https://github.com/voxelmc/dnalg-gleam
A DNA manipulation library written in Gleam.
https://github.com/voxelmc/dnalg-gleam
biochemistry bioinformatics cli dna gleam
Last synced: 3 months ago
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A DNA manipulation library written in Gleam.
- Host: GitHub
- URL: https://github.com/voxelmc/dnalg-gleam
- Owner: VoxelMC
- License: mit
- Created: 2024-11-05T23:31:37.000Z (11 months ago)
- Default Branch: main
- Last Pushed: 2025-01-13T18:22:34.000Z (9 months ago)
- Last Synced: 2025-07-10T00:20:55.299Z (3 months ago)
- Topics: biochemistry, bioinformatics, cli, dna, gleam
- Language: Gleam
- Homepage:
- Size: 89.8 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Roadmap: ROADMAP.md
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README
# dnalg
DNAlg is a DNA sequence manipulation library. This is my implementation in Gleam.
> For a more portable version of this project, I will rewrite it in Go whenever I choose to learn Go.
## Plans
- Restriction enzyme operations such as
- Simulated digestion
- Counting cut sites
- Silent mutation of cut sites
## Usage
To use `dnalg`, run it in the command line.
The easiest way to use it is by piping in a DNA sequence and pipe the output to a file.
You can also use the -i flag to specify an input file and the -o flag to specify an output file.
```sh
cat input.txt > dnalg [subcommand] > output.txt
```
The input can be a text file, or in FASTA format. I will look at adding support for `.dna` and `.gb` files in the future.
### Subcommands
#### `silent-mutate`
`silent-mutate` will silently mutate any restriction sites within the provided DNA sequence.
- Sends the new DNA sequence to stdout.
```sh
dnalg silent-mutate [-r|--restriction string]
```
## Roadmap
You can find the roadmap for this project here: [ROADMAP.md](ROADMAP.md)
## Contributing
### Running the project
```sh
gleam run # Run the project
gleam test # Run the tests
```
### Adding functionality
- Use the built-in `cli/` module to add subcommands to the CLI command (when it is complete);
- Add new modules according to the flow outlines in the next section.
### Module management
Module structure is as follows:
- `core/` is for primitives and shared functionality;
- `actions/` are abstractions for core for use in commands;
- `commands/` are primary functions which run via the CLI.
This is done to keep the code clean and avoid circular dependencies.
Try to have modules in `actions/` only import from `core/` and `commands/`
only import from `core/` or `actions/` where possible.
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