# Bioutils
<h2 id="quick-start" class="section-header"><a href="#quick-start">Simple Biological Utilities in Rust</a></h2>
<p>Bioutils provides simple biological utilities including:
<ul> Functions to create new random IUPAC sequences</ul>
<ul> Functions to download human and mouse Gencode reference files</ul>
<ul> Common genomic sequences (PhiX and ERCC) </ul>
<ul> Functions to download fastq files</ul>
<ul> Functions to replace N or gaps with pseudorandom nucleotides</ul>
<ul> Functions to check sequence validity and content (palindromes too!)</ul>
<ul>complete iupac and quality character sets</ul>
</p>
<p> Pull requests welcome, suggestions for improvement always welcome!</p>
</p></pre></div>
</div><h2 id='modules' class='section-header'><a href="#modules">Modules</a></h2>
<table><tr class='module-item'><td><a class="mod" href="charsets/index.html" title='bioutils::charsets mod'>charsets</a></td><td class='docblock-short'><p>Numerous IUPAC character sets to either use directly or create your own mix and match.</p></td></tr><tr class='module-item'><td><a class="mod" href="files/index.html" title='bioutils::files mod'>files</a></td><td class='docblock-short'><p>Download fastq sample files with curl using a url. See step 2 download files example in bioutils/examples.</p></td></tr><tr class='module-item'><td><a class="mod" href="references/index.html" title='bioutils::references mod'>references</a></td><td class='docblock-short'><p>Currently includes human NCBI gencode GRCh38. Automatically downloads the latest version of user's choice. See step 2 download files example in bioutils/examples.</p>
</td></tr><tr class='module-item'><td><a class="mod" href="utils/index.html" title='bioutils::utils mod'>utils</a></td><td class='docblock-short'><p>Functions for sequence checks, pseudorandom replacement of N or gaps, and functions to create new pseudoranndom sequences.</p></td></tr>
<tr class='module-item'><td><a class="mod" href="charsets/index.html" title='bioutils::charsets mod'>image</a></td><td class='docblock-short'><p>Create images from biological data. See Image example in bioutils/examples.</p></td></tr>
</table></section><section id="search" class="content hidden"></section><section class="footer"></section>
<h2 id="quick-start" class="section-header"><a href="#quick-start">TL;DR</a></h2>
<div class="example-wrap"><pre class="rust rust-example-rendered"><p>
//! // Examples for using checks:
//!
//! use bioutils::charsets;
//! use bioutils::utils;
//! use bioutils::utils::check::value::CheckU8;
//! use bioutils::utils::new::random::random_dna;
//! use bioutils::utils::new::random::random_quality;
//! use bioutils::utils::mutate::random::AsMutRandomU8;
//! use rand::rngs::ThreadRng;
//! use rand::seq::SliceRandom;
//! use std::string::String;
//! use std::str;
//!
//! let dna = b"ACTG";
//! let rna = b"ACUG";
//! let homopolymerN = b"NNNN";
//! let homopolymerA = b"AAAA";
//! let gapna = b"AC-G";
//! let nna = b"ACnG";
//! let quality = b"@ABC";
//!
//! assert!(homopolymerN.is_homopolymer());
//! assert!(homopolymerA.is_homopolymer_not_n());
//! assert!(homopolymerN.is_homopolymer_n());
//!
//! assert!(gapna.has_gap());
//! assert!(nna.has_n());
//! assert!(dna.is_iupac());
//! assert!(rna.is_basic_rna());
//!
//! assert!(quality.is_phred33());
//! assert!(quality.is_phred64());
//! assert!(quality.is_solexa());
//!
//! // Examples for creating a new random sequence and quality
//!
//! let mut rng1 = rand::thread_rng(); // Create a random number generator
//! let dna = random_dna(4,rng1); // Create a random dna sequence
//! let mut rng2 = rand::thread_rng();
//! let quality = random_quality(4,rng2); // Create a random quality string
//! println!("{:?}", dna.to_owned());
//! println!("{:?}", quality.to_owned());
//!
//! // Examples for replacing nucleotides
//!
//! let mut rng3 = rand::thread_rng(); //create a random number generator
//! let mut rng4 = rand::thread_rng(); //create a random number generator
//! let mut seq = b"acugnnnqqq".to_owned(); // or by *: let mut seq = *b"acugnnnqqq";
//! let mut seq = seq.mut_random_replace_non_basic("RNA", rng4).mut_random_replace_n("RNA", rng3).mut_to_upper_basic();
//! let printseq = str::from_utf8(seq).unwrap();
//! println!("{:?}", printseq);