/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.phosphosite;
import org.biojava.nbio.structure.align.util.AtomCache;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.*;
import java.net.URL;
import java.nio.channels.FileChannel;
import java.nio.file.Files;
import java.nio.file.StandardCopyOption;
import java.util.ArrayList;
import java.util.List;
/**
* Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from
*
* http://www.phosphosite.org/staticDownloads.do
*
* Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations.
*
* Please cite : “Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.”.
*
*
*
* Created by ap3 on 31/10/2014.
*/
public class Dataset {
private static final Logger logger = LoggerFactory.getLogger(Dataset.class);
public static final String ACETYLATION = "http://www.phosphosite.org/downloads/Acetylation_site_dataset.gz";
public static final String DISEASE_ASSOC = "http://www.phosphosite.org/downloads/Disease-associated_sites.gz";
public static final String METHYLATION = "http://www.phosphosite.org/downloads/Methylation_site_dataset.gz";
public static final String PHOSPHORYLATION = "http://www.phosphosite.org/downloads/Phosphorylation_site_dataset.gz";
public static final String REGULATORY = "http://www.phosphosite.org/downloads/Regulatory_sites.gz";
public static final String SUMOYLATION = "http://www.phosphosite.org/downloads/Sumoylation_site_dataset.gz";
public static final String UBIQUITINATION = "http://www.phosphosite.org/downloads/Ubiquitination_site_dataset.gz";
public Dataset(){
}
private String[] getRemoteFiles(){
String[] files = new String[]{ACETYLATION,DISEASE_ASSOC,METHYLATION,PHOSPHORYLATION,REGULATORY,SUMOYLATION,UBIQUITINATION};
return files;
}
public File[] getLocalFiles(){
String[] rfiles = getRemoteFiles();
File dir = getLocalDir();
List<File> files = new ArrayList<File>();
for ( String f : rfiles) {
int slashIndex = f.lastIndexOf("/");
String fileName = f.substring(slashIndex);
File localFile = new File(dir+"/" + fileName);
if ( localFile.exists()){
files.add(localFile);
}
}
return files.toArray(new File[files.size()]);
}
public File getLocalDir(){
AtomCache cache = new AtomCache();
String path = cache.getCachePath();
File dir = new File(path+"/phosphosite");
return dir;
}
public void download(){
logger.warn("Downloading data from www.phosposite.org. Data is under CC-BY-NC-SA license. Please link to site and cite: ");
logger.warn("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.");
File dir = getLocalDir();
if ( ! dir.exists()) {
// need to download all...
dir.mkdir();
}
String[] files = getRemoteFiles();
for ( String f : files){
try {
int slashIndex = f.lastIndexOf("/");
String fileName = f.substring(slashIndex);
File localFile = new File(dir+"/" + fileName);
if ( ! localFile.exists()){
URL u = new URL(f);
downloadFile(u, localFile);
}
} catch (Exception e){
e.printStackTrace();
}
}
}
public void downloadFile(URL u, File localFile) throws IOException {
logger.info("Downloading " + u);
File tmp = File.createTempFile("tmp","phosphosite");
InputStream is = u.openStream();
BufferedInputStream in = new BufferedInputStream(is);
FileOutputStream w = new FileOutputStream(tmp);
int i= 0;
byte[] bytesIn = new byte[300000];
while ((i = in.read(bytesIn)) >= 0) {
w.write(bytesIn,0,i);
}
in.close();
w.close();
// now copy tmp file to localFile
copyFile(tmp, localFile);
}
public static void copyFile(File src, File dst) throws IOException
{
Files.copy(src.toPath(), dst.toPath(), StandardCopyOption.REPLACE_EXISTING);
}
public static void main(String[] args) {
Dataset ds = new Dataset();
ds.download();
try {
for (File f : ds.getLocalFiles()) {
logger.info(f.getAbsolutePath());
List<Site> sites = Site.parseSites(f);
logger.info("Got " + sites.size() + " sites");
for (Site s : sites) {
if (s.getUniprot().equals("P50225") || s.getUniprot().equals("P48025")) {
logger.info(s.toString());
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}
}