# nucgen
A fast and simple configurable nucleotide generator for testing bioinformatics tools with random fasta and fastq files.
All nucleotides `{A,C,T,G}` are generated randomly with equal probability.
## Installation
```bash
cargo install nucgen
```
## Usage (CLI)
All the options are configurable via the command line.
You can see the available options by running:
```bash
nucgen --help
```
## Examples
Generate 10,000 reads of length 100bp in a FASTQ format and output to stdout:
```bash
nucgen -n 10000 -l 100 -fq
```
Generate a paired-end dataset of 100 reads with R1 length 30 and R2 length 50.
Output as FASTA format and write to files in gzip format.
```bash
nucgen -n 100 -l 30 -L 50 -fa reads_R1.fasta.gz reads_R2.fasta.gz
```
Seed the random number generator with a specific value:
```bash
nucgen -n 100 -l 100 -fq -S 42
```
## Usage (Library)
Add `nucgen` as a dependency in your `Cargo.toml`:
```bash
cargo add nucgen
```
You can use the `Sequence` struct to generate random nucleotide sequences:
```rust
use nucgen::{Sequence, write_fasta};
// Generate a cursor to write the output to
let mut out = Cursor::new(Vec::new());
// Initialize the random number generator
let mut rng = rand::thread_rng();
// Initialize the sequence struct
let mut seq = Sequence::new();
// Generate 100 random nucleotides into the sequence
seq.fill_buffer(&mut rng, 100);
// Write the sequence to the output cursor
write_fasta(&mut out, 0, seq.bytes())?;
// Generate another 100 random nucleotides
seq.fill_buffer(&mut rng, 100);
// Write the second sequence to the output cursor
write_fasta(&mut out, 1, seq.bytes())?;
```