Created
May 6, 2014 08:34
-
-
Save ianyfchang/254b893eb71529651f1d to your computer and use it in GitHub Desktop.
Splitting each chromosome position in BED-like format into bins
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import java.util.zip.*; | |
| import java.io.*; | |
| import java.util.*; | |
| public class GenerateBinsForRegionsAndReverseByStrand{ | |
| static LinkedHashMap<String, String> data = new LinkedHashMap<String, String>(); | |
| public static void main(String[] args) throws Exception { | |
| if(args.length!=2){ | |
| System.err.println("java -Xmx14g GenerateBinsForRegionsAndReverseByStrand bed-like binsize"); | |
| System.exit(1); | |
| } | |
| String block= new File(args[0]).getName().indexOf(".gz")>-1?new File(args[0]).getName().replaceAll(".gz",""):new File(args[0]).getName(); | |
| int bin = Integer.parseInt(args[1]); | |
| BufferedReader br = new BufferedReader(new FileReader(args[0])); | |
| /* | |
| chr1 703405 705146 - bt126 uc001abo.1 - 0 uc001abo.1 - -276 0 | |
| chr1 751975 753075 + bt126 uc009vjn.1 + 0 uc009vjn.1 + 0 0 | |
| chr1 794294 795479 + bt126 uc001abt.2 - 6851 uc001abt.2 - 5667 0 | |
| chr1 829557 831008 + bt126 uc001abu.1 + -6119 uc001abu.1 + -4669 0 | |
| */ | |
| String tmp = ""; | |
| int idx=0; | |
| while ((tmp = br.readLine()) != null) { | |
| String tmpstr0=tmp.replaceAll("\t",","); | |
| String[] tmpstr = tmp.split("\t"); | |
| int tmpS = Integer.parseInt(tmpstr[1])+1; // start MUST add 1 to fix UCSC zero-based start, after divided into bins, substract 1 to restore zero-base for bigwig query | |
| int tmpE = Integer.parseInt(tmpstr[2]);// end | |
| //divide into bins | |
| int size = (tmpE-tmpS+1)/bin; | |
| ArrayList<int[]> tmpdata = new ArrayList<int[]>(); | |
| for (int i = 0; i < bin ; i++){ | |
| int last = 0; | |
| if (i==bin-1){ // last bin | |
| last=tmpE; | |
| }else{ | |
| last=tmpS+((i+1)*size); | |
| } | |
| int[] tmpPos = {0,tmpS+(i*size),last}; | |
| tmpdata.add(tmpPos); | |
| } | |
| if(tmpstr[3].equals("-")){ | |
| Collections.reverse(tmpdata); | |
| } | |
| for (int j = 0 ; j < tmpdata.size(); j++){ | |
| int[] tmppos = tmpdata.get(j); | |
| int chr = tmppos[0]; // chromosome | |
| int start = tmppos[1]-1; | |
| int end = tmppos[2];// end | |
| int realstart=start>=0?start:0; | |
| int realend=end>=0?end:0; | |
| //bed format: chr, start, end, name, score, strand | |
| System.out.println(tmpstr[0]+"\t"+realstart+"\t"+realend+"\t"+tmpstr[0]+","+start+","+end+","+(j+1)+","+tmpstr0); | |
| } | |
| System.err.print(++idx+"\r"); | |
| } | |
| br.close(); | |
| } | |
| } |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment