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package data.cerevisiae.huesca2011swr1d;
import fork.lib.base.file.FileName;
import fork.lib.base.file.io.txt.ReadTable;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.data.microarray.ArrayProbeMapping;
import fork.lib.bio.data.microarray.IDMapperAffy;
import java.io.File;
import java.util.HashMap;
import java.util.Iterator;
/**
* @deprecated
* @author man-mqbpjmg4
*/
public class MapID {
public static void main(String[] args) throws Exception { //debug
File dir= Dirs.getFile("dir");
File anno= new File(dir+"\\anno\\microarray\\affymetrix/Yeast_2.na33.annot.csv");
File d= new File(dir+"/other_datasets/huesca2011swr1d/raw/processed");
File[] fs= d.listFiles();
for( int i=0; i<fs.length; i++ ){
File f= fs[i];
if(f.isFile()){
IDMapperAffy map = new IDMapperAffy(anno);
ReadTable rt= new ReadTable(f);
rt.param().setSkipRows(0);
HashMap<String, String> hm= rt.getHashMap(0, 1);
HashMap<String, Double> idv= new HashMap();
Iterator<String> it= hm.keySet().iterator();
while(it.hasNext()){
String id= it.next();
idv.put(id, Double.parseDouble(hm.get(id)));
}
ArrayProbeMapping ap= new ArrayProbeMapping(map, idv){
protected boolean ifWriteID(String id)throws Exception {
if(id.indexOf("Y")==0){
return true;
}
return false;
}
};
File od= new File(d+"/idmap");
od.mkdirs();
File out= new File(od+"/id_"+FileName.getBaseName(f)+".txt");
ap.writeToFile(out);
}
}
}
}