Mercurial > repos > timpalpant > java_genomics_toolkit
diff src/edu/unc/genomics/nucleosomes/NRLCalculator.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/edu/unc/genomics/nucleosomes/NRLCalculator.java Mon Feb 13 22:12:06 2012 -0500 @@ -0,0 +1,93 @@ +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.ArrayList; +import java.util.Collections; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import org.apache.log4j.Logger; + +import com.beust.jcommander.Parameter; + +import edu.unc.genomics.CommandLineTool; +import edu.unc.genomics.Interval; +import edu.unc.genomics.ReadablePathValidator; +import edu.unc.genomics.io.IntervalFile; + +public class NRLCalculator extends CommandLineTool { + + private static final Logger log = Logger.getLogger(NRLCalculator.class); + + @Parameter(names = {"-i", "--input"}, description = "Input file (nucleosome calls)", required = true, validateWith = ReadablePathValidator.class) + public Path inputFile; + @Parameter(names = {"-l", "--loci"}, description = "Genomic loci (Bed format)", required = true) + public IntervalFile<? extends Interval> lociFile; + @Parameter(names = {"-o", "--output"}, description = "Output file (NRL for each gene)", required = true) + public Path outputFile; + + private Map<String,List<NucleosomeCall>> nucs = new HashMap<>(); + + private List<NucleosomeCall> getIntervalNucleosomes(Interval i) { + List<NucleosomeCall> intervalNucs = new ArrayList<>(); + for (NucleosomeCall call : nucs.get(i.getChr())) { + if (call.getDyad() >= i.low() && call.getDyad() <= i.high()) { + intervalNucs.add(call); + } + } + + return intervalNucs; + } + + @Override + public void run() throws IOException { + log.debug("Initializing input file"); + NucleosomeCallsFile nucsFile = new NucleosomeCallsFile(inputFile); + log.debug("Loading all nucleosomes"); + for (NucleosomeCall nuc : nucsFile) { + if (nuc == null) continue; + if (!nucs.containsKey(nuc.getChr())) { + nucs.put(nuc.getChr(), new ArrayList<NucleosomeCall>()); + } + nucs.get(nuc.getChr()).add(nuc); + } + nucsFile.close(); + + log.debug("Initializing output file"); + try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) { + log.debug("Calculating nucleosome spacing for each interval"); + NucleosomeCall.DyadComparator comparator = new NucleosomeCall.DyadComparator(); + for (Interval interval : lociFile) { + writer.write(interval.toBed()); + + // Get all of the nucleosomes within this interval + List<NucleosomeCall> intervalNucs = getIntervalNucleosomes(interval); + + if (intervalNucs.size() > 1) { + // Sort the list by nucleosome position + Collections.sort(intervalNucs, comparator); + if (interval.isCrick()) { + Collections.reverse(intervalNucs); + } + + for (int i = 1; i < Math.min(intervalNucs.size(), 10); i++) { + writer.write("\t" + Math.abs(intervalNucs.get(i).getDyad()-intervalNucs.get(i-1).getDyad())); + } + } + + writer.newLine(); + } + } + + lociFile.close(); + } + + public static void main(String[] args) throws IOException { + new NRLCalculator().instanceMain(args); + } +} \ No newline at end of file