feat(graph): implement graph analysis

Cargo.toml

@@ -10,7 +10,7 @@ documentation = "https://github.com/cauliyang/rboss"
 license = "MIT"
 description = "Rust Bioinformatics Toolbox"
 keywords = ["Bioinformatics", "Graph", "Toolbox"]
-categories = ["Bioinformatics"]
+categories = ["command-line-interface"]
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [profile.dev.package."*"]
@@ -53,11 +53,12 @@ noodles-fasta = "0.30"
 noodles-fastq = "0.9"
 noodles-sam = "0.46"
 
-petgraph = "0.6"
-regex = "1.10"
-serde_json = "1.0"
+petgraph = { version = "0.6", features = ["serde-1"] }
+regex = { version = "1.10" }
+serde = { version = "1.0" }
+serde_json = { version = "1.0" }
 
-walkdir = "2.4"
+walkdir = { version = "2.4" }
 
 # standard crate data is left out
 [dev-dependencies]

src/fa2fq.rs

@@ -5,7 +5,6 @@ use std::path::Path;
 
 pub fn fa2fq<P: AsRef<Path>>(input: P) -> Result<()> {
     let mut reader = fasta::reader::Builder.build_from_path(input)?;
-
     let mut writer = fastq::Writer::new(std::io::stdout());
 
     for result in reader.records() {

src/graph.rs

@@ -1,14 +1,45 @@
+use anyhow::Result;
 use clap::Args;
 use clap::ValueHint;
+use std::io::BufWriter;
+use std::io::Write;
 use std::path::PathBuf;
 
 mod analysis;
 mod data;
 mod load;
 
+use analysis::GraphAnalysis;
+use log::warn;
+
 #[derive(Args, Debug)]
 pub struct GraphArgs {
     /// Graph input file
     #[arg(value_hint = ValueHint::FilePath)]
     input: PathBuf,
 }
+
+pub fn analyze_nlgraph(args: &GraphArgs) -> Result<()> {
+    let mut nlgraph = load::load_cygraph_from_file(&args.input)?;
+
+    if !nlgraph.is_weakly_connected() {
+        warn!("Graph is weakly connected");
+        return Ok(());
+    }
+
+    if nlgraph.is_cyclic_directed() {
+        warn!("Graph is cyclic");
+        return Ok(());
+    }
+
+    nlgraph.node_degree();
+    nlgraph.degree_centrality();
+    nlgraph.closeness_centrality();
+    nlgraph.local_clustering_coefficient();
+
+    let stdout = std::io::stdout().lock();
+    let mut handle = BufWriter::new(stdout); // optional: wrap that handle in a buffer
+    writeln!(handle, "{}", nlgraph.to_cyjson())?;
+
+    Ok(())
+}