Simple parsing of tabular output from HMMER::nhmmer --tblout ...
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Run this example using cargo run --example print_coordinates ./data/test.tbl
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use hmm_tblout;
fn main() -> Result<(), Box<dyn std::error::Error>> {
// get the command line args, only parse the
// first one which should be a fasta file
let args: Vec<String> = std::env::args().collect();
if args.len() < 2 {
println!("Usage: print_coordinates <tblout_file>");
std::process::exit(1);
}
let reader = hmm_tblout::Reader::from_path(args[1].clone())?;
for record in reader.into_records() {
let r = record?;
let tname = r.target_name();
let strand = r.strand().unwrap();
let alifrom = r.ali_from().unwrap();
let alito = r.ali_to().unwrap();
println!("{}\t{}\t{}\t{}", tname, strand, alifrom, alito);
}
Ok(())
}
May handle these in the future. Or feel free to contribute!
- Does not handle the description column, as this may contain spaces.