Crate pilercr_parser

Parses the output produced by PILER-CR (https://www.drive5.com/pilercr/), a CRISPR array annotation tool.

PILER-CR v1.06 (at least) reports incorrect coordinates if any of the repeat sequences contains gaps. This parses will correct those errors, and also determines the actual repeat sequence of each repeat-spacer (which is given only as a difference pattern to the consensus in the PILER-CR output).

Example

use std::fs::File;
use std::io::{BufReader, Read};

let file = File::open("examples/example.txt").unwrap();
let mut reader = BufReader::new(file);
let mut input = String::new();
reader.read_to_string(&mut input).unwrap();
let arrays = pilercr_parser::parse(&input).unwrap();
for array in arrays {
    println!(
        "{} has {} arrays",
        array.accession,
        array.repeat_spacers.len()
    );
}

Structs

Array

A single CRISPR array.

RepeatSpacer

A single repeat-spacer.

Functions

parse

Parses the output of PILER-CR for a single contig/genome.