search for alternative Reading frames in human Genome (hg18) ( http://biostar.stackexchange.com/questions/3034)

BioStar3034.java

/**
 * search for alternative Reading frames in human Genome (hg18)
 * Pierre Lindenbaum 2010
 * http://biostar.stackexchange.com/questions/3034
 */
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.net.URL;
import java.util.Arrays;
import java.util.zip.GZIPInputStream;


public class BioStar3034
    {
    private static final byte NIL=(byte)99;
    private static final byte ALT_FRAME=(byte)80;
  
    /** scans each transcript from knownGene.txt.gz */
    private void run() throws Exception
        {
        
        //an array of frame 0/1/2 or NIL if not filled
        byte genome[]=new byte[247249800];//~ size of human chr1
        //download UCSC knownGene
        BufferedReader r=new BufferedReader(new InputStreamReader(
                new GZIPInputStream( new URL(
                "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/knownGene.txt.gz").openStream())
                ));
        String line;
        String prevChrom=null;
        while((line=r.readLine())!=null)
            {
            String tokens[]=line.split("[\t]");
           
            String chrom=tokens[1];
            if(prevChrom==null || !(prevChrom.equals(chrom)))
                {
                Arrays.fill(genome,0,genome.length,NIL);//all the frame
                prevChrom=chrom;
                }

            int cdsStart=Integer.parseInt(tokens[5]);
            int cdsEnd=Integer.parseInt(tokens[6]);
            int exonsCount=Integer.parseInt(tokens[7]);

            String exonStarts[]=tokens[8].split("[,]");
            String exonEnds[]=tokens[9].split("[,]");

            int starts[]=new int[exonsCount];
            int ends[]=new int[exonsCount];
            for(int i=0;i< exonsCount;++i)
                {
                starts[i]=Integer.parseInt(exonStarts[i]);
                ends[i]=Integer.parseInt(exonEnds[i]);
                }
                
             int cDNA=0;
             
             //orientation is forward
             if(tokens[2].equals("+"))
               {
               int position=cdsStart;
               
               //loop over the cDNA and flag the frames 0/1/2
               while(position<cdsEnd)
                  {
                  //check position is in an exon
                  for(int exon=0;exon < exonsCount;++exon)
                     {   
                     if(!(starts[exon]<=position &&  position< ends[exon])) continue;
                     byte frame=(byte)(cDNA%3);
                     //we have been there before and it was not the same frame !
                     if( genome[position]!=NIL &&
                           genome[position]!=frame)
                           {
                           genome[position]=ALT_FRAME;
                           System.out.println(chrom+":"+(position+1)+"-"+(position+2)+" (+)");
                           }
                     else
                           {
                           genome[position]=frame;
                           }
                     cDNA++;
                     break;
                     }
                  ++position;
                  }
               }
            else //gene on reverse strand'
               {
               int position=cdsEnd-1;
               
               //loop over the cDNA and flag the frames 0/1/2
               while(position>=cdsStart)
                  {
                   //check position is in an exon
                  for(int exon=0;exon < exonsCount;++exon)
                     {   
                     if(!(starts[exon]<=position &&  position< ends[exon])) continue;
                     byte frame=(byte)(10+cDNA%3);//add 10 to flag reverse orientation
                     //we have been there before and it was not the same frame !
                     if( genome[position]!=NIL &&
                           genome[position]!=frame)
                           {
                           genome[position]=ALT_FRAME;
                           System.out.println(chrom+":"+(position+1)+"-"+(position+2)+" (-)");
                           }
                     else
                           {
                           genome[position]=frame;
                           }
      
                     genome[position]=frame;
                     cDNA++;
                     break;
                     }
      
                  --position;
                  }

               }
            }
        r.close();
        
      
        }
    public static void main(String[] args)
        {
        try {
            BioStar3034 app=new  BioStar3034();
            app.run();
            } 
        catch (Exception e)
            {
            e.printStackTrace();
            }
        }
    }