readme

Cargo.toml

@@ -1,14 +1,11 @@
 [workspace]
-members = [
-    "ncbi",
-    "kr2r",
-    "seqkmer"]
+members = ["ncbi", "kr2r", "seqkmer"]
 resolver = "2"
 
 [profile.release]
 lto = true
-opt-level = "s" # 或者 "z"
+opt-level = "s"          # 或者 "z"
 debug-assertions = false
 # panic = 'abort'
 codegen-units = 1 # Compile crates one after another so the compiler can optimize better
-strip = true # Remove debug symbols
+strip = true      # Remove debug symbols

README.md

@@ -105,7 +105,7 @@ This will build the kr2r and ncbi project in release mode.
 Next, run the example script that demonstrates how to use the `kun_peng` binary. Execute the following command from the root of the workspace:
 
 ``` sh
-cargo run --release --example build_and_classify --package kr2r
+cargo run --release --example build_and_classify --package kun_peng
 ```
 
 This will run the build_and_classify.rs example located in the kr2r project's examples directory.
@@ -124,42 +124,42 @@ kun_peng direct error: [any direct errors here]
 
 This output confirms that the `kun_peng` commands were executed successfully and the files were processed as expected.
 
-## ncbi tool
+## ncbi_dl tool
 
 
 #### Run the `ncbi` Example
 
 Run the example script in the ncbi project to download the necessary files. Execute the following command from the root of the workspace:
 
 ``` sh
-cargo run --release --example run_download --package ncbi
+cargo run --release --example run_download --package ncbi_dl
 ```
 
 This will run the run_download.rs example located in the ncbi project's examples directory. The script will:
 
 1.  Ensure the necessary directories exist.
 2.  Download the required files using the ncbi binary with the following commands:
 
--   ./target/release/ncbi -d downloads gen -g archaea
--   ./target/release/ncbi -d downloads tax
+-   ./target/release/ncbi_dl -d downloads gen -g archaea
+-   ./target/release/ncbi_dl -d downloads tax
 
 Example Output You should see output similar to the following:
 
 ``` txt
-Executing command: /path/to/workspace/target/release/ncbi -d /path/to/workspace/downloads gen -g archaea
+Executing command: /path/to/workspace/target/release/ncbi_dl -d /path/to/workspace/downloads gen -g archaea
 NCBI binary output: [download output here]
 
-Executing command: /path/to/workspace/target/release/ncbi -d /path/to/workspace/downloads tax
+Executing command: /path/to/workspace/target/release/ncbi_dl -d /path/to/workspace/downloads tax
 NCBI binary output: [download output here]
 ```
 
-The ncbi binary is used to download resources from the NCBI website. Here is the help manual for the ncbi binary:
+The ncbi_dl binary is used to download resources from the NCBI website. Here is the help manual for the ncbi_dl binary:
 
 ``` sh
-./target/release/ncbi -h
-ncbi download resource
+./target/release/ncbi_dl -h
+ncbi_dl download resource
 
-Usage: ncbi [OPTIONS] <COMMAND>
+Usage: ncbi_dl [OPTIONS] <COMMAND>
 
 Commands:
   taxonomy  Download taxonomy files from NCBI (alias: tax)

ncbi/README.md

@@ -1,12 +1,12 @@
-## ncbi tool
+## ncbi_dl tool
 
-The ncbi binary is used to download resources from the NCBI website. Here is the help manual for the ncbi binary:
+The ncbi_dl binary is used to download resources from the NCBI website. Here is the help manual for the ncbi_dl binary:
 
 ``` sh
-./target/release/ncbi -h
-ncbi download resource
+./target/release/ncbi_dl -h
+ncbi_dl download resource
 
-Usage: ncbi [OPTIONS] <COMMAND>
+Usage: ncbi_dl [OPTIONS] <COMMAND>
 
 Commands:
   taxonomy  Download taxonomy files from NCBI (alias: tax)

ncbi/examples/run_download.rs

@@ -9,7 +9,7 @@ fn main() {
         .to_path_buf();
 
     // Run the NCBI binary to download files
-    let ncbi_binary = workspace_root.join("target/release/ncbi");
+    let ncbi_binary = workspace_root.join("target/release/ncbi_dl");
     let download_dir = workspace_root.join("downloads");
     // Ensure the download directory exists
     fs::create_dir_all(&download_dir).expect("Failed to create download directory");