gget

What this skill does

# gget

## Overview

gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, expression data, and disease associations through a consistent interface. All gget modules work both as command-line tools and as Python functions.

**Important**: The databases queried by gget are continuously updated, which sometimes changes their structure. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary.

## Installation

Install gget in a clean virtual environment to avoid conflicts:

```bash
# Using uv (recommended)
uv uv pip install gget

# Or using pip
uv pip install --upgrade gget

# In Python/Jupyter
import gget
```

## Quick Start

Basic usage pattern for all modules:

```bash
# Command-line
gget <module> [arguments] [options]

# Python
gget.module(arguments, options)
```

Most modules return:
- **Command-line**: JSON (default) or CSV with `-csv` flag
- **Python**: DataFrame or dictionary

Common flags across modules:
- `-o/--out`: Save results to file
- `-q/--quiet`: Suppress progress information
- `-csv`: Return CSV format (command-line only)

## Module Categories

### 1. Reference & Gene Information

#### gget ref - Reference Genome Downloads

Retrieve download links and metadata for Ensembl reference genomes.

**Parameters**:
- `species`: Genus_species format (e.g., 'homo_sapiens', 'mus_musculus'). Shortcuts: 'human', 'mouse'
- `-w/--which`: Specify return types (gtf, cdna, dna, cds, cdrna, pep). Default: all
- `-r/--release`: Ensembl release number (default: latest)
- `-l/--list_species`: List available vertebrate species
- `-liv/--list_iv_species`: List available invertebrate species
- `-ftp`: Return only FTP links
- `-d/--download`: Download files (requires curl)

**Examples**:
```bash
# 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
# Python
gget.ref("homo_sapiens")
gget.ref("mus_musculus", which="gtf", download=True)
```

#### gget search - Gene Search

Locate genes by name or description across species.

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

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

**Examples**:
```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 or translated DNA alignment using DIAMOND.

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

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

**Examples**:
```bash
# 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
# Python
gget.diamond("GGETISAWESQME", reference="reference.fasta", threads=4)
```

### 3. Structural & Protein Analysis

#### gget pdb - Protein Structures

Query RCSB Protein Data Bank for structure and metadata.

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

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

**Examples**:
```bash
# Download PDB structure
gget pdb 7S7U -o 7S7U.pdb

# Get metadata
gget pdb 7S7U -r entry
```

```python
# Python
gget.pdb("7S7U", sav