https://github.com/zeqianli/tgv
Terminal Genome Viewer
https://github.com/zeqianli/tgv
bioinformatics genome-viewer ratatui rust
Last synced: 29 days ago
JSON representation
Terminal Genome Viewer
- Host: GitHub
- URL: https://github.com/zeqianli/tgv
- Owner: zeqianli
- License: mit
- Created: 2025-03-20T19:31:46.000Z (about 1 month ago)
- Default Branch: main
- Last Pushed: 2025-03-20T19:41:15.000Z (about 1 month ago)
- Last Synced: 2025-03-20T20:58:33.312Z (about 1 month ago)
- Topics: bioinformatics, genome-viewer, ratatui, rust
- Language: Rust
- Homepage:
- Size: 4.92 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
- Roadmap: ROADMAP.md
Awesome Lists containing this project
- awesome-ratatui - tgv - Explore human genomes in the terminal. (💻 Apps / 🌌 Other)
README
# Terminmal Genome Viewer
*This is a work in progress.*
Light, fast, in terminal, vim motion.
## Installation
### Prerequisites
1. Install Rust:
```bash
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
```
2. Add Rust to your path (or restart your terminal):
```bash
source "$HOME/.cargo/env"
```
### Install TGV
```bash
# Clone the repository
git clone https://github.com/zeqianli/tgv.git
cd tgv
cargo install --path .
```
## Usage
Currently, TGV only supports BAM files (sorted and indexed) for hg19 / hg38 genomes.
```bash
# Help
tgv -h
# Start by a coordinate
tgv sorted.bam -r 12:25398142 -g hg19
# Start at a gene
tgv sorted.bam -r TP53 -g hg19
```
## Key bindings
Quit: `:q`
Normal mode
| Command | Notes | Example |
|---------|-------------|---------|
| `:` | Enter command mode | |
| `h/j/k/l` | Move left / down / up / right | |
| `y/p` | Fast move left / right | |
| `w/b` | Beginning of the next / last exon | |
| `e/ge` | End of the next / last exon | |
| `W/B` | Begining of the next / last gene | |
| `E/gE` | End of the next / last gene | |
| `z/o` | Zoom in / out | |
| `_number_` + `_movement_` | Move by `_number_` steps | `20h`: left by 20 bases; `2z`: Zoom-in twice |
Command mode:
|Command |Notes| Example|
|---------|-------------|---------|
| `:q` | Quit | |
| `:_pos_` | Go to position on same contig | `:1000` |
| `:_contig_:_pos_` | Go to position on specific contig | `:17:7572659` |
| `:_gene_` | Go to `_gene_`.| `:KRAS`|
| `Esc` | Switch to Normal Mode | |
Compare TGV and Vim concepts:
|Command|TGV|Vim|Notes|
|-------|-----|--|--|
|`h/l`|Horizontal movement|Character ||
|`y/p`|Fast horizontal movement|NA|`y/p` do different things in Vim|
|`w/b/e/ge`|Exon|word||
| `W/B/E/gE` | Gene |WORD||
|`j/k/gg/G`|Alignment track|Line||
|`z/o`| Zoom | NA | Note that `o` does a different thing in Vim.|
See `ROADMAP.md` for future key bindings ideas.
# FAQ
- **How to quit TGV?**
[Just like vim :)](https://stackoverflow.com/questions/11828270/how-do-i-exit-vim) Press `Esc` to ensure you're in normal mode, then type `:q` and press Enter.
- **What file formats are supported?**
BAM files (sorted and indexed) for hg19 / hg38 genomes.
Future plans: BED, VCF, S3 BAM files, HTTP BAM files. See `ROADMAP.md`.
- **Where does the reference genome data come from?**
- Reference sequences: [UCSC Genome Browser API](https://genome.ucsc.edu/goldenPath/help/api.html)
- Uses endpoint: `https://api.genome.ucsc.edu/getData/sequence`
- Gene annotations: [UCSC MariaDB](https://genome.ucsc.edu/goldenPath/help/mysql.html)
- Server: `genome-mysql.soe.ucsc.edu`
- Database: `hg19` / `hg38`
- Table: `ncbiRefSeqSelect` (same as IGV's default)