For a related bioinformatics resource and walkthough: Bioinformatics in Rust
Bioutils provides simple biological utilities including:
Pull requests and suggestions for improvement always welcome!
| utils | Sequence checks / find sequences, subsequence cuts and edits, pseudorandom replacement of N or gaps, functions to create new pseudorandom sequences |
| charsets | IUPAC character sets to either use directly or create your own mix and match. |
| files | Download fastq sample files with curl using a url. See step 2 download files example in bioutils/examples. |
| references | Currently includes human NCBI gencode GRCh38. Automatically downloads the latest version of user's choice. See step 2 download files example in bioutils/examples. |
| image | Create images from biological data. Includes common colors and color names (port from colorbrewers) for ease of use with rust Image. See Image example in bioutils/examples. |
//! // Downloading reference files //! // Download grch38 fasta gz and gtf gz to current directory //! let path = Path::new("./"); //! download_grch38_primary_assembly_genome_fa_gz(&path); //! download_gencode_vxx_primary_assembly_annotation_gtf_gz(&path); //! //! // Download files through http //! let fastq_ftp = "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR170/009/SRR1700869/"; //! let fastq_gz = "SRR1700869.fastq.gz"; //! let out_directory = Path::new("./") //! bioutils::files::http::curl(fastq_ftp, fastq_gz, &out_directory); //! //! // 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()); //! //! // 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);