/*
* The MIT License
*
* Copyright (c) 2009 The 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 htsjdk.samtools.reference;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.util.Random;
/**
* Tests for the reading of reference sequences in various formats.
*
* @author Tim Fennell
*/
public class ReferenceSequenceTests {
private static final byte[] BASES = "acgtACGTN".getBytes();
private final Random random = new Random();
@Test(dataProvider="fastaTestParameters")
public void testSingleShortSequence(int chroms, int basesPerChrom) throws Exception {
File f = makeRandomReference(chroms, basesPerChrom);
ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(f);
for (int i=1; i<=chroms; ++i) {
ReferenceSequence seq = ref.nextSequence();
Assert.assertNotNull(seq);
Assert.assertEquals(seq.length(), basesPerChrom);
Assert.assertEquals(seq.getName(), "chr" + i);
Assert.assertEquals(seq.getContigIndex(), i-1);
}
Assert.assertNull(ref.nextSequence());
}
@DataProvider
Object[][] fastaTestParameters() {
return new Object[][] {
new Object[] { 1, 60},
new Object[] { 2, 60},
new Object[] {10, 60},
new Object[] { 1, 1000},
new Object[] { 2, 1000},
new Object[] {10, 1000},
new Object[] { 1, 250000},
new Object[] { 2, 250000},
new Object[] {10, 250000}
};
}
/** Utility method to write a random reference sequence of specified length. */
private File makeRandomReference(int chroms, int basesPerChrom) throws Exception {
File file = File.createTempFile("reference.", ".fasta");
file.deleteOnExit();
BufferedWriter out = new BufferedWriter(new FileWriter(file));
for (int i=1; i<=chroms; ++i) {
out.write("> chr" + i);
out.newLine();
for (int j=1; j<=basesPerChrom; ++j) {
out.write(BASES[random.nextInt(BASES.length)]);
if (j % 80 == 0 || j == basesPerChrom) out.newLine();
}
}
out.flush();
out.close();
return file;
}
}