysis
-
-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 genes
-- `plot`: Python-only; 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
-
-**Examples**:
-```bash
-# 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
-# Python with plot
-gget.enrichr(["ACE2", "AGT", "AGTR1"], database="ontology", plot=True)
-```
-
-#### gget bgee - Orthology & Expression
-
-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**:
-- **Orthologs mode**: Matching genes across species with IDs, names, taxonomic info
-- **Expression mode**: Anatomical entities, confidence scores, expression status
-
-**Examples**:
-```bash
-# Get orthologs
-gget bgee ENSG00000169194
-
-# Get expression data
-gget bgee ENSG00000169194 -t expression
-
-# Multiple genes
-gget bgee ENSBTAG00000047356 ENSBTAG00000018317 -t expression
-```
-
-```python
-# Python
-gget.bgee("ENSG00000169194", type="orthologs")
-```
-
-#### gget opentargets - Disease & Drug Associations
-
-Retrieve disease and drug associations from OpenTargets.
-
-**Parameters**:
-- Ensembl gene ID (required)
-- `-r/--resource`: diseases (default), drugs, tractability, pharmacogenetics, expression, depmap, interactions
-- `-l/--limit`: Cap results count
-- `--filters`: Exact-match filters using returned OpenTargets column names; repeat on the CLI or pass a Python dict
-- `-or/--or`: CLI-only; combine filters with OR logic instead of the default AND logic
-
-**Current notes**:
-- gget 0.30.5 rewrote this module for the newer OpenTargets API; some output column names differ from older releases.
-- The older `--filter_mode` argument was removed upstream.
-
-**Examples**:
-```bash
-# Get associated diseases
-gget opentargets ENSG00000169194 -r diseases -l 5
-
-# Get associated drugs
-gget opentargets ENSG00000169194 -r drugs -l 10
-
-# Filter interactions by returned column names
-gget opentargets ENSG00000169194 -r interactions --filters protein_a_id=P35225 --filters gene_b_id=ENSG00000077238
-```
-
-```python
-# Python
-gget.opentargets("ENSG00000169194", resource="diseases", limit=5)
-gget.opentargets(
-    "ENSG00000169194",
-    resource="interactions",
-    filters={"protein_a_id": "P35225", "gene_b_id": "ENSG00000077238"},
-)
-```
-
-#### gget cbio - cBioPortal Cancer Genomics
-
-Plot cancer genomics heatmaps using cBioPortal data.
-
-**Two subcommands**:
-
-**search** - Find study IDs:
-```bash
-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 window
-- `-nc/--no_confirm`: Skip download confirmations
-
-**Examples**:
-```bash
-# 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
-# Python
-gget.cbio_search(["esophag", "ovary"])
-gget.cbio_plot(["msk_impact_2017"], ["AKT1", "ALK"], stratification="tissue")
-```
-
-#### gget cosmic - COSMIC Database
-
-Search COSMIC (Catalogue Of Somatic Mutations In Cancer) database.
-
-**Important**: License fees apply for commercial use. Requires COSMIC account credentials.
-Avoid passing COSMIC credentials directly as CLI arguments on shared systems because command-line arguments can be exposed in shell history, process listings, and logs. Prefer the interactive prompt (`gget cosmic --download_cosmic ...`) or named environment variables read inside Python.
-
-**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, cancer_example, 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 credentials for non-interactive downloads; prefer prompt or Python env vars
-
-**Examples**:
-```bash
-# First download database; gget prompts for COSMIC email/password
-gget cosmic --download_cosmic --cosmic_project cancer
-
-# Then query
-gget cosmic EGFR --cosmic_tsv_path "CancerMutationCensus_AllData_Tsv_v101_GRCh37/CancerMutationCensus_AllData_v101_GRCh37.tsv" -l 10
-```
-
-```python
-# Python
-import os
-
-gget.cosmic(
-    searchterm=None,
-    download_cosmic=True,
-    cosmic_project="cancer",
-    email=os.environ["COSMIC_EMAIL"],
-    password=os.environ["COSMIC_PASSWORD"],
-)
-gget.cosmic("EGFR", cosmic_tsv_path="cosmic_data.tsv", limit=10)
-```
-
-### 5. Viral & Mouse Specificity Data
-
-#### gget virus - Viral Sequence Downloads
-
-Download viral nucleotide sequences plus linked metadata from INSDC sources via NCBI Virus, with optional GenBank metadata enrichment. Results are saved to an output folder as FASTA, CSV, JSONL, and a command summary file.
-
-**Parameters**:
-- `virus`: Virus taxon name, taxon ID, accession, space-separated accessions, or path to a text file of accessions
-- `-a/--is_accession`: Treat `virus` as accession input
-- `--is_sars_cov2`, `--is_alphainfluenza`: Use optimized cached NCBI datasets paths for SARS-CoV-2 or Influenza A
-- `--host`: Host organism name or NCBI taxonomy ID
-- `--nuc_completeness`: complete or partial
-- `--min_seq_length`, `--max_seq_length`: Sequence length filters
-- `-g/--genbank_metadata`: Fetch detailed GenBank metadata; auto-enabled by some annotation filters
-- `--segment`, `--vaccine_strain`, `--annotated`, `--lab_passaged`, `--source_database`: Common viral metadata filters
-- `--download_all_accessions`: Apply filters across all viral accessions
-- `--baseline`, `--merge-results`: Resume or merge with prior metadata from partial/previous runs
-
-**Important**: Do not use `--download_all_accessions` without restrictive filters; it can attempt to download the entire Viruses taxonomy and consume substantial time, bandwidth, and disk.
-
-**Examples**:
-```bash
-# Complete Zika genomes from human hosts
-gget virus "Zika virus" --nuc_completeness complete --host human --out zika_data
-
-# SARS-CoV-2 reference genome by accession
-gget virus NC_045512.2 --is_accession --is_sars_cov2
-```
-
-```python
-# Python
-gget.virus(
-    "SARS-CoV-2",
-    host="human",
-    nuc_completeness="complete",
-    min_seq_length=29000,
-    genbank_metadata=True,
-    is_sars_cov2=True,
-    outfolder="covid_data",
-)
-```
-
-#### gget 8cube - Mouse Specificity & Expression
-
-Query 8cubeDB for snRNA-seq gene specificity metrics and normalized expression values across mouse strains, tissues, sexes, and individuals.
-
-**Subcommands**:
-- `gget 8cube specificity <genes...>`: Return gene-level psi/zeta specificity statistics
-- `gget 8cube psi_block <genes...> --analysis_level <level> --analysis_type <type>`: Return block-level specificity
-- `gget 8cube expression <genes...> --analysis_level <level> --analysis_type <type>`: Return mean/variance normalized expression
-
-**Examples**:
-```bash
-gget 8cube specificity Acsm2 ENSMUSG00000046623.9
-gget 8cube psi_block Acsm2 --analysis_level Kidney --analysis_type "Sex:Celltype"
-gget 8cube expression Gjb4 --analysis_level Across_tissues --analysis_type Strain
-```
-
-```python
-# Python
-from gget import specificity, psi_block, gene_expression
-
-specificity(["Acsm2", "ENSMUSG00000046623.9"])
-psi_block(["Acsm2"], analysis_level="Kidney", analysis_type="Sex:Celltype")
-gene_expression(["Gjb4"], analysis_level="Across_tissues", analysis_type="Strain")
-```
-
-### 6. Additional Tools
-
-#### gget mutate - Generate Mutated Sequences
-
-Generate mutated nucleotide sequences from mutation annotations.
-
-**Current scope**: gget 0.29.1 simplified `mutate` to focus on applying standard mutation annotations to supplied nucleotide sequences and returning/saving mutated FASTA records. The broader variant-screening workflow moved upstream to the `kvar` project.
-
-**Parameters**:
-- `sequences`: FASTA file path or direct nucleotide sequence input (string/list)
-- `-m/--mutations`: Mutation string/list, CSV/TSV path, 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 (default: same as mut_column)
-- `-k/--k`: Length of flanking sequences (default: 30 nucleotides)
-- `-o/--out`: Output FASTA path; without it Python returns a list of mutated sequences
-
-**Returns**: Mutated sequences in FASTA format
-
-**Examples**:
-```bash
-# Single mutation
-gget mutate ATCGCTAAGCT -m "c.4G>T"
-
-# Multiple sequences with one mutation per sequence
-gget mutate ATCGCTAAGCT TAGCTA -m "c.4G>T" "c.1_3inv" -o mutated.fasta
-```
-
-```python
-# Python
-gget.mutate("ATCGCTAAGCT", "c.4G>T")
-gget.mutate(["ATCGCTAAGCT", "TAGCTA"], ["c.4G>T", "c.1_3inv"], out="mutated.fasta")
-```
-
-#### gget gpt - OpenAI Text Generation
-
-Generate natural language text using OpenAI's API.
-
-**Setup Required**:
-```bash
-gget setup gpt
-```
-
-**Important**: Requires an OpenAI API key. Do not hard-code the key in notebooks, scripts, shell history, or committed files. Prefer a named environment variable such as `OPENAI_API_KEY`, and set monthly billing limits before use.
-
-**Parameters**:
-- `prompt`: Text input for generation (required)
-- `api_key`: OpenAI authentication (required by the upstream API)
-- Model configuration: model, temperature, top_p, stop, max_tokens, frequency_penalty, presence_penalty, logit_bias
-- Default model: gpt-3.5-turbo (upstream default; verify available models in your OpenAI account)
-
-**Examples**:
-For CLI usage, `gget gpt` expects the API key as an argument. Avoid this on shared systems because process arguments can be visible to other users.
-
-```python
-# Python
-import os
-
-gget.gpt("Explain CRISPR", api_key=os.environ["OPENAI_API_KEY"])
-```
-
-#### gget setup - Install Dependencies
-
-Install/download third-party dependencies for specific modules.
-
-As of gget 0.29.2, `gget setup` tries `uv pip install` first for Python dependencies and falls back to plain `pip install` if uv is unavailable or fails.
-
-**Parameters**:
-- `module`: Module name requiring dependency installation
-- `-o/--out`: Output folder path (elm module only)
-
-**Modules requiring setup**:
-- `alphafold` - Downloads ~4GB of model parameters
-- `cellxgene` - Installs cellxgene-census (may require Python 3.9/3.10 if the latest Python is unsupported)
-- `elm` - Downloads local ELM database
-- `gpt` - Installs/configures OpenAI integration dependencies
-
-**Examples**:
-```bash
-# Setup AlphaFold
-gget setup alphafold
-
-# Setup ELM with custom directory
-gget setup elm -o /path/to/elm_data
-```
-
-```python
-# Python
-gget.setup("alphafold")
-```