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Stairpainter.java
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/**
*
* Copyright (c) @author Xiaoming Liu, Ph.D.
* Associate Professor,
* USF Genomics,
* College of Public Health,
* University of South Florida at Tampa
*
* This source code is distributed under the Artistic License 2.0
*
* The license can be found at
* https://opensource.org/licenses/Artistic-2.0
*/
import java.util.*;
import java.io.*;
public class Stairpainter {
public static void main(String[] args)throws Exception{
if(args.length!=1){
System.out.println("Usage: java Stairpainter blueprint_file");
System.exit(1);
}
String blueprint_file=args[0];
BufferedReader in=new BufferedReader(new FileReader(blueprint_file));
String batchfile=blueprint_file+".plot.sh";
if(System.getProperty("os.name").startsWith("Windows"))batchfile=blueprint_file+".plot.bat";
String popid="";
int nseq=0;
double L=0;
boolean folded=true;
double[] sfs=new double[0];
double dimFactor=2000;
double pct_training=0.67;
int[] rand=new int[0];
String project_dir="";
String stairway_plot_dir="";
int ninput=0;
String inputstem="";
while(in.ready()){
String line=in.readLine();
if(line.indexOf("#")!=-1)line=line.substring(0,line.indexOf("#"));//remove comments
StringTokenizer t=new StringTokenizer(line,":#");
int nt=t.countTokens();
if(nt!=2)continue;
String tmp=t.nextToken().trim();
if(tmp.equalsIgnoreCase("popid"))popid=t.nextToken().trim();
else if(tmp.equalsIgnoreCase("inputstem"))inputstem=t.nextToken().trim();
else if(tmp.equalsIgnoreCase("nseq"))nseq=Integer.parseInt(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("L"))L=Double.parseDouble(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("whether_folded"))folded=Boolean.parseBoolean(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("SFS")){
String temp=t.nextToken();
StringTokenizer t2=new StringTokenizer(temp);
int nt2=t2.countTokens();
if(folded){
if(nt2!=(nseq/2)){
System.out.println("SFS error: shall have nseq/2 numbers");
if(nt2==(nseq-1)){
System.out.println("Assuming the nseq-1 numbers are unfolded counts");
double[] sfs0=new double[nseq];
for(int i=1;i<=nseq-1;i++)sfs0[i]=Double.parseDouble(t2.nextToken());
sfs=new double[nseq/2];
for(int i=1;i<=nseq/2;i++){
if(i!=nseq-i){
sfs[i-1]=sfs0[i]+sfs0[nseq-i];
}
else sfs[i-1]=sfs0[i];
}
}
else System.exit(1);
}
else{
sfs=new double[nseq/2];
for(int i=0;i<nseq/2;i++)sfs[i]=Double.parseDouble(t2.nextToken());
}
}
else{
if(nt2!=(nseq-1)){
System.out.println("SFS error: shall have nseq-1 numbers");
System.exit(1);
}
else{
sfs=new double[nseq-1];
for(int i=0;i<nseq-1;i++)sfs[i]=Double.parseDouble(t2.nextToken());
}
}
}
else if(tmp.equalsIgnoreCase("dimFactor"))dimFactor=Integer.parseInt(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("pct_training"))pct_training=Double.parseDouble(t.nextToken().trim());
else if(tmp.equalsIgnoreCase("nrand")){
String temp=t.nextToken();
StringTokenizer t2=new StringTokenizer(temp);
int nt2=t2.countTokens();
rand=new int[nt2];
for(int i=0;i<nt2;i++)rand[i]=Integer.parseInt(t2.nextToken());
Arrays.sort(rand);
}
else if(tmp.equalsIgnoreCase("project_dir"))project_dir=t.nextToken().trim();
else if(tmp.equalsIgnoreCase("stairway_plot_dir"))stairway_plot_dir=t.nextToken().trim();
else if(tmp.equalsIgnoreCase("ninput"))ninput=Integer.parseInt(t.nextToken().trim());
}
in.close();
if(inputstem.isEmpty())inputstem=popid+"-";
int ngroup=rand.length;
double[] average=new double[ngroup];
double[] median=new double[ngroup];
String sep=File.separator;
for(int i=0;i<ngroup;i++){
String dir=correctDirectory(project_dir+sep+"rand"+rand[i]);
if(!confirm_dir(dir)) System.exit(1);
File folder = new File(dir);
File[] listOfFiles = folder.listFiles();
String[] infiles=folder.list();
ArrayList list=new ArrayList();
for(int ii=0;ii<infiles.length;ii++){
if(infiles[ii].endsWith(".addTheta"))list.add(infiles[ii]);
}
int n1=list.size();
String[] infiles1=(String[])list.toArray(new String[n1]);
double[] fitness1=new double[n1];
double total1=0;
for(int ii=0;ii<n1;ii++){
System.out.println(dir+infiles1[ii]);
in=new BufferedReader(new FileReader(dir+infiles1[ii]));
String line=in.readLine();
double fitness=0;
while(line.indexOf("final model:")==-1)line=in.readLine();
StringTokenizer t=new StringTokenizer(line,"\t");
t.nextToken();
fitness=Double.parseDouble(t.nextToken());
fitness1[ii]=fitness;
total1+=fitness;
in.close();
}
Arrays.sort(fitness1);
average[i]=total1/n1;
median[i]=fitness1[n1/2];
}
int bestaverage=0;
int bestmedian=0;
double averagefit=Double.MAX_VALUE;
double medianfit=Double.MAX_VALUE;
for(int i=0;i<ngroup;i++){
if(averagefit-average[i]>3.841/2){
averagefit=average[i];
bestaverage=i;
}
else break;
}
for(int i=0;i<ngroup;i++){
if(medianfit-median[i]>3.841/2){
medianfit=median[i];
bestmedian=i;
}
else break;
}
int bestrand=Math.min(bestaverage,bestmedian);
int bestbreak=rand[bestrand];
//output batch file
String comment="# ";
String mv="mv -f";
String cp="cp -f";
if(System.getProperty("os.name").startsWith("Windows")){
comment="REM ";
mv="MOVE /y";
cp="COPY >nul";
}
PrintWriter out=new PrintWriter(new FileWriter(batchfile),true);
for(int i=0;i<ngroup;i++) {
out.println(comment+"rand"+rand[i]+": average logLikelihood="+(-average[i])+" median logLikelihood="+(-median[i]));
}
out.println(comment+"best number of break points (average logLikelihood):"+rand[bestaverage]);
out.println(comment+"best number of break points (median logLikelihood):"+rand[bestmedian]);
System.out.println(comment+"best number of break points (average logLikelihood):"+rand[bestaverage]);
System.out.println(comment+"best number of break points (median logLikelihood):"+rand[bestmedian]);
out.println(comment+"Step 1: estimations for the \"final\" result");
if(!confirm_or_create_dir(correctDirectory(project_dir+sep+"final"))) System.exit(1);
for(int i=1;i<=ninput;i++) {
out.println(cp+" "+correctDirectory(project_dir+sep+"rand"+rand[bestrand])+inputstem+i+"."+rand[bestrand]+"_"+pct_training+".addTheta"+" "+correctDirectory(project_dir+sep+"final"));
}
out.println(comment+"Step 2: create summaries and plots");
out.println("java -Xmx4g -cp "+correctDirectory(stairway_plot_dir)+System.getProperty("path.separator")+correctDirectory(stairway_plot_dir)+"gral-core-0.11.jar"+System.getProperty("path.separator")+correctDirectory(stairway_plot_dir)+"VectorGraphics2D-0.9.3.jar"+" "+"Stairway_output_summary_plot2"+" "+blueprint_file);
for(int ii=0;ii<rand.length;ii++){
if(!confirm_dir(correctDirectory(project_dir+sep+"rand"+rand[ii]))) System.exit(1);
out.println("java -Xmx4g -cp "+correctDirectory(stairway_plot_dir)+System.getProperty("path.separator")+correctDirectory(stairway_plot_dir)+"gral-core-0.11.jar"+System.getProperty("path.separator")+correctDirectory(stairway_plot_dir)+"VectorGraphics2D-0.9.3.jar"+" "+"Stairway_output_summary_plot2"+" "+blueprint_file+" rand"+rand[ii]);
}
out.close();
}
private static String correctDirectory(String dir){
StringTokenizer t=new StringTokenizer (dir,"/\\\"\'");
int nt=t.countTokens();
String sep=File.separator;
String dir2="";
for(int i=0;i<nt;i++)dir2+=t.nextToken()+sep;
if((dir.charAt(0)=='\"'||dir.charAt(0)=='\'')&&(dir.charAt(1)=='/'||dir.charAt(1)=='\\'))dir2=sep+dir2;
else if(dir.charAt(0)=='/'||dir.charAt(0)=='\\')dir2=sep+dir2;
return dir2;
}
private static boolean confirm_dir(String dir){
File f = new File(dir);
if (!f.exists()){
System.out.println("Error: Directory: "+ dir + "does not exists");
return false;
}
else if(!f.isDirectory()){
System.out.println("Error: "+dir + "exists but is not a directory");
return false;
}
return true;
}
private static boolean confirm_or_create_dir(String dir){
File f = new File(dir);
if (!f.exists()){
boolean success = (new File(dir)).mkdir();
if (success) {
System.out.println("Warnning: Directory: "+ dir + " created");
return true;
}
else {
System.out.println("Error: Directory: "+ dir + "does not exists and cannot be created");
return false;
}
}
else if(!f.isDirectory()){
System.out.println("Error: "+dir + "exists but is not a directory");
return false;
}
return true;
}
}