-
Notifications
You must be signed in to change notification settings - Fork 379
/
CGIAlignmentReader.java
231 lines (195 loc) · 7.81 KB
/
CGIAlignmentReader.java
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
/*
* 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
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
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.broad.igv.logging.*;
import org.broad.igv.Globals;
import org.broad.igv.sam.Alignment;
import org.broad.igv.sam.SAMAlignment;
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 = LogManager.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 = HttpUtils.createURL(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 = HttpUtils.createURL(getHeaderURL());
is = HttpUtils.getInstance().openConnectionStream(url);
LineReader reader = new BufferedLineReader(is);
SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
header = codec.decode(reader, null);
} catch (Exception ex) {
log.error("Error loading header : ", ex);
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 = HttpUtils.createURL(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<SAMAlignment> iterator() {
try {
URL url = HttpUtils.createURL(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<SAMAlignment> 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 = HttpUtils.createURL(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 true;
}
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<SAMAlignment> iter = reader.query(chr, start, end, false);
while (iter.hasNext()) {
Alignment a = iter.next();
System.out.println(a);
}
}
}