Mercurial > repos > timpalpant > java_genomics_toolkit
view src/edu/unc/genomics/nucleosomes/MapDyads.java @ 2:e16016635b2a
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author | timpalpant |
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date | Mon, 13 Feb 2012 22:12:06 -0500 |
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package edu.unc.genomics.nucleosomes; 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.PositiveIntegerValidator; import edu.unc.genomics.io.IntervalFile; public class MapDyads extends CommandLineTool { private static final Logger log = Logger.getLogger(MapDyads.class); @Parameter(names = {"-i", "--input"}, description = "Input file (reads)", required = true) public IntervalFile<? extends Interval> inputFile; @Parameter(names = {"-s", "--size"}, description = "Mononucleosome length (default: read length)", validateWith = PositiveIntegerValidator.class) public Integer nucleosomeSize; @Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true) public Assembly assembly; @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 " + inputFile.getPath().getFileName()); header.setDescription("Converted " + inputFile.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 = inputFile.query(chr, start, stop); while (it.hasNext()) { Interval entry = it.next(); if (nucleosomeSize == null) { count[entry.center()-start]++; } else { count[entry.getStart()+nucleosomeSize-start]++; } mapped++; } // Write the average 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 MapDyads().instanceMain(args); } }