/*
* Copyright (C) 2014 wangqion
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
package edu.msu.cme.rdp.multicompare;
import edu.msu.cme.rdp.multicompare.taxon.MCTaxon;
import edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor;
import edu.msu.cme.rdp.taxatree.ConcretRoot;
import edu.msu.cme.rdp.taxatree.TaxonHolder;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.List;
/**
*
* @author wangqion
*/
public class MergeTaxonCount {
private MultiClassifierResult result = null;
public MultiClassifierResult getResult(){
return result;
}
public void processOneHierFile(String file) throws IOException{
BufferedReader reader = new BufferedReader(new FileReader(file));
String line = null;
ArrayList<String[]> oneHierBlock = new ArrayList<String[]> () ;
while ( (line= reader.readLine())!= null){
if ( line.trim().equals("")) continue;
if ( line.startsWith("taxid")){
if ( oneHierBlock.size() > 0){
processOneHierBlock(oneHierBlock);
}
oneHierBlock = new ArrayList<String[]> ();
}
oneHierBlock.add(line.split("\\t"));
}
if ( oneHierBlock.size() > 0){
processOneHierBlock(oneHierBlock);
}
reader.close();
}
public void processOneHierBlock( ArrayList<String[]> oneHierBlock) throws IOException{
// get the samples names
int offset = 4;
String[] values = oneHierBlock.get(0);
List<MCSample> curSampleList = new ArrayList<MCSample>();
for ( int i = offset; i< values.length; i++){
if ( result != null){
MCSample sample = result.getSample(values[i]);
if( sample == null){
sample = new MCSample(values[i]);
result.addSample(sample);
}
curSampleList.add(sample);
}else {
MCSample sample = new MCSample(values[i]);
curSampleList.add(sample);
}
}
//taxid lineage name rank sample sample .....
// the first line should be the root, we need to handle this specially because a previous bug printed out the root taxon differenly
values = oneHierBlock.get(1);
if( result == null){
// the first line should be the root taxon
ConcretRoot root = new ConcretRoot<MCTaxon>(new MCTaxon(Integer.parseInt(values[0]), values[2], values[3]) );
result = new MultiClassifierResult(root);
result.addSampleList(curSampleList);
}
MCTaxon curTaxon = (MCTaxon)(result.getRoot().getRootTaxonHodler().getTaxon());
// add counts
for ( int i = offset; i< values.length; i++){
curTaxon.incCount(curSampleList.get(i-offset), Double.parseDouble(values[i]));
}
for ( int ln = 2; ln < oneHierBlock.size(); ln++){
values = oneHierBlock.get(ln);
int taxid = Integer.parseInt(values[0]);
// find the parent taxon
String[] lineage = values[1].split(";");
TaxonHolder parentTaxon = result.getRoot().getRootTaxonHodler();
for ( int i= 2; i< lineage.length-2; i+=2){ // the first taxon should be the root
TaxonHolder temp = parentTaxon.getImediateChildTaxon(lineage[i]);
if ( temp == null){
throw new IOException("Error: Something is wrong with input file, can not find parent node " + lineage[i] + " in line: "+ values[1] );
}
parentTaxon = temp;
}
//check if the name and rank match the existing one, in case the result from different version
TaxonHolder tempChild = parentTaxon.getImediateChildTaxon(values[2]);
if ( tempChild != null){
curTaxon = (MCTaxon) tempChild.getTaxon();
if ( curTaxon.getTaxid() != taxid ){
throw new IOException("Error: Something is wrong with input file: taxon name " + values[2] + " with taxid " + taxid
+ " does not match previous processed taxon " + curTaxon.getName() + " with taxid " + curTaxon.getTaxid()
+ ". Possibly from different training sets ??");
}
}else {
curTaxon = new MCTaxon(taxid, values[2], values[3], false);
result.getRoot().addChild(curTaxon, parentTaxon.getTaxon().getTaxid());
curTaxon.setLineage(values[1]);
}
// add counts
for ( int i = offset; i< values.length; i++){
curTaxon.incCount(curSampleList.get(i-offset), Double.parseDouble(values[i]));
}
}
}
public static void main(String[] args) throws Exception{
String usage = "Usage: out_merged_count.txt in_taxoncount.txt n_taxoncount.txt ...\n" +
" This program merges multiple taxon count files to into one count file, keeping one column for each unique sample.\n" +
" If same sample occurred more than once, the taxon count for this sample will be combined.";
if (args.length < 2){
System.err.println(usage);
System.exit(1);
}
File outFile = new File(args[0]);
if ( outFile.exists()){
System.err.println("Error: output file " + args[0] + " already exists!");
System.exit(1);
}
try {
MergeTaxonCount theObj = new MergeTaxonCount();
for ( int i = 1; i < args.length; i++){
theObj.processOneHierFile(args[i]);
}
PrintStream hier_out = new PrintStream(outFile);
DefaultPrintVisitor printVisitor = new DefaultPrintVisitor(hier_out, theObj.getResult().getSamples());
theObj.getResult().getRoot().topDownVisit(printVisitor);
hier_out.close();
}catch (Exception ex){
outFile.delete();
throw ex;
}
}
}