com.github.autoprimer3.SequenceFromDasUcsc.java Source code

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Here is the source code for com.github.autoprimer3.SequenceFromDasUcsc.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.HashMap;
import java.util.Iterator;
import org.dom4j.Attribute;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.QName;
import org.dom4j.io.SAXReader;

/**
 *
 * @author David A. Parry <d.a.parry@leeds.ac.uk>
 */
public class SequenceFromDasUcsc {
    HashMap<String, String> buildToMapMaster = new HashMap<>();//maps build name to url e.g. hg19 => http://genome.cse.ucsc.edu:80/cgi-bin/das/hg19

    SequenceFromDasUcsc() {//get build names and DAS urls
        try {
            SAXReader reader = new SAXReader();
            URL url = new URL("http://genome.ucsc.edu/cgi-bin/das/dsn");//usa    
            //URL url = new URL("http://genome-euro.ucsc.edu/cgi-bin/das/dsn");    
            Document dasXml;
            dasXml = reader.read(url);
            Element root = dasXml.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");
                buildToMapMaster.put(build.getValue(), mapmaster.getText());
            }
        } catch (DocumentException | MalformedURLException ex) {
            //TO DO - handle (throw) this error properly
            ex.printStackTrace();
        }
    }

    //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 (!buildToMapMaster.containsKey(build)) {
            return null;
        } else {
            String chromNumber = chrom.replaceFirst("chr", "");
            int length = 0;
            URL entryPointUrl = new URL(buildToMapMaster.get(build) + "/entry_points");
            Document dasXml;
            SAXReader reader = new SAXReader();
            dasXml = reader.read(entryPointUrl);
            Element root = dasXml.getRootElement();
            for (Iterator i = root.elementIterator("ENTRY_POINTS"); i.hasNext();) {
                Element dsn = (Element) i.next();
                for (Iterator j = dsn.elementIterator("SEGMENT"); j.hasNext();) {
                    Element seg = (Element) j.next();
                    String id = seg.attributeValue("id");
                    if (id != null && id.equals(chromNumber)) {
                        String stop = seg.attributeValue("stop");
                        length = Integer.valueOf(stop);
                        break;
                    }
                }
            }
            if (length > 0) {
                end = end <= length ? end : length;
            }
            StringBuilder dna = new StringBuilder();
            URL genomeUrl = new URL(
                    buildToMapMaster.get(build) + "/dna?segment=" + chrom + ":" + (start + 1) + "," + end);
            dasXml = reader.read(genomeUrl);
            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();

        }

    }
}