TestSiteSnpIndelAnno.java

package fionaApp;
import org.junit.Assert;

import com.novelbio.analysis.seq.fasta.SeqFasta;
import com.novelbio.analysis.seq.genome.GffChrAbs;
import com.novelbio.database.model.species.Species;

public class TestSiteSnpIndelAnno {
	
		GffChrAbs gffChrAbs;
		
		public void before() {
			Species species = new Species(9606);
			species.setVersion("hg19_GRCh37");
			gffChrAbs = new GffChrAbs(species);
		}
		
		public void testSnpAnnoNormCis() {
			SiteSnpIndelAnno siteSnpIndelAnno = new SiteSnpIndelAnno(gffChrAbs);
			String chrId = "chr1";
			int startLoc = 218578574;
			String refNr = "T", thisNr = "A";
			siteSnpIndelAnno.setSite(chrId, refNr, thisNr);
			siteSnpIndelAnno.anno();
			Assert.assertEquals("ATG", siteSnpIndelAnno.getRefNr().toString());
			Assert.assertEquals("AAG", siteSnpIndelAnno.getThisNr().toString());
			
			chrId = "chr1";
			startLoc = 218578573;
			refNr = "A"; thisNr = "G";
			siteSnpIndelAnno.setSite(chrId, refNr, thisNr);
			siteSnpIndelAnno.anno();
			Assert.assertEquals("ATG".toLowerCase(), siteSnpIndelAnno.getRefNr().toString());
			Assert.assertEquals("GTG".toLowerCase(), siteSnpIndelAnno.getThisNr().toString());
			
			chrId = "chr1";
			startLoc = 218578575;
			refNr = "G"; thisNr = "C";
			siteSnpIndelAnno.setSite(chrId, refNr, thisNr);
			siteSnpIndelAnno.anno();
			Assert.assertEquals("ATG".toLowerCase(), siteSnpIndelAnno.getRefNr().toString());
			Assert.assertEquals("ATC".toLowerCase(), siteSnpIndelAnno.getThisNr().toString());
		}
		
		public void testSnpAnnoNormTrans() {
			SiteSnpIndelAnno siteSnpIndelAnno = new SiteSnpIndelAnno(gffChrAbs);
			String chrId = "chr17";
			int startLoc = 7577534;
			String refNr = "C", thisNr = "A";
			siteSnpIndelAnno.setSite(chrId, refNr, thisNr);
			siteSnpIndelAnno.anno();
			Assert.assertEquals("AGG", siteSnpIndelAnno.getRefNr().toString());
			Assert.assertEquals("AGT", siteSnpIndelAnno.getThisNr().toString());
			
			chrId = "chr1";
			startLoc = 7577535;
			refNr = "C"; thisNr = "G";
			siteSnpIndelAnno.setSite(chrId, refNr, thisNr);
			siteSnpIndelAnno.anno();
			Assert.assertEquals("AGG".toLowerCase(), siteSnpIndelAnno.getRefNr().toString());
			Assert.assertEquals("ACG".toLowerCase(), siteSnpIndelAnno.getThisNr().toString());
			
			chrId = "chr1";
			startLoc = 7577536;
			refNr = "T"; thisNr = "C";
			siteSnpIndelAnno.setSite(chrId, refNr, thisNr);
			siteSnpIndelAnno.anno();
			Assert.assertEquals("AGG".toLowerCase(), siteSnpIndelAnno.getRefNr().toString());
			Assert.assertEquals("GGG".toLowerCase(), siteSnpIndelAnno.getThisNr().toString());
		}
		
		
		
		
	}

}