public static void transform2idx(String inFile, String outFile) throws Exception {
BufferedReader br = new BufferedReader(new FileReader(inFile));
BufferedWriter bw = new BufferedWriter(new FileWriter(outFile));
String line;
while ((line = br.readLine()) != null) {
if (line.startsWith("###")) {
bw.write(line + "\n");
continue;
}
String[] spt = line.split("\t");
String idx1 = EntityIndex.getIdx(spt[0]);
String idx2 = EntityIndex.getIdx(spt[1]);
if (idx1 != null && idx2 != null) bw.write(idx1 + "\t" + idx2 + "\n");
}
br.close();
bw.close();
LogInfo.logs("Job Done.");
}
public static void main(String[] args) throws Exception {
// processFile(args[0], args[1]);
EntityIndex.initialize(args[2]);
transform2idx(args[0], args[1]);
}