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use std::path::PathBuf;

use crate::gfa::gfa::GFAtk;
use crate::load::{load_gfa, load_gfa_stdin};
use crate::utils;
use anyhow::{bail, Result};

/// Print a fasta representation of the sequences in a GFA.
///
/// For example:
/// ```bash
/// gfatk fasta in.gfa > out.fasta
/// ```
pub fn fasta(matches: &clap::ArgMatches) -> Result<()> {
    // read in path and parse gfa
    let gfa_file = matches.get_one::<PathBuf>("GFA");

    let gfa: GFAtk = match gfa_file {
        Some(f) => {
            let ext = f.extension();
            match ext {
                Some(e) => {
                    if e == "gfa" {
                        GFAtk(load_gfa(f)?)
                    } else {
                        bail!("Input is not a GFA.")
                    }
                }
                None => bail!("Could not read file."),
            }
        }
        None => match utils::is_stdin() {
            true => GFAtk(load_gfa_stdin(std::io::stdin().lock())?),
            false => bail!("No input from STDIN. Run `gfatk extract -h` for help."),
        },
    };

    // None here, as we aren't lookiing/care about
    // subgraphs.
    gfa.print_sequences(None)?;

    Ok(())
}