org.snpeff.ped.PedPedigree 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.ped;

import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Set;

import org.snpeff.collections.AutoHashMap;
import org.snpeff.util.Gpr;

/**
 * A pedigree of PedEntries
 * 
 * @author pcingola
 */
public class PedPedigree implements Iterable, Comparable {

	boolean verbose = false;
	HashMap tfamEntryById = new HashMap();
	List tfamEntries;
	PlinkMap plinkMap;

	public PedPedigree() {
		tfamEntryById = new HashMap();
		tfamEntries = new ArrayList();
	}

	public PedPedigree(String tfamFileName) {
		tfamEntryById = new HashMap();
		tfamEntries = new ArrayList();
		loadTfam(tfamFileName);
	}

	/**
	 * Add an entry to this pedigree
	 * @param tfamEntry
	 */
	public void add(TfamEntry tfamEntry) {
		tfamEntryById.put(tfamEntry.getId(), tfamEntry);
		tfamEntries.add(tfamEntry);
	}

	@Override
	public int compareTo(PedPedigree ped) {
		return getFamilyId().compareTo(ped.getFamilyId());
	}

	/**
	 * Split data into families
	 * @return
	 */
	public Collection families() {
		AutoHashMap families = new AutoHashMap(new PedPedigree());

		// Add each individual to its corresponding family
		for (TfamEntry ind : this) {
			String fid = ind.getFamilyId();
			PedPedigree ped = families.getOrCreate(fid);
			ped.add(ind);
		}

		return families.values();
	}

	public TfamEntry get(String id) {
		return tfamEntryById.get(id);
	}

	public String getFamilyId() {
		if (tfamEntries.isEmpty()) return "";
		return tfamEntries.get(0).getFamilyId();
	}

	public PlinkMap getPlinkMap() {
		return plinkMap;
	}

	/**
	 * Get a list of sample IDs
	 * @return
	 */
	public List getSampleIds() {
		ArrayList sampleIds = new ArrayList();
		for (TfamEntry te : tfamEntries)
			sampleIds.add(te.id);
		return sampleIds;
	}

	@Override
	public Iterator iterator() {
		return tfamEntries.iterator();
	}

	public Set keySet() {
		return tfamEntryById.keySet();
	}

	/**
	 * Load a pedigree from a PED and MAP file pair
	 * 
	 * @param pedFileName
	 */
	public void load(String pedFileName) {
		String pedBaseFileName = Gpr.removeExt(pedFileName);
		String mapFile = pedBaseFileName + ".map";

		PedFileIterator pedFile = new PedFileIterator(pedFileName, mapFile);

		// Load all entries for this family
		int count = 1;
		for (PedEntry pe : pedFile) {
			if (verbose) Gpr.showMarkStderr(count++, 1);
			add(pe);
		}

		plinkMap = pedFile.getPlinkMap();
	}

	/**
	 * Load a TFAM file
	 * @param tfamFileName
	 */
	public void loadTfam(String tfamFileName) {
		String tfamStr = Gpr.readFile(tfamFileName);
		if (tfamStr.isEmpty()) throw new RuntimeException("Cannot read file '" + tfamFileName + "'");

		for (String line : tfamStr.split("\n")) {
			if (line.startsWith("#")) continue; // Skip comments

			try {
				TfamEntry te = new TfamEntry(line);
				add(te);
			} catch (Throwable t) {
				throw new RuntimeException("Error parsing line from PED/TFAM file:\n\tFile name : '" + tfamFileName + "\n\tLine: '" + line + "'", t);
			};
		}
	}

	/**
	 * Save pedigree as a TFAM file
	 * @param fileName
	 */
	public void saveTfam(String fileName) {
		StringBuilder sb = new StringBuilder();
		for (TfamEntry te : this)
			sb.append(te + "\n");

		Gpr.toFile(fileName, sb.toString());
	}

	public void setVerbose(boolean verbose) {
		this.verbose = verbose;
	}

	public int size() {
		return tfamEntryById.size();
	}

	@Override
	public String toString() {
		StringBuilder sb = new StringBuilder();
		for (TfamEntry te : this)
			sb.append(te.toString() + "\n");
		return sb.toString();
	}

	public Collection values() {
		return tfamEntryById.values();
	}
}