Mercurial > repos > timpalpant > java_genomics_toolkit
diff java-genomics-toolkit/src/edu/unc/genomics/nucleosomes/Phasogram.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/nucleosomes/Phasogram.java Mon Feb 13 21:55:55 2012 -0500 @@ -0,0 +1,71 @@ +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 org.apache.log4j.Logger; + +import com.beust.jcommander.Parameter; + +import edu.unc.genomics.CommandLineTool; +import edu.unc.genomics.CommandLineToolException; +import edu.unc.genomics.io.WigFile; +import edu.unc.genomics.io.WigFileException; + +public class Phasogram extends CommandLineTool { + + private static final Logger log = Logger.getLogger(Phasogram.class); + + @Parameter(names = {"-i", "--input"}, description = "Input wig file (read counts)", required = true) + public WigFile inputFile; + @Parameter(names = {"-m", "--max"}, description = "Maximum phase shift", required = true) + public int maxPhase; + @Parameter(names = {"-o", "--output"}, description = "Output file (histogram)", required = true) + public Path outputFile; + + public void run() throws IOException { + long[] phaseCounts = new long[maxPhase+1]; + + // Process each chromosome in the assembly + for (String chr : inputFile.chromosomes()) { + log.debug("Processing chromosome " + chr); + + int start = inputFile.getChrStart(chr); + while (start < inputFile.getChrStop(chr)) { + int stop = start + DEFAULT_CHUNK_SIZE - 1; + + try { + float[] data = WigFile.flattenData(inputFile.query(chr, start, stop), start, stop); + for (int i = 0; i < data.length-maxPhase; i++) { + for (int j = 0; j <= maxPhase; j++) { + phaseCounts[j] += data[i]; + } + } + + } catch (WigFileException e) { + log.fatal("Error querying data from Wig file!"); + e.printStackTrace(); + throw new CommandLineToolException("Error querying data from Wig file!"); + } + + // Process the next chunk + start = stop - maxPhase + 1; + } + } + + log.debug("Writing output to disk"); + try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { + for (int i = 0; i < phaseCounts.length; i++) { + writer.write(i+"\t"+phaseCounts[i]); + writer.newLine(); + } + } + } + + public static void main(String[] args) { + new Phasogram().instanceMain(args); + } +} \ No newline at end of file