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package data.cerevisiae.histmod.liu2005_histmods;
import fork.lib.base.file.FileName;
import fork.lib.base.file.management.Dirs;
import fork.lib.bio.data.microarraychip.ChipArrayParser;
import java.io.File;
/**
*
* @author man-mqbpjmg4
*/
public class ProcessData {
public static void main(String[] args) throws Exception { //debug
File dir= Dirs.getFile("dir");
File d= new File(dir+"/other_datasets/liu_2005_hist-mods");
File dd= new File(d+"/data");
File od= new File(dd+"/wig");
//File pf= new File(d+"/array/sort_array_6-9.sam");
File pf= new File(d+"/array/sort_array_10p.sam");
/*
File[] afs= new File[]{
new File(dd+"/a_h2bk16ac_r1_9.txt"),
new File(dd+"/a_h3k4me1_r1_8.txt"),
new File(dd+"/a_h3k4me2_r1_8.txt"),
new File(dd+"/a_h3k4me3_r1_9.txt"),
new File(dd+"/a_h3k9ac_r1_8.txt"),
new File(dd+"/a_h3k14ac_r1_8.txt"),
new File(dd+"/a_h4k5ac_r1_8.txt"),
new File(dd+"/a_h4k8ac_r1_8.txt"),
new File(dd+"/a_h4k12ac_r1_6.txt"),
new File(dd+"/a_h4k16ac_r1_8.txt"),
};
*/
File[] afs= new File[]{
new File(dd+"/b_h2az_r1_11.txt"),
//new File(dd+"/b_h3k18ac_r1_11.txt"),
//new File(dd+"/b_h3k14ac-grunstein_r1_11.txt"),
};
for( int i=0; i<afs.length; i++ ){
File af= afs[i];
ChipArrayParser cp = new ChipArrayParser(af, pf, 0, 2);
File out= new File(od+"/"+FileName.getBaseName(af)+".wig");
cp.writeToFile(out, FileName.getBaseName(af));
}
}
}