TestDinucCovariate.java

// Copyright (C) 2011-2012 CRS4.
//
// This file is part of Seal.
//
// Seal is free software: you can redistribute it and/or modify it
// under the terms of the GNU General Public License as published by the Free
// Software Foundation, either version 3 of the License, or (at your option)
// any later version.
//
// Seal is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
// or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
// for more details.
//
// You should have received a copy of the GNU General Public License along
// with Seal.  If not, see <http://www.gnu.org/licenses/>.

package tests.it.crs4.seal.recab;

import it.crs4.seal.recab.DinucCovariate;
import it.crs4.seal.common.TextSamMapping;

import org.junit.*;
import static org.junit.Assert.*;

import java.util.List;
import java.util.Arrays;

import org.apache.hadoop.io.Text;

public class TestDinucCovariate
{
	private static final String dna = "AGCTTC";
	private static final String complement = "TCGAAG";
	private static final String sam = "id	flag	chr6	1	37	22M	=	41	60	" + dna + "	5:CB:C	RG:Z:myrg";

	private DinucCovariate cov;
	private TextSamMapping mapping;
	private List<String> answers;

	@Before
	public void setup()
	{
		cov = new DinucCovariate();
		mapping = null;
		answers = null;
	}

	@Test
	public void testForwardRead()
	{
		String record = sam.replace("flag", "67"); // forward, read 1
		mapping = new TextSamMapping( new Text(record) );
		cov.applyToMapping(mapping);

		answers = Arrays.asList( "NN", "AG", "GC", "CT", "TT", "TC" );

		for (int i = 0; i < dna.length(); ++i)
			assertEquals(("at index " + i), answers.get(i), cov.getValue(i));
	}

	@Test
	public void testReverseRead()
	{
		String record = sam.replace("flag", "83"); // reverse strand, read 1
		mapping = new TextSamMapping(new Text(record));
		cov.applyToMapping(mapping);

		answers = Arrays.asList( "CT", "GC", "AG", "AA", "GA", "NN" );

		for (int i = 0; i < dna.length(); ++i)
			assertEquals(("at index " + i), answers.get(i), cov.getValue(i));
	}

	@Test
	public void testReadWithN()
	{
		String record = sam.replace("flag", "67"); // forward, read 1
		record = record.replace(dna, "AGCNTC"); // forward, read 1
		mapping = new TextSamMapping( new Text(record) );
		cov.applyToMapping(mapping);

		answers = Arrays.asList( "NN", "AG", "GC", "CN", "NN", "TC" );

		for (int i = 0; i < answers.size(); ++i)
			assertEquals(("at index " + i), answers.get(i), cov.getValue(i));
	}

	@Test
	public void testReverseReadWithN()
	{
		String record = sam.replace("flag", "83"); // revese strand, read 1
		record = record.replace(dna, "AGCNTC");
		mapping = new TextSamMapping( new Text(record) );
		cov.applyToMapping(mapping);

		answers = Arrays.asList( "CT", "GC", "NN", "AN", "GA", "NN" );

		for (int i = 0; i < answers.size(); ++i)
			assertEquals(("at index " + i), answers.get(i), cov.getValue(i));
	}

	@Test(expected=RuntimeException.class)
	public void testDidntCallApplyToMapping()
	{
		cov.getValue(1);
	}

	@Test(expected=IndexOutOfBoundsException.class)
	public void testOutOfBounds()
	{
		String record = sam.replace("flag", "67");
		mapping = new TextSamMapping( new Text(record) );
		cov.applyToMapping(mapping);
		cov.getValue(100);
	}

	public static void main(String args[]) {
		org.junit.runner.JUnitCore.main(TestDinucCovariate.class.getName());
	}
}