com.github.autoprimer3.GetUcscBuildsAndTables.java Source code

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Here is the source code for com.github.autoprimer3.GetUcscBuildsAndTables.java

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/*
 * Copyright (C) 2014 David A. Parry <d.a.parry@leeds.ac.uk>
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
package com.github.autoprimer3;

import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashMap;
import org.dom4j.Attribute;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;

/**
 *
 * @author David A. Parry <d.a.parry@leeds.ac.uk>
 * 
 * Connect to DAS server on UCSC and retrieve all genome builds in constructor
 * The method getAvailableTables returns all available tables for a given build
 */
public class GetUcscBuildsAndTables {

    private HashMap<String, String> buildToMapMaster = new HashMap<>();
    //maps build name to url e.g. hg19 => http://genome.cse.ucsc.edu:80/cgi-bin/das/hg19
    //a list of IDs so we can retrieve them in the same order they're given
    private LinkedHashMap<String, String> buildToDescription = new LinkedHashMap<>();
    //maps build name to description e.g. hg19 => 'Human Feb. 2009 (GRCh37/hg19) Genome at UCSC'

    private Document dasGenomeXml;

    //get build names and DAS urls
    public void connectToUcsc() throws DocumentException, MalformedURLException {
        SAXReader reader = new SAXReader();
        URL url = new URL("http://genome.ucsc.edu/cgi-bin/das/dsn");
        //URL url = new URL("http://genome-euro.ucsc.edu/cgi-bin/das/dsn");
        dasGenomeXml = reader.read(url);
        readDasGenomeXmlDocument();
    }

    public void readDasGenomeXmlDocument() {
        if (dasGenomeXml == null) {
            return;
        }
        Element root = dasGenomeXml.getRootElement();
        for (Iterator i = root.elementIterator("DSN"); i.hasNext();) {
            Element dsn = (Element) i.next();
            Element source = dsn.element("SOURCE");
            Attribute build = source.attribute("id");
            Element mapmaster = dsn.element("MAPMASTER");
            Element desc = dsn.element("DESCRIPTION");
            buildToMapMaster.put(build.getValue(), mapmaster.getText());
            buildToDescription.put(build.getValue(), desc.getText());
        }
    }

    public Document getDasGenomeXmlDocument() {
        return dasGenomeXml;
    }

    public void setDasGenomeXmlDocument(Document document) {
        dasGenomeXml = document;
    }

    public HashMap<String, String> getBuildToMapMaster() {
        return buildToMapMaster;
    }

    public LinkedHashMap<String, String> getBuildToDescription() {
        return buildToDescription;
    }

    public ArrayList<String> getBuildIds() {
        return new ArrayList<>(buildToDescription.keySet());
    }

    public String getGenomeDescription(String genome) {
        return buildToDescription.get(genome);
    }

    public Document getTableXmlDocument(String build) throws DocumentException, MalformedURLException {
        SAXReader reader = new SAXReader();
        URL url = new URL("http://genome.ucsc.edu/cgi-bin/das/" + build + "/types");
        Document dasXml;
        dasXml = reader.read(url);
        return dasXml;
    }

    //uses 0-based coordinates for compatibility with gene tables, bed etc., although DAS uses 1-based
    public String retrieveSequence(String build, String chrom, Integer start, Integer end)
            throws DocumentException, MalformedURLException {
        if (buildToDescription.isEmpty()) {
            this.connectToUcsc();
        }
        if (!buildToMapMaster.containsKey(build)) {
            return null;
        } else {
            StringBuilder dna = new StringBuilder();
            URL genomeUrl = new URL(
                    buildToMapMaster.get(build) + "/dna?segment=" + chrom + ":" + (start + 1) + "," + end);
            SAXReader reader = new SAXReader();
            Document dasXml;
            dasXml = reader.read(genomeUrl);
            Element root = dasXml.getRootElement();
            for (Iterator i = root.elementIterator("SEQUENCE"); i.hasNext();) {
                Element dsn = (Element) i.next();
                Element seq = dsn.element("DNA");
                String text = seq.getText().replaceAll("\n", "");
                dna.append(text);
                //dna.append(seq.getText());
            }
            return dna.toString();

        }

    }

}