v0.0.1

README.md

@@ -1,2 +1,39 @@
 # asmkit
 Toolkit for genome assembly
+
+## Introduction  
+
+`asmkit` provide some useful tools for genome scaffold, such as [ALLHiC](https://github.com/tangerzhang/ALLHiC).
+
+## Installation
+The easiest way to install `asmkit` is to download the latest binary from the [releases](https://github.com/wangyibin/asmkit/releases/latest)  
+
+Build from source with:
+```console
+go get -u -t -v github.com/wangyibin/asmkit/...
+go install github.com/wangyibin/asmkit
+```
+## Usage
+### <kbd>agp2assembly</kbd>
+
+```console
+asmkit agp2assembly input.agp output.assembly
+```
+### <kbd>bam2links</kdb>
+```console
+asmkit bam2links input.bam output.links
+```
+
+
+
+
+## Example
+### From bam to juicebox assembly tool
+> Depend on [3D-DNA](https://github.com/aidenlab/3d-dna), please first downloand it.
+
+```console
+asmkit agp2assembly sample.agp sample.assembly
+asmkit bam2links sample.bwa_mem.bam sample.links
+bash ~/software/3d-dna/visualize/run-assembly-visualizer.sh sample.assembly sample.links
+```
+And then import `sample.hic` and `sample.assembly` into [juicebox](https://github.com/aidenlab/Juicebox) to manual curate genome assembly

agp2assembly.go

@@ -6,11 +6,8 @@ import (
 	"os"
 	"strconv"
 	"strings"
-
-	"github.com/op/go-logging"
 )
 
-
 // Agp2assembler
 type Agp2assembler struct {
 	Agpfile      string
@@ -150,4 +147,5 @@ func (r *Agp2assembler) Run() error {
 	if err != nil {
 		return err
 	}
+	return nil
 }

asmkit.go

@@ -4,9 +4,9 @@ import (
 	"github.com/spf13/cobra"
 )
 
-var rootCmd = &cobra.Command {
-	Use: "asmkit",
-	Short: "Toolkit for genome assembly",
+var rootCmd = &cobra.Command{
+	Use:     "asmkit",
+	Short:   "Toolkit for genome assembly",
 	Version: Version,
 }
 
@@ -15,31 +15,43 @@ func Execute() error {
 }
 
 func init() {
-	bam2linkCmd := &cobra.Command {
-		Use:  "bam2links",
+	bam2linkCmd := &cobra.Command{
+		Use:   "bam2links <input.bam> <output.links>",
+		Short: "Extract mnd links from bam",
+		Long: `
+bam2link function:
+Given a bamfile, to extract links and store as mnd links file for juicebox assembly tools.
+`,
 		Args: cobra.ExactArgs(2),
 		Run: func(cmd *cobra.Command, args []string) {
 			bamfile := args[0]
 			linkfile := args[1]
-			p := Bam2link{Bamfile: bamfile, Linkfile: linkfile}
+			p := Bam2linker{Bamfile: bamfile, Linkfile: linkfile}
 			err := p.Run()
 			if err != nil {
 				log.Fatal(err)
 			}
 		},
 	}
 
-	agp2assembly := &cobra.Command {
-		Use: "agp2assembly",
+	agp2assemblyCmd := &cobra.Command{
+		Use:   "agp2assembly <input.agp> <output.assembly>",
+		Short: "Convert agp file into 3d-dna assembly.",
+		Long: `
+agp2assembly function:
+Convert agp file into 3d-dna assembly for juicebox assembly tool.		
+`,
 		Args: cobra.ExactArgs(2),
-		Run: func(cmd *cobra.Command, args []string){
+		Run: func(cmd *cobra.Command, args []string) {
 			agpfile := args[0]
 			assemblyfile := args[1]
-			p := Agp2assembly{Agpfile: agpfile, Assemblyfile: assemblyfile}
-			err : p.Run()
+			p := Agp2assembler{Agpfile: agpfile, Assemblyfile: assemblyfile}
+			err := p.Run()
 			if err != nil {
 				log.Fatal(err)
 			}
 		},
 	}
+
+	rootCmd.AddCommand(agp2assemblyCmd, bam2linkCmd)
 }

bam2links.go

@@ -111,4 +111,5 @@ func (r *Bam2linker) Run() error {
 	if err != nil {
 		return err
 	}
+	return nil
 }