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predictBatchSPMAP.java

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import java.io.BufferedReader;

import java.io.File;

import java.io.FileReader;

import java.io.IOException;

import java.io.PrintWriter;

import java.nio.file.Files;

import java.nio.file.Paths;

import java.util.Date;

import java.util.HashMap;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.StringTokenizer;

import java.util.Vector;

public class predictBatchSPMAP {

public static void main(String[] args, Vector<String> ecnums, long time, String ROOTPATH, List<String> test_ids, String fastaFile, String tempDir)

throws IOException, InterruptedException

{

int sigTh = -15;

int subseqlen = 5;

String predictProg = ROOTPATH.substring(0, ROOTPATH.length() - 3) + "/svmlight/svm_classify";

String method = "spmap";

for (int i = 0; i < ecnums.size(); i++)

{

File workdir = new File(tempDir + File.separator + "testResult" + File.separator + time + File.separator + ecnums.get(i));

workdir.mkdirs();

String path = ROOTPATH + File.separator + ecnums.get(i) + File.separator + method;

String testpath = workdir + File.separator + method;

String modelfile = path + File.separator + "model.svm";

workdir = new File(testpath);

workdir.mkdirs();

String predFile = testpath + File.separator + ecnums.get(i) + ".preds";

String confFile = testpath + File.separator + ecnums.get(i) + ".confs";

String batchVect = testpath + File.separator + "test.vec";

String posPredFile = path + File.separator + "ppreds.txt";

String negPredFile = path + File.separator + "npreds.txt";

seq2vectPSSMtest seqtest = new seq2vectPSSMtest();

seq2vectPSSMtest.calculateVectors(sigTh, subseqlen, ecnums.get(i), test_ids, fastaFile, time, ROOTPATH, tempDir);

String cmd = predictProg + " " + batchVect + " " + modelfile + " " + predFile;

ProcessBuilder pb = new ProcessBuilder(cmd.split(" "));

Process process = pb.start();

try

{

process.waitFor();

int exitVal = process.exitValue();

}

catch (InterruptedException e)

{

System.out.print("Svm_classify is not working!");

e.printStackTrace();

}

utils u = new utils();

utils.calculateConfidence(posPredFile, negPredFile, predFile, confFile);

}

}

}