Mercurial > repos > timpalpant > java_genomics_toolkit
diff java-genomics-toolkit/src/edu/unc/genomics/converters/IntervalToWig.java @ 0:1daf3026d231
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author | timpalpant |
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date | Mon, 13 Feb 2012 21:55:55 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/java-genomics-toolkit/src/edu/unc/genomics/converters/IntervalToWig.java Mon Feb 13 21:55:55 2012 -0500 @@ -0,0 +1,91 @@ +package edu.unc.genomics.converters; + +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.Interval; +import edu.unc.genomics.CommandLineTool; +import edu.unc.genomics.ValuedInterval; +import edu.unc.genomics.io.IntervalFile; + +public class IntervalToWig extends CommandLineTool { + + private static final Logger log = Logger.getLogger(IntervalToWig.class); + + @Parameter(names = {"-i", "--input"}, description = "Input file (Bed/BedGraph)", required = true) + public IntervalFile<? extends Interval> intervalFile; + @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.info(intervalFile.count() + " entries in input"); + + log.debug("Initializing output file"); + 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]; + float[] sum = new float[length]; + + Iterator<? extends Interval> it = intervalFile.query(chr, start, stop); + while (it.hasNext()) { + ValuedInterval entry = (ValuedInterval) it.next(); + if (entry.getValue() != null) { + for (int i = entry.getStart(); i <= entry.getStop(); i++) { + sum[i-start] += entry.getValue().floatValue(); + count[i-start]++; + } + } + } + + // Write the average at each base pair to the output file + for (int i = 0; i < sum.length; i++) { + if (count[i] == 0) { + writer.write(String.valueOf(Float.NaN)); + } else { + writer.write(String.valueOf(sum[i]/count[i])); + } + writer.newLine(); + } + + // Process the next chunk + start = stop + 1; + } + } + } + } + + public static void main(String[] args) { + new IntervalToWig().instanceMain(args); + } + +}