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package data.cerevisiae.inhouse.spikein;
import data.cerevisiae.inhouse.jointable.JoinTable;
import fork.lib.base.file.io.txt.ReadTable;
import fork.lib.base.file.management.Dirs;
import java.io.File;
/**
*
* @author man-mqbpjmg4
*/
public class JoinTableERCC extends JoinTable{
public static void main(String[] args) throws Exception { //debug
File dir= Dirs.getFile("dir");
File d= new File(dir+"/data\\spikein\\score");
File refd= new File(dir+"/anno/genomes/spikein/ercc_rna");
File ref= new File(refd+"/ercc-rna_spike-in.bed");
JoinTable jj= new JoinTable();
jj.initRows(ref);
ReadTable rt= new ReadTable(new File(refd+"/anno_ercc-rna_spike-in.txt"));
rt.param().setSkipRows(0);
jj.addHashMapIDToVal(rt.getHashMap(1, 3), "conc");
jj.addBedFile(new File(d+"/569-4kr-cen_sd-ura_20140313-r1_pe1_read.bed"));
jj.addBedFile(new File(d+"/569-4kr-cen_sd-ura_20140313-r2_pe1_read.bed"));
jj.addBedFile(new File(d+"/666-htz1-cen_sd-ura_20140313-r1_pe1_read.bed"));
jj.addBedFile(new File(d+"/666-htz1-cen_sd-ura_20140313-r2_pe1_read.bed"));
jj.addBedFile(new File(d+"/749-htz1oe_ypg_20140313-r1_pe1_read.bed"));
jj.addBedFile(new File(d+"/749-htz1oe_ypg_20140313-r2_pe1_read.bed"));
jj.addBedFile(new File(d+"/1054-wt-gdna_sd-ura_20140313-r1_pe1_read.bed"));
jj.addBedFile(new File(d+"/1054-wt-gdna_sd-ura_20140313-r2_pe1_read.bed"));
jj.addBedFile(new File(d+"/1057-htz1-2um_sd-ura_20140313-r1_pe1_read.bed"));
jj.addBedFile(new File(d+"/1057-htz1-2um_sd-ura_20140313-r2_pe1_read.bed"));
jj.addBedFile(new File(d+"/1058-4kr-2um_sd-ura_20140313-r1_pe1_read.bed"));
jj.addBedFile(new File(d+"/1058-4kr-2um_sd-ura_20140313-r2_pe1_read.bed"));
jj.addBedFile(new File(d+"/by4741-wt_ypg_20140313-r1_pe1_read.bed"));
jj.addBedFile(new File(d+"/by4741-wt_ypg_20140313-r2_pe1_read.bed"));
jj.writeToFile(new File(d+"/combine.txt"));
}
}