default taxo path

eric9n · Sep 9, 2024 · dc87a40 · dc87a40
1 parent 8dd9aec
commit dc87a40
Show file tree

Hide file tree

Showing 3 changed files with 17 additions and 3 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "clade"
-version = "0.1.1"
+version = "0.1.2"
 edition = "2021"
 description = "A tool for phlyo tree, a phylogenetic tree construction software."
 license = "MIT"

diff --git a/src/main.rs b/src/main.rs
@@ -6,6 +6,7 @@ use clade::ncbi;
 use clade::taxo::{prune_taxonomy, prune_taxonomy_by_names, Taxonomy};
 use clade::update::update_taxdump;
 use clap::{Parser, Subcommand};
+use std::env;
 use std::{error::Error, fs::File, io::Write, path::PathBuf};
 
 #[derive(clap::Parser, Debug)]
@@ -14,10 +15,23 @@ struct Args {
     #[clap(subcommand)]
     pub cmd: Command,
 
-    #[clap(short, long, help = "The path to store the taxdump files")]
+    #[clap(
+        short,
+        long,
+        help = "The path to store the taxdump files",
+        default_value_os_t = default_taxo_path()
+    )]
     pub taxo_path: PathBuf,
 }
 
+fn default_taxo_path() -> PathBuf {
+    env::var_os("HOME")
+        .or_else(|| env::var_os("USERPROFILE"))
+        .map(PathBuf::from)
+        .map(|p| p.join(".clade"))
+        .unwrap_or_else(|| PathBuf::from(".clade"))
+}
+
 #[derive(Subcommand, Debug)]
 enum Command {
     #[clap(about = "Update NCBI taxdump files")]