org.snpeff.snpEffect.commandLine.SnpEffCmdDump Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation
Variant annotation and effect prediction package.
The newest version!
package org.snpeff.snpEffect.commandLine;

import org.snpeff.SnpEff;
import org.snpeff.interval.Cds;
import org.snpeff.interval.Exon;
import org.snpeff.interval.Gene;
import org.snpeff.interval.Intron;
import org.snpeff.interval.Marker;
import org.snpeff.interval.Transcript;
import org.snpeff.interval.Utr;
import org.snpeff.interval.tree.Itree;
import org.snpeff.util.Timer;

/**
 * Command line program: Build database
 *
 * @author pcingola
 */
public class SnpEffCmdDump extends SnpEff {

	public enum DumpFormat {
		DUMP, BED, TXT
	}

	DumpFormat dumpFormat = DumpFormat.DUMP;
	String chrStr = "";

	public SnpEffCmdDump() {
		super();
	}

	/**
	 * Parse command line arguments
	 * 
	 * @param args
	 */
	@Override
	public void parseArgs(String[] args) {
		this.args = args;
		for (int i = 0; i < args.length; i++) {

			// Argument starts with '-'?
			if (args[i].startsWith("-")) {
				if (args[i].equalsIgnoreCase("-chr"))
					chrStr = args[++i];
				else if (args[i].equals("-bed")) {
					dumpFormat = DumpFormat.BED;
					// inOffset = outOffset = 0;
				} else if (args[i].equals("-txt")) {
					dumpFormat = DumpFormat.TXT;
					// inOffset = outOffset = 1;
				} else
					usage("Unknown option '" + args[i] + "'");
			} else if (genomeVer.length() <= 0)
				genomeVer = args[i];
			else
				usage("Unknown parameter '" + args[i] + "'");
		}

		// Check: Do we have all required parameters?
		if (genomeVer.isEmpty())
			usage("Missing genomer_version parameter");
	}

	/**
	 * Show all intervals in BED format References:
	 * http://genome.ucsc.edu/FAQ/FAQformat.html#format1
	 */
	void print() {
		// Show title
		if (dumpFormat == DumpFormat.TXT)
			System.out.println(
					"chr\tstart\tend\tstrand\ttype\tid\tgeneName\tgeneId\tnumberOfTranscripts\tcanonicalTranscriptLength\ttranscriptId\tcdsLength\tnumerOfExons\texonRank\texonSpliceType");

		for (Itree tree : config.getSnpEffectPredictor().getIntervalForest()) {
			for (Marker i : tree) {
				try {
					print(i);

					// Show gene specifics
					if (i instanceof Gene) {
						Gene g = (Gene) i;

						// Show transcripts: UTR and Exons
						for (Transcript t : g) {
							print(t);

							for (Cds c : t.getCds())
								print(c);

							for (Utr u : t.getUtrs())
								print(u);

							for (Exon e : t)
								print(e);

							for (Intron intron : t.introns())
								print(intron);
						}
					}
				} catch (Throwable t) {
					t.printStackTrace();
				}
			}
		}
	}

	/**
	 * Print a marker
	 */
	void print(Marker marker) {
		if (dumpFormat == DumpFormat.BED)
			printBed(marker);
		else if (dumpFormat == DumpFormat.TXT)
			printTxt(marker);
	}

	/**
	 * Show a marker in BED format
	 */
	void printBed(Marker marker) {
		String chr = chrStr + marker.getChromosome().getId();
		int start = marker.getStart(); // The starting position of the feature in the chromosome or scaffold. The first
										// base in a chromosome is numbered 0.
		int end = marker.getEnd() + 1; // The ending position of the feature in the chromosome or scaffold. The
										// chromEnd base is not included in the display of the feature.
		String name = marker.getClass().getSimpleName() + "_" + marker.getId();
		System.out.println(chr + "\t" + start + "\t" + end + "\t" + name);
	}

	/**
	 * Print as a TXT format
	 */
	void printTxt(Marker marker) {
		String chr = chrStr + marker.getChromosome().getId();
		int start = marker.getStart(); // The starting position of the feature in the chromosome or scaffold. The first
										// base in a chromosome is numbered 0.
		int end = marker.getEnd() + 1; // The ending position of the feature in the chromosome or scaffold. The
										// chromEnd base is not included in the display of the feature.

		StringBuilder info = new StringBuilder();
		info.append(chr);
		info.append("\t" + start);
		info.append("\t" + end);
		info.append("\t" + (marker.isStrandPlus() ? "+1" : "-1"));
		info.append("\t" + marker.getClass().getSimpleName());
		info.append("\t" + marker.getId());

		// Add gene info
		Gene gene = null;
		if (marker instanceof Gene)
			gene = (Gene) marker;
		else if (marker != null)
			gene = (Gene) marker.findParent(Gene.class);

		if (gene != null) {
			Transcript canonical = gene.canonical();
			info.append("\t" + gene.getGeneName() //
					+ "\t" + gene.getId() //
					+ "\t" + gene.numChilds() //
					+ "\t" + (canonical == null ? 0 : canonical.cds().length()) //
			);
		} else
			info.append("\t\t\t\t");

		// Add transcript info
		Transcript tr = null;
		if (marker instanceof Transcript)
			tr = (Transcript) marker;
		else if (marker != null)
			tr = (Transcript) marker.findParent(Transcript.class);

		if (tr != null)
			info.append("\t" + tr.getId() //
					+ "\t" + tr.cds().length() //
					+ "\t" + tr.numChilds() //
			);
		else
			info.append("\t\t\t");

		// Add exon info
		Exon exon = null;
		if (marker instanceof Exon)
			exon = (Exon) marker;
		else if (marker != null)
			exon = (Exon) marker.findParent(Exon.class);

		if (exon != null)
			info.append("\t" + exon.getRank() //
					+ "\t" + exon.getSpliceType() //
			);
		else
			info.append("\t\t");

		System.out.println(info);
	}

	/**
	 * Run according to command line options
	 */
	@Override
	public boolean run() {
		// ---
		// Dump database
		// ---
		loadConfig(); // Read config file
		loadDb();

		// Build forest
		if (verbose)
			Timer.showStdErr("Building interval forest");
		config.getSnpEffectPredictor().buildForest();
		if (verbose)
			Timer.showStdErr("Done.");

		// Dump database
		if (dumpFormat == DumpFormat.DUMP)
			config.getSnpEffectPredictor().print();
		else if ((dumpFormat == DumpFormat.BED) || (dumpFormat == DumpFormat.TXT))
			print();
		else
			throw new RuntimeException("Unimplemented format '" + dumpFormat + "'");

		return true;
	}

	/**
	 * Show 'usage;' message and exit with an error code '-1'
	 * 
	 * @param message
	 */
	@Override
	public void usage(String message) {
		if (message != null)
			System.err.println("Error: " + message + "\n");
		System.err.println("snpEff version " + VERSION);
		System.err.println("Usage: snpEff dump [options] genome_version");
		System.err.println("\t-bed                    : Dump in BED format (implies -0)");
		System.err.println(
				"\t-chr            : Prepend 'string' to chromosome name (e.g. 'chr1' instead of '1')");
		System.err.println("\t-txt                    : Dump as a TXT table (implies -1)");
		System.err.println("\nGeneric options:");
		System.err.println("\t-0                      : Output zero-based coordinates. ");
		System.err.println("\t-1                      : Output one-based coordinates");
		System.exit(-1);
	}
}