Created
May 5, 2014 13:17
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Extracting TSS, Exons, Introns, 5'UTR and 3' UTR from UCSC knownGene.txt and kgXref.txt
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| import java.io.*; | |
| import java.util.*; | |
| public class ExtractIntronExonUTRFromKnownGeneAndKgXref { | |
| public static void main(String[] args) throws Exception { | |
| BufferedReader br = new BufferedReader(new FileReader(args[1])); | |
| HashMap<String,String> xref=new HashMap<String,String>(); | |
| String tmp = ""; | |
| while ((tmp = br.readLine()) != null) { | |
| String[] x = tmp.split("\t"); | |
| xref.put(x[0],x[4]); | |
| } | |
| br.close(); | |
| int tss=Integer.parseInt(args[2]); | |
| BufferedWriter bwTSS = new BufferedWriter(new FileWriter(new File(args[0]).getName().replaceAll("txt","")+"tss"+tss+".bed")); | |
| BufferedWriter bwI = new BufferedWriter(new FileWriter(new File(args[0]).getName().replaceAll("txt","")+"introns.bed")); | |
| BufferedWriter bwE = new BufferedWriter(new FileWriter(new File(args[0]).getName().replaceAll("txt","")+"exons.bed")); | |
| BufferedWriter bw3U = new BufferedWriter(new FileWriter(new File(args[0]).getName().replaceAll("txt","")+"3UTR.bed")); | |
| BufferedWriter bw5U = new BufferedWriter(new FileWriter(new File(args[0]).getName().replaceAll("txt","")+"5UTR.bed")); | |
| br = new BufferedReader(new FileReader(args[0])); | |
| tmp = ""; | |
| while ((tmp = br.readLine()) != null) { | |
| // chr1 1115 4121 + 3 1115,2475,3083, 2090,2584,4121, uc001aaa.2 | |
| // BC032353 | |
| String[] x = tmp.split("\t"); | |
| String geneinfo = x[0]+":"+xref.get(x[0])+":"; // put strand and kgid to mimic kg.cg format | |
| int exonsize = Integer.parseInt(x[7]); | |
| String[] exonstart = x[8].split(","); | |
| String[] exonend = x[9].split(","); | |
| for (int i = 0 ; i < exonsize ; i++){ | |
| if(x[2].equals("+")){//forward strand | |
| bwE.write(x[1]+"\t"+exonstart[i]+"\t"+exonend[i]+"\t"+geneinfo+"Exon" + (i + 1) +"\n"); | |
| if(exonsize>0 && i<exonsize-1){//having intron | |
| bwI.write(x[1]+"\t"+exonend[i]+"\t"+exonstart[i+1]+"\t"+geneinfo+"Intron" + (i + 1) +"\n"); | |
| } | |
| }else{ | |
| bwE.write(x[1]+"\t"+exonstart[i]+"\t"+exonend[i]+"\t"+geneinfo+"Exon" + (exonsize-i) +"\n"); | |
| if(exonsize>0 && i<exonsize-1){//having intron | |
| bwI.write(x[1]+"\t"+exonend[i]+"\t"+exonstart[i+1]+"\t"+geneinfo+"Intron" + (exonsize-i-1) +"\n"); | |
| } | |
| } | |
| } | |
| int txstart=Integer.parseInt(x[3]); | |
| int txend=Integer.parseInt(x[4]); | |
| int cdsstart=Integer.parseInt(x[5]); | |
| int cdsend =Integer.parseInt(x[6]); | |
| // write TSS | |
| if(x[2].equals("+")){ | |
| int tssstart=(txstart-tss)<0?0:(txstart-tss); | |
| int tssend=txstart+tss; | |
| bwTSS.write(x[1]+"\t"+tssstart+"\t"+tssend+"\t"+geneinfo+x[2]+"\n"); | |
| } | |
| else{ | |
| int tssstart=(txend-tss)<0?0:(txend-tss); | |
| int tssend=txend+tss; | |
| bwTSS.write(x[1]+"\t"+tssstart+"\t"+tssend+"\t"+geneinfo+x[2]+"\n"); | |
| } | |
| if(cdsstart!=cdsend){ //having 3'UTR or 5'UTR | |
| if(x[2].equals("+")){ | |
| if(txstart!=cdsstart){ | |
| bw5U.write(x[1]+"\t"+x[3]+"\t"+(cdsstart-1)+"\t"+geneinfo+"5'UTR"+"\n"); | |
| } | |
| if(txend!=cdsend){ | |
| bw3U.write(x[1]+"\t"+(cdsend+1)+"\t"+x[4]+"\t"+geneinfo+"3'UTR"+"\n"); | |
| } | |
| }else{ | |
| if(txstart!=cdsstart){ | |
| bw3U.write(x[1]+"\t"+x[3]+"\t"+(cdsstart-1)+"\t"+geneinfo+"3'UTR"+"\n"); | |
| } | |
| if(txend!=cdsend){ | |
| bw5U.write(x[1]+"\t"+(cdsend+1)+"\t"+x[4]+"\t"+geneinfo+"5'UTR"+"\n"); | |
| } | |
| } | |
| } | |
| } | |
| bwTSS.close(); | |
| bwI.close(); | |
| bwE.close(); | |
| bw3U.close(); | |
| bw5U.close(); | |
| } | |
| } | |
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