Address comments: move out of main.rs; fix CLI help text

src/cli.rs

@@ -394,31 +394,31 @@ pub(crate) enum Command {
     /// Reconstruct a phylogenetic tree given a Phylip distance matrix input file.
     #[structopt(author = "Ragnar Groot Koerkamp <ragnar.grootkoerkamp@gmail.com>")]
     Phylogeny {
-        /// The reconstruction method to use. `UPGMA` and `NeighborJoining`.
-        #[structopt(long = "method")]
+        #[structopt(
+            long = "method",
+            help = "The reconstruction method to use. `UPGMA` or `NeighborJoining`"
+        )]
         method: PhylogenyMethod,
-
-        /// Path of Phylip distance matrix file.
-        #[structopt(parse(from_os_str))]
+        #[structopt(parse(from_os_str), help = "Input Phylip distance matrix file.")]
         input: PathBuf,
-
-        /// Path to store the phylogeny in Newick format, or stdout otherwise.
-        #[structopt(parse(from_os_str))]
+        #[structopt(
+            parse(from_os_str),
+            help = "Optional output Newick file. Stdout by default."
+        )]
         output: Option<PathBuf>,
     },
 
     /// Compute the Robinson-Foulds distance between two phylogenetic trees.
     #[structopt(author = "Ragnar Groot Koerkamp <ragnar.grootkoerkamp@gmail.com>")]
     RobinsonFoulds {
-        /// The path of the first phylogeny in Newick format.
-        #[structopt(parse(from_os_str))]
+        #[structopt(parse(from_os_str), help = "First input Newick file.")]
         newick_1: PathBuf,
-        /// The path of the second phylogeny in Newick format.
-        #[structopt(parse(from_os_str))]
+        #[structopt(parse(from_os_str), help = "Second input Newick file.")]
         newick_2: PathBuf,
-
-        /// The path to write the distance to, or stdout otherwise.
-        #[structopt(parse(from_os_str))]
+        #[structopt(
+            parse(from_os_str),
+            help = "Optional file to write distance to. Stdout by default."
+        )]
         output: Option<PathBuf>,
     },
 }

src/main.rs

@@ -16,6 +16,7 @@ mod cli;
 pub mod common;
 pub mod csv;
 pub mod fastq;
+pub mod phylogeny;
 pub mod sequences_stats;
 
 fn main() -> Result<()> {
@@ -284,43 +285,12 @@ fn main() -> Result<()> {
             method,
             input,
             output,
-        } => {
-            let dm = bio_types::distancematrix::DistanceMatrix::from_file(&input)?;
-            let phylogeny = (match method {
-                cli::PhylogenyMethod::UPGMA => bio::phylogeny::upgma,
-                cli::PhylogenyMethod::NeighborJoining => bio::phylogeny::neighbor_joining,
-            })(&dm);
-            match output {
-                Some(path) => {
-                    let mut f = fs::File::create(path)?;
-                    f.write_all(phylogeny.to_string().as_bytes())?;
-                    f.write(b"\n")?;
-                }
-                None => {
-                    println!("{}", phylogeny.to_string());
-                }
-            }
-        }
+        } => phylogeny::phylogeny(input, method, output)?,
         RobinsonFoulds {
-            ref newick_1,
-            ref newick_2,
+            newick_1,
+            newick_2,
             output,
-        } => {
-            let dist = bio::phylogeny::robinson_foulds_distance(
-                &bio::io::newick::from_file(newick_1)?,
-                &bio::io::newick::from_file(newick_2)?,
-            );
-            match output {
-                Some(path) => {
-                    let mut f = fs::File::create(path)?;
-                    f.write_all(dist.to_string().as_bytes())?;
-                    f.write(b"\n")?;
-                }
-                None => {
-                    println!("{}", dist.to_string());
-                }
-            }
-        }
+        } => phylogeny::robinson_foulds_distance(&newick_1, &newick_2, output)?,
     }
     Ok(())
 }

src/phylogeny.rs

@@ -0,0 +1,56 @@
+//! Compute a phylogeny from a distance matrix, or the distance between two phylogenies.
+//!
+//! ## Usage:
+//!
+//! ```
+//! $ rbt phylogeny --method {UPGMA,NeighborJoining} phylip.dist [newick.tree]
+//! $ rbt robinsonfoulds newick1.tree newick2.tree [outfile]
+//! ```
+
+use anyhow::Error;
+use std::fs::File;
+
+use crate::cli::PhylogenyMethod;
+
+pub fn phylogeny(
+    input: std::path::PathBuf,
+    method: PhylogenyMethod,
+    output: Option<std::path::PathBuf>,
+) -> Result<(), Error> {
+    let dm = bio_types::distancematrix::DistanceMatrix::from_file(&input)?;
+    let phylogeny = (match method {
+        PhylogenyMethod::UPGMA => bio::phylogeny::upgma,
+        PhylogenyMethod::NeighborJoining => bio::phylogeny::neighbor_joining,
+    })(&dm);
+    Ok(match output {
+        Some(path) => {
+            let mut f = File::create(path)?;
+            f.write_all(phylogeny.to_string().as_bytes())?;
+            f.write(b"\n")?;
+        }
+        None => {
+            println!("{}", phylogeny.to_string());
+        }
+    })
+}
+
+pub fn robinson_foulds_distance(
+    newick_1: &std::path::PathBuf,
+    newick_2: &std::path::PathBuf,
+    output: Option<std::path::PathBuf>,
+) -> Result<(), Error> {
+    let dist = bio::phylogeny::robinson_foulds_distance(
+        &bio::io::newick::from_file(newick_1)?,
+        &bio::io::newick::from_file(newick_2)?,
+    );
+    Ok(match output {
+        Some(path) => {
+            let mut f = File::create(path)?;
+            f.write_all(dist.to_string().as_bytes())?;
+            f.write(b"\n")?;
+        }
+        None => {
+            println!("{}", dist.to_string());
+        }
+    })
+}