https://github.com/luispedro/fna2faa.rs
https://github.com/luispedro/fna2faa.rs
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/luispedro/fna2faa.rs
- Owner: luispedro
- License: mit
- Created: 2023-08-18T09:46:24.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2024-04-19T11:55:02.000Z (about 2 years ago)
- Last Synced: 2025-02-13T13:46:47.941Z (over 1 year ago)
- Language: Rust
- Size: 40 KB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: ChangeLog
- License: COPYING.MIT
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README
# Convert nucleotide FASTA to amino acid FASTA
Very fast conversion of nucleotide to amino acids FASTA. Correctly handles ambiguous nucleotides in IUPAC notation (_i.e._, if if all possible underlying nucleotides translate to the same codon, then this codon is output).
## Example
```bash
fna2faa examples/gmsc10.fna > gmsc10.faa
```
## Speed
Compared to the [C++ implementation](https://github.com/luispedro/fna2faa), this is >10x faster. It is even 7x than the C++ version using the same approach that does not support ambiguous nucleotides.
| Test | Rust (this one) | C++ (full) | C++ (no ambiguous) |
| ---------- | ---------------- | ---------- | ------------------ |
| 2.5M genes | 0.85s | 11s32 | 6s37 |
- _Author_: [Luis Pedro Coelho](http://luispedro.org)
- _License_: MIT