rsomics-tree-tipdist 0.1.0

use std::fs;
use std::io::{BufWriter, Write};
use std::path::PathBuf;

use clap::Parser;
use rsomics_common::{CommonFlags, Result, RsomicsError, Tool, ToolMeta};
use rsomics_help::{Example, FlagSpec, HelpSpec, Origin, Section};
use rsomics_phylo_tree::Tree;

use rsomics_tree_tipdist::tip_tip_distances;

pub const META: ToolMeta = ToolMeta {
    name: env!("CARGO_PKG_NAME"),
    version: env!("CARGO_PKG_VERSION"),
};

#[derive(Parser, Debug)]
#[command(name = "rsomics-tree-tipdist", version, about, long_about = None, disable_help_flag = true)]
pub struct Cli {
    /// Newick tree; reads stdin when "-" or omitted.
    #[arg(default_value = "-")]
    input: PathBuf,

    /// Count branches between tips instead of summing branch lengths.
    #[arg(long, default_value_t = false)]
    count: bool,

    /// Output path; writes stdout when "-".
    #[arg(short = 'o', long, default_value = "-")]
    output: String,

    #[command(flatten)]
    pub common: CommonFlags,
}

impl Tool for Cli {
    fn meta() -> ToolMeta {
        META
    }
    fn common(&self) -> &CommonFlags {
        &self.common
    }

    fn execute(self) -> Result<()> {
        let newick = if self.input.as_os_str() == "-" {
            std::io::read_to_string(std::io::stdin().lock()).map_err(RsomicsError::Io)?
        } else {
            fs::read_to_string(&self.input)
                .map_err(|e| RsomicsError::InvalidInput(format!("{}: {e}", self.input.display())))?
        };
        let tree = Tree::from_newick(&newick)
            .map_err(|e| RsomicsError::InvalidInput(format!("newick parse: {e}")))?;

        let dm = tip_tip_distances(&tree, !self.count)
            .map_err(|e| RsomicsError::InvalidInput(e.to_string()))?;

        let mut out: Box<dyn Write> = if self.output == "-" {
            Box::new(BufWriter::new(std::io::stdout().lock()))
        } else {
            Box::new(BufWriter::new(
                fs::File::create(&self.output).map_err(RsomicsError::Io)?,
            ))
        };
        dm.write_lsmat(&mut out).map_err(RsomicsError::Io)?;
        out.flush().map_err(RsomicsError::Io)
    }
}

pub static HELP: HelpSpec = HelpSpec {
    name: env!("CARGO_PKG_NAME"),
    version: env!("CARGO_PKG_VERSION"),
    tagline: "Patristic tip-to-tip distance matrix from a phylogenetic tree.",
    origin: Some(Origin {
        upstream: "scikit-bio skbio.tree.TreeNode.cophenet / tip_tip_distances",
        upstream_license: "BSD-3-Clause",
        our_license: "MIT OR Apache-2.0",
        paper_doi: Some("10.1186/1471-2148-6-1"),
    }),
    usage_lines: &["[tree.nwk] [-o dm.tsv]"],
    sections: &[Section {
        title: "OPTIONS",
        flags: &[
            FlagSpec {
                short: None,
                long: "count",
                aliases: &[],
                value: None,
                type_hint: None,
                required: false,
                default: Some("false"),
                description: "Count branches between tips instead of summing lengths.",
                why_default: None,
            },
            FlagSpec {
                short: Some('o'),
                long: "output",
                aliases: &[],
                value: Some("<path>"),
                type_hint: Some("path"),
                required: false,
                default: Some("-"),
                description: "Output path (- for stdout).",
                why_default: None,
            },
        ],
    }],
    examples: &[
        Example {
            description: "Cophenetic distance matrix to stdout",
            command: "rsomics-tree-tipdist tree.nwk",
        },
        Example {
            description: "From stdin, branch counts, to a file",
            command: "cat tree.nwk | rsomics-tree-tipdist --count -o dm.tsv",
        },
    ],
    json_result_schema_doc: None,
};

#[cfg(test)]
mod tests {
    use super::*;
    use clap::CommandFactory;

    #[test]
    fn cli_debug_assert() {
        Cli::command().debug_assert();
    }
}