antisequence_sciseq3.rs

gistfile1.txt

use antisequence::*;

fn main() {
    // 1{b[9-10]f[CAGAGC]u[8]b[10]}2{r:}
    let patterns = r#"
        name: anchor 
        patterns:
            - pattern: "CAGAGC"
    "#;

    iter_fastq1("example_data/sciseq3_r1.fastq", 256)
        .unwrap_or_else(|e| panic!("{e}"))
        .match_any(
            sel!(),
            tr!(seq1.* -> seq1.barcode1, seq1.anchor, seq1.rest),
            patterns,
            LocalAln {
                identity: 0.83,
                overlap: 1.0,
            },
        )
        .retain(sel!(seq1.anchor))
        .cut(
            sel!(),
            tr!(seq1.rest -> seq1.umi, seq1.tail1),
            LeftEnd(8)
        )
        .cut(
            sel!(),
            tr!(seq1.tail1 -> seq1.barcode2, seq1.junk),
            LeftEnd(10)
        )
        .dbg(sel!())
        .run()
        .unwrap_or_else(|e| panic!("{e}"));
}