document update

README.md

@@ -21,6 +21,25 @@ With the MAP graph, we can use the "principal bundle decomposition" to study com
 
 ## Documentation, Usage and Examples
 
+Command Line Tools:
+
+PGR-TK provides the following tool to 
+
+- create the PGR-TK sequence and index database
+	-  `pgr-mdb`: create pgr minimizer database with AGC backend
+	-  `pgr-make-frgdb`: create PGR-TK fragment minimizer database with frg format backend
+- query the database to fetch sequences
+	- `pgr-query`: query a PGR-TK pangenome sequence database, ouput the hit summary and generate fasta files from the target sequences
+- generate MAP-graph in GFA format and principal bundle decomposition bed file
+	- `pgr-pbundle-decomp`: generat the principal bundle decomposition though MAP Graph from a fasta file
+- generate SVG from the principal bundle decomposition bed file
+	- `pgr-pbundle-bed2svg`: generate SVG from a principal bundle bed file
+- auxiliary tools
+	- `pgr-pbundle-bed2sorted`: generate annotation file with a sorting order from the principal bundle decomposition
+	- `pgr-pbundle-bed2dist`: generate alignment scores between sequences using bundle decomposition from a principal bundle bed file
+
+For each comannd, `command --help` provides the detail usage information. 
+
 The API documentation is at https://sema4-research.github.io/pgr-tk/
 
 A collection of Jupyter Notebooks are at https://github.com/sema4-Research/pgr-tk-notebooks/

pgr-bin/src/bin/pgr-fetch-seqs.rs

@@ -6,10 +6,11 @@ use std::fs::File;
 use std::io::{self, BufRead, BufReader, BufWriter, Write};
 use std::path::Path;
 
+/// List or fetch sequences from a PGR-TK database
 #[derive(Parser, Debug)]
 #[clap(name = "pgr-fetch-seqs")]
 #[clap(author, version)]
-#[clap(about = "list or fetch sequences from a pgr database", long_about = None)]
+#[clap(about, long_about = None)]
 struct CmdOptions {
     /// the prefix to a PGR-TK sequence database
     pgr_db_prefix: String,

pgr-bin/src/bin/pgr-make-frgdb.rs

@@ -8,10 +8,11 @@ use std::fs::File;
 use std::io::{BufRead, BufReader};
 use std::path::Path;
 
+/// Create PGR-TK fragment minimizer database with frg format backend
 #[derive(Parser, Debug)]
 #[clap(name = "pgr-make-frgdb")]
 #[clap(author, version)]
-#[clap(about = "create PGR-TK fragment minimizer database with frg format backend", long_about = None)]
+#[clap(about, long_about = None)]
 struct CmdOptions {
     /// the path to the file contains the paths to the fastx files to load
     filepath: String,

pgr-bin/src/bin/pgr-mdb.rs

@@ -10,10 +10,11 @@ use std::io::{BufRead, BufReader};
 
 use pgr_db::seq_db;
 
+/// Create pgr minimizer database with AGC backend
 #[derive(Parser, Debug)]
 #[clap(name = "pgr-mdb")]
 #[clap(author, version)]
-#[clap(about = "create pgr minimizer db", long_about = None)]
+#[clap(about, long_about = None)]
 struct CmdOptions {
     filepath: String,
     prefix: String,

pgr-bin/src/bin/pgr-pbundle-bed2dist.rs

@@ -6,12 +6,15 @@ use std::io::{BufRead, BufReader, BufWriter, Write};
 use std::path::Path;
 use std::{fs::File, path};
 
+/// Generate alignment scores between sequences using bundle decomposition from a principal bundle bed file
 #[derive(Parser, Debug)]
 #[clap(name = "pgr-pbundle-bed2dist")]
 #[clap(author, version)]
-#[clap(about = "generate alignment scores between contigs using bundle decomposition from a principal bundle bed file", long_about = None)]
+#[clap(about, long_about = None)]
 struct CmdOptions {
+    /// the path to the pricipal bundle bed file
     bed_file_path: String,
+    /// the prefix of the output file
     output_prefix: String,
 }
 

pgr-bin/src/bin/pgr-pbundle-bed2sorted.rs

@@ -5,10 +5,11 @@ use std::io::{BufRead, BufReader, BufWriter, Write};
 use std::path::Path;
 use std::{fs::File, path};
 
+/// Generate annotation file with a sorting order from the principal bundle decomposition
 #[derive(Parser, Debug)]
 #[clap(name = "pgr-pbundle-bed2sorted")]
 #[clap(author, version)]
-#[clap(about = "sort the contig by bunldes", long_about = None)]
+#[clap(about, long_about = None)]
 struct CmdOptions {
     /// the path to the pricipal bundle bed file
     bed_file_path: String,

pgr-bin/src/bin/pgr-pbundle-bed2svg.rs

@@ -6,10 +6,11 @@ use std::{fs::File, path};
 use svg::node::{self, element, Node};
 use svg::Document;
 
+/// Generate SVG from a principal bundle bed file
 #[derive(Parser, Debug)]
 #[clap(name = "pgr-pbundle-bed2svg")]
 #[clap(author, version)]
-#[clap(about = "generate SVG from a principal bundle bed file", long_about = None)]
+#[clap(about, long_about = None)]
 struct CmdOptions {
     /// the path to the pricipal bundle bed file
     bed_file_path: String,

pgr-bin/src/bin/pgr-pbundle-decomp.rs

@@ -10,10 +10,11 @@ use std::{
     path::Path,
 };
 
+/// Generat the principal bundle decomposition though MAP Graph from a fasta file
 #[derive(Parser, Debug)]
 #[clap(name = "pgr-pbundle-decomp")]
 #[clap(author, version)]
-#[clap(about = "take a fasta file and output the principal bundle decomposition though MAP Graph", long_about = None)]
+#[clap(about, long_about = None)]
 struct CmdOptions {
     /// the path to the input fasta file
     fastx_path: String,

pgr-bin/src/bin/pgr-query.rs

@@ -7,10 +7,12 @@ use std::fs::File;
 use std::io::{self, BufWriter, Write};
 use std::path::Path;
 
+/// Query a PGR-TK pangenome sequence database, 
+/// ouput the hit summary and generate fasta files from the target sequences
 #[derive(Parser, Debug)]
 #[clap(name = "pgr-query")]
 #[clap(author, version)]
-#[clap(about = "query a pgr pangenome database and ouput the hits", long_about = None)]
+#[clap(about, long_about = None)]
 struct CmdOptions {
     /// the prefix to a PGR-TK sequence database
     pgr_db_prefix: String,