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package org.snpeff.snpEffect.testCases.unity;

import org.junit.Test;
import org.snpeff.motif.Jaspar;
import org.snpeff.util.Gpr;

import junit.framework.Assert;

/**
 * Test case for Jaspar parsing
 *
 * @author pcingola
 */
public class TestCasesJaspar extends TestCasesBase {

	public TestCasesJaspar() {
		super();
	}

	@Test
	public void test_01() {
		Gpr.debug("Test");
		Jaspar jaspar = new Jaspar();
		jaspar.load(path("jaspar_old.txt.gz"));

		String actual = jaspar.getPwm("MA0001.1").toString().replace('\t', ' ');

		// Trim each line
		StringBuilder sb = new StringBuilder();
		for (String s : actual.split("\n"))
			sb.append(s.trim() + "\n");
		actual = sb.toString();

		// Compare to expected
		String expected = "Name: AGL3 Id: MA0001.1\n" //
				+ "Counts:\n" //
				+ "A          0           3          79          40          66          48          65          11          65           0\n" //
				+ "C         94          75           4           3           1           2           5           2           3           3\n" //
				+ "G          1           0           3           4           1           0           5           3          28          88\n" //
				+ "T          2          19          11          50          29          47          22          81           1           6\n" //
				+ "Max:          C           C           A           T           A           A           A           T           A           G\n" //
				+ "\n" //
				+ "Weights:\n" //
				+ "A       0.01        0.03        0.18        0.14        0.17        0.15        0.17        0.06        0.17        0.01\n" //
				+ "C       0.10        0.11        0.03        0.02        0.01        0.02        0.03        0.02        0.02        0.02\n" //
				+ "G       0.01        0.01        0.02        0.02        0.01        0.01        0.03        0.02        0.07        0.05\n" //
				+ "T       0.02        0.08        0.06        0.13        0.10        0.12        0.08        0.14        0.01        0.04\n" //
				+ "Max:          C           C           A           A           A           A           A           T           A           G\n" //
		;

		Assert.assertEquals(expected, actual);
	}

	@Test
	public void test_02() {
		Gpr.debug("Test");
		Jaspar jaspar = new Jaspar();
		jaspar.load(path("jaspar_2013.txt.gz"));

		String actual = jaspar.getPwm("MA0001.1").toString().replace('\t', ' ');

		// Trim each line
		StringBuilder sb = new StringBuilder();
		for (String s : actual.split("\n"))
			sb.append(s.trim() + "\n");
		actual = sb.toString();

		// Compare to expected
		String expected = "Name: SEP4 Id: MA0001.1\n" //
				+ "Counts:\n" //
				+ "A          0           3          79          40          66          48          65          11          65           0\n" //
				+ "C         94          75           4           3           1           2           5           2           3           3\n" //
				+ "G          1           0           3           4           1           0           5           3          28          88\n" //
				+ "T          2          19          11          50          29          47          22          81           1           6\n" //
				+ "Max:          C           C           A           T           A           A           A           T           A           G\n" //
				+ "\n" //
				+ "Weights:\n" //
				+ "A       0.01        0.03        0.18        0.14        0.17        0.15        0.17        0.06        0.17        0.01\n" //
				+ "C       0.10        0.11        0.03        0.02        0.01        0.02        0.03        0.02        0.02        0.02\n" //
				+ "G       0.01        0.01        0.02        0.02        0.01        0.01        0.03        0.02        0.07        0.05\n" //
				+ "T       0.02        0.08        0.06        0.13        0.10        0.12        0.08        0.14        0.01        0.04\n" //
				+ "Max:          C           C           A           A           A           A           A           T           A           G\n" //
		;

		Assert.assertEquals(expected, actual);
	}

}