/*
* 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
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.cli_plugin;
import org.broad.igv.Globals;
import org.broad.igv.track.FeatureSource;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.track.TrackLoader;
import org.broad.igv.track.TribbleFeatureSource;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.RuntimeUtils;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.Feature;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.BufferedReader;
import java.io.FileReader;
import java.util.*;
import static org.junit.Assert.*;
/**
* User: jacob
* Date: 2012/05/01
*/
public class BEDToolsPluginSourceTest extends AbstractPluginTest {
@BeforeClass
public static void setUpClass() throws Exception {
pluginPath = "resources/bedtools_plugin.xml";
AbstractPluginTest.setUpClass();
}
@Test
public void testBedToolsPath() throws Exception {
String resp = RuntimeUtils.executeShellCommand(new String[]{toolPath}, null, null);
String line0 = resp.split("\n")[0];
assertEquals("bedtools: flexible tools for genome arithmetic and DNA sequence analysis.", line0.trim());
}
@Test
public void testGetPath() throws Exception {
String path = System.getenv("PATH");
//System.out.println("System path: " + path);
assertNotNull(path);
}
private List<Feature> tstOperationBED3(String cmdArg, int expectedNumFeatures) throws Exception {
String pathA = TestUtils.DATA_DIR + "bed/test.bed";
String pathB = TestUtils.DATA_DIR + "bed/test2.bed";
return tstOperationBED(new String[]{pathA, pathB}, cmdArg, expectedNumFeatures);
}
private List<Feature> tstOperationBED6(String cmdArg, int expectedNumFeatures) throws Exception {
String pathA = TestUtils.DATA_DIR + "bed/H3K4me1_sample_bed6.bed";
String pathB = TestUtils.DATA_DIR + "bed/H3K4me3_sample_bed6.bed";
return tstOperationBED(new String[]{pathA, pathB}, cmdArg, expectedNumFeatures);
}
private List<Feature> tstOperationBED(String[] paths,
String cmd, int expectedNumFeatures) throws Exception {
PluginSpecReader.Command command = findCommandElementByName(tool, cmd);
List<Argument> argumentList = command.argumentList;
LinkedHashMap<Argument, Object> arguments = new LinkedHashMap<Argument, Object>(argumentList.size());
int argnum = 0;
int numArgsSet = 0;
if(cmd.equalsIgnoreCase("intersect")){
numArgsSet = 2;
}else if(cmd.equalsIgnoreCase("coverage")){
numArgsSet = 1;
}
for(; argnum < numArgsSet; argnum++){
Argument argument = argumentList.get(argnum);
Object value = argumentList.get(argnum).getDefaultValue();
if(argument.getType() == Argument.InputType.BOOL){
value = Boolean.parseBoolean((String) value);
}
arguments.put(argument, value);
}
List<FeatureTrack> trackList = new ArrayList<FeatureTrack>(paths.length);
TrackLoader loader = new TrackLoader();
for (String path : paths) {
TestUtils.createIndex(path);
FeatureTrack track = (FeatureTrack) loader.load(new ResourceLocator(path), genome).get(0);
trackList.add(track);
}
if (cmd.equals("multiinter")) {
arguments.put(argumentList.get(argnum++), trackList);
} else {
for (FeatureTrack ft : trackList) {
arguments.put(argumentList.get(argnum++), ft);
}
}
//Optional arguments
arguments.put(argumentList.get(argnum), argumentList.get(argnum).getDefaultValue());
List<String> commands = Arrays.asList(toolPath, cmd);
PluginFeatureSource combinedFeatureSource = new PluginFeatureSource(commands, arguments, command.outputList.get(0), pluginPath);
Iterator<Feature> features = combinedFeatureSource.getFeatures("chr1", 0, (int) 1e6);
List<Feature> featureList = new ArrayList(10);
while (features.hasNext()) {
featureList.add(features.next());
}
assertEquals("Unexpected number of features in result of " + cmd, expectedNumFeatures, featureList.size());
return featureList;
}
@Test
public void testOperationsBED3() throws Exception {
Map<String, Integer> expectedNumFeatures = new HashMap(6);
expectedNumFeatures.put("intersect", 4);
expectedNumFeatures.put("subtract", 2);
expectedNumFeatures.put("closest", 6);
expectedNumFeatures.put("window", 9);
expectedNumFeatures.put("coverage", 3);
expectedNumFeatures.put("multiinter", 3);
for (Map.Entry<String, Integer> entry : expectedNumFeatures.entrySet()) {
tstOperationBED3(entry.getKey(), entry.getValue());
}
}
@Test
public void testOperationsBED6() throws Exception {
Map<String, Integer> expectedNumFeatures = new HashMap(6);
expectedNumFeatures.put("intersect", 5);
expectedNumFeatures.put("subtract", 18);
expectedNumFeatures.put("closest", 19);
expectedNumFeatures.put("window", 12);
expectedNumFeatures.put("coverage", 14);
expectedNumFeatures.put("multiinter", 3);
for (Map.Entry<String, Integer> entry : expectedNumFeatures.entrySet()) {
tstOperationBED6(entry.getKey(), entry.getValue());
}
}
@Test
public void testIntersectBED() throws Exception {
List<Feature> actFeatures = tstOperationBED3("intersect", 4);
String expectedPath = TestUtils.DATA_DIR + "bed/isect_res.bed";
TestUtils.createIndex(expectedPath);
FeatureSource expFeatureSource = TribbleFeatureSource.getFeatureSource(new ResourceLocator(expectedPath), genome);
Iterator<Feature> expFeatures = expFeatureSource.getFeatures("chr1", 0, (int) 1e6);
TestUtils.assertFeatureListsEqual(expFeatures, actFeatures.iterator());
}
@Test
public void testClosestBED() throws Exception {
List<Feature> actFeatures = tstOperationBED3("closest", 6);
String expectedPath = TestUtils.DATA_DIR + "bed/closest_res.bed";
BufferedReader reader = new BufferedReader(new FileReader(expectedPath));
int ind = 0;
String line = null;
while ((line = reader.readLine()) != null) {
String[] tokens = Globals.singleTabMultiSpacePattern.split(line);
String expChr = tokens[3];
int expStart = Integer.parseInt(tokens[4]);
int expEnd = Integer.parseInt(tokens[5]);
if (expChr.equalsIgnoreCase(".")) {
continue;
}
Feature actFeature = actFeatures.get(ind);
assertEquals(expChr, actFeature.getChr());
assertEquals(expStart, actFeature.getStart());
assertEquals(expEnd, actFeature.getEnd());
ind++;
}
}
@Test
public void testMultiinterBED() throws Exception {
String beddir = TestUtils.DATA_DIR + "bed/";
String[] bedfiles = new String[]{beddir + "test.bed", beddir + "test2.bed", beddir + "isect_res.bed"};
Iterator<Feature> features = tstOperationBED(bedfiles, "multiinter", 3).iterator();
int ind = 0;
int[] expStarts = new int[]{100, 200, 300};
int[] expEnds = new int[]{101, 201, 301};
while (features.hasNext()) {
Feature feat = features.next();
assertEquals(expStarts[ind], feat.getStart());
assertEquals(expEnds[ind], feat.getEnd());
ind++;
}
}
/**
* Test to make sure we are parsing the 2nd files features
*
* @throws Exception
*/
@Test
public void testWindow() throws Exception {
List<Feature> features = tstOperationBED3("window", 9);
Set<Integer> startsSet = new HashSet<Integer>(Arrays.asList(100, 150, 175));
Set<Integer> endsSet = new HashSet<Integer>(Arrays.asList(101, 201, 375));
for (Feature feat : features) {
assertTrue("Feature start not found in expected set", startsSet.contains(feat.getStart()));
assertTrue("Feature end not found in expected set", endsSet.contains(feat.getEnd()));
}
}
}