annotate java-genomics-toolkit/src/edu/unc/genomics/ngs/BaseAlignCounts.java @ 0:1daf3026d231

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package edu.unc.genomics.ngs;

import java.io.BufferedWriter;
import java.io.IOException;
import java.nio.charset.Charset;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.Iterator;

import org.apache.log4j.Logger;

import com.beust.jcommander.Parameter;

import edu.ucsc.genome.TrackHeader;
import edu.unc.genomics.Assembly;
import edu.unc.genomics.CommandLineTool;
import edu.unc.genomics.Interval;
import edu.unc.genomics.io.IntervalFile;

public class BaseAlignCounts extends CommandLineTool {
	
	private static final Logger log = Logger.getLogger(BaseAlignCounts.class);
		
	@Parameter(names = {"-i", "--input"}, description = "Input file (reads)", required = true)
	public IntervalFile<? extends Interval> intervalFile;
	@Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true)
	public Assembly assembly;
	@Parameter(names = {"-x", "--extend"}, description = "Extend reads from 5' end (default = read length)")
	public Integer extend;
	@Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true)
	public Path outputFile;
	
	@Override
	public void run() throws IOException {
		log.debug("Initializing output file");
		int mapped = 0;
		try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
			// Write the Wiggle track header to the output file
			TrackHeader header = new TrackHeader("wiggle_0");
			header.setName("Converted " + intervalFile.getPath().getFileName());
			header.setDescription("Converted " + intervalFile.getPath().getFileName());
			writer.write(header.toString());
			writer.newLine();
			
			// Process each chromosome in the assembly
			for (String chr : assembly) {
				log.debug("Processing chromosome " + chr);
				// Write the contig header to the output file
				writer.write("fixedStep chrom="+chr+" start=1 step=1 span=1");
				writer.newLine();
				
				int start = 1;
				while (start < assembly.getChrLength(chr)) {
					int stop = start + DEFAULT_CHUNK_SIZE - 1;
					int length = stop - start + 1;
					int[] count = new int[length];
					
					Iterator<? extends Interval> it = intervalFile.query(chr, start, stop);
					while (it.hasNext()) {
						Interval entry = it.next();
						int entryStop = entry.getStop();
						if (extend != null) {
							if (entry.isWatson()) {
								entryStop = entry.getStart() + extend;
							} else {
								entryStop = entry.getStart() - extend;
							}
						}
						
						for (int i = entry.getStart(); i <= entryStop; i++) {
							count[i-start]++;
						}
						mapped++;
					}
					
					// Write the count at each base pair to the output file
					for (int i = 0; i < count.length; i++) {
						writer.write(count[i]);
						writer.newLine();
					}
					
					// Process the next chunk
					start = stop + 1;
				}
			}
		}
		
		log.info("Mapped "+mapped+" reads");
	}
	
	public static void main(String[] args) {
		new BaseAlignCounts().instanceMain(args);
	}
}