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* Copyright (c) 2007-2015 Broad Institute
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package org.broad.igv.feature.genome;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.IOException;
import java.util.Map;
import static org.junit.Assert.assertEquals;
/**
* @author Jim Robinson
* @date 3/26/12
*/
public class FastaSequenceParserTest {
static InMemorySequence fastaSequence;
@BeforeClass
public static void setup() throws IOException {
String path = "http://data.broadinstitute.org/igvdata/test/fasta/ci2_test.fa";
Map<String, byte[]> sequenceMap = FastaSequenceParser.parseFasta(path);
fastaSequence = new InMemorySequence(sequenceMap);
}
@Test
public void testReadSequence() throws Exception {
String chr = "chr02q";
int start = 3531385;
int end = 3531425;
String expectedSequence = "TAATTTTTACGTCTTATTTAAACACATATAATGAATAGGT";
byte[] seq = fastaSequence.getSequence(chr, start, end);
String seqString = new String(seq);
assertEquals(expectedSequence, seqString);
}
@Test
public void testReadEnd() throws Exception {
String chr = "chr02q";
int chrLen = 8059593;
int start = chrLen - 10;
int end = chrLen + 10;
byte[] bytes = fastaSequence.getSequence(chr, start, end);
assertEquals(10, bytes.length);
byte[] expectedSequence = "TTTTTCCCAG".getBytes();
for (int i = 0; i < 10; i++) {
assertEquals(expectedSequence[i], bytes[i]);
}
}
}