/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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package org.broad.igv.sam.reader;
import htsjdk.samtools.*;
import htsjdk.samtools.util.BufferedLineReader;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.LineReader;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.sam.Alignment;
import org.broad.igv.sam.PicardAlignment;
import org.broad.igv.util.HttpUtils;
import org.broad.igv.util.stream.IGVSeekableStreamFactory;
import java.io.*;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
/**
* Reader for querying a CGI service for SAM (note not BAM) files.
*
* @author Jim Robinson
* @date 12/15/11
* <p/>
* Example URLs:
* http://host/query.cgi?file=input.sam&start=800&end=900&contained=true
* http://host/samHeader.cgi?file=input.sam
* http://phhost/getSequenceNames.cgi?file=input.sam
*/
public class CGIAlignmentReader implements AlignmentReader {
private static Logger log = Logger.getLogger(CGIAlignmentReader.class);
private final SamReaderFactory factory;
String baseURL;
String queryScript = "query.cgi";
String headerScript = "samHeader.cgi";
String seqNameScript = "getSequenceNames.cgi";
String query;
SAMFileHeader header;
List<String> sequenceNames;
public CGIAlignmentReader(String url) throws MalformedURLException {
URL u = new URL(url);
int port = u.getPort();
baseURL = u.getProtocol() + "://" + u.getHost();
if (port > 0) baseURL += ":" + port;
baseURL += u.getPath();
query = u.getQuery();
factory = SamReaderFactory.makeDefault().
validationStringency(ValidationStringency.SILENT);
loadHeader();
}
// The URL methods are package-scope to allow unit testing
String getHeaderURL() {
return baseURL.replace(queryScript, headerScript) + "?" + query;
}
String getSequenceNamesURL() {
return baseURL.replace(queryScript, seqNameScript) + "?" + query;
}
String getQueryURL() {
return baseURL + "?" + query;
}
public void close() throws IOException {
//Nothing to do. Could notify server that we are done, if that is useful
}
/**
* Try to load header, if there are any errors just set to null and continue. The header is optional
*/
private void loadHeader() {
InputStream is = null;
try {
URL url = new URL(getHeaderURL());
is = HttpUtils.getInstance().openConnectionStream(url);
LineReader reader = new BufferedLineReader(is);
SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
header = codec.decode(reader, null);
} catch (Exception ex) {
log.info("Error loading header : " + ex.getMessage());
header = null;
} finally {
if (is != null) {
try {
is.close();
} catch (IOException ex) {
log.error("Error closing url stream", ex);
}
}
}
}
public List<String> getSequenceNames() {
if (sequenceNames == null) {
InputStream is = null;
try {
URL url = new URL(getSequenceNamesURL());
is = HttpUtils.getInstance().openConnectionStream(url);
BufferedReader br = new BufferedReader(new InputStreamReader(is));
sequenceNames = new ArrayList<String>();
String nextLine;
while ((nextLine = br.readLine()) != null) {
String[] tokens = nextLine.split("\\s+");
for (String seq : tokens) {
sequenceNames.add(seq);
}
}
} catch (IOException e) {
log.error("Error fetching sequence names", e);
return null;
} finally {
if (is != null) try {
is.close();
} catch (IOException e) {
log.error(e);
}
}
}
return sequenceNames;
}
public Set<String> getPlatforms() {
return AlignmentReaderFactory.getPlatforms(getFileHeader());
}
public SAMFileHeader getFileHeader() {
if(header == null) {
loadHeader();
}
return header;
}
public CloseableIterator<PicardAlignment> iterator() {
try {
URL url = new URL(getQueryURL());
InputStream is = HttpUtils.getInstance().openConnectionStream(url);
BufferedInputStream stream = new BufferedInputStream(is, 500000);
SamInputResource resource = SamInputResource.of(stream);
SamReader reader = factory.open(resource);
CloseableIterator<SAMRecord> iter = reader.iterator();
return new SAMQueryIterator(iter);
} catch (IOException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
return null;
}
}
public CloseableIterator<PicardAlignment> query(String sequence, int start, int end, boolean contained) throws IOException {
try {
//
final String parameters = "&chr=" + sequence + "&start=" + start + "&end=" + end +
"&contained=" + contained;
//String encodedParameters = URLEncoder.encode(parameters);
URL url = new URL(getQueryURL() + parameters);
InputStream is = HttpUtils.getInstance().openConnectionStream(url);
BufferedInputStream stream = new BufferedInputStream(is, 500000);
SamInputResource resource = SamInputResource.of(stream);
SamReader reader = factory.open(resource);
CloseableIterator<SAMRecord> iter = reader.iterator();
return new SAMQueryIterator(sequence, start, end, contained, iter);
} catch (IOException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
return null;
}
}
public boolean hasIndex() {
return false; //To change body of implemented methods use File | Settings | File Templates.
}
public static void main(String[] args) throws IOException {
Globals.setHeadless(true);
CGIAlignmentReader reader = new CGIAlignmentReader("http://philtest.batcave.net/query.cgi?file=input.sam");
String chr = "gi|66043271|ref|NC_007005.1|";
int start = 800;
int end = 900;
CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, false);
while (iter.hasNext()) {
Alignment a = iter.next();
System.out.println(a);
}
}
}