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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.program.indexdb;
import java.io.File;
import java.io.IOException;
import java.net.URL;
import junit.framework.TestCase;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.db.SequenceDBLite;
import org.biojava.bio.seq.db.flat.FlatSequenceDB;
import org.biojava.bio.seq.io.SeqIOConstants;
/**
* <code>IndexToolsTest</code> tests indexing of flat files.
*
* @author Keith James
*/
public class IndexToolsTest extends TestCase
{
protected String location;
public IndexToolsTest(String name)
{
super(name);
}
protected void setUp() throws IOException
{
location = System.getProperty("java.io.tmpdir")
+ System.getProperty("file.separator")
+ "IndexToolsTest."
+ System.currentTimeMillis()
+ ".idx";
}
public void testIndexFastaDNA() throws Exception
{
File [] files = getDBFiles(new String [] { "dna1.fasta",
"dna2.fasta" });
IndexTools.indexFasta("test", new File(location),
files, SeqIOConstants.DNA);
SequenceDBLite db = new FlatSequenceDB(location, "dna");
Sequence seq1 = db.getSequence("id1");
assertEquals("gatatcgatt", seq1.seqString());
Sequence seq2 = db.getSequence("id2");
assertEquals("ggcgcgcgcg", seq2.seqString());
Sequence seq3 = db.getSequence("id3");
assertEquals("ccccccccta", seq3.seqString());
Sequence seq4 = db.getSequence("id4");
assertEquals("tttttcgatt", seq4.seqString());
Sequence seq5 = db.getSequence("id5");
assertEquals("ggttcgcgcg", seq5.seqString());
Sequence seq6 = db.getSequence("id6");
assertEquals("nnnnnnttna", seq6.seqString());
}
public void testIndexFastaRNA() throws Exception
{
File [] files = getDBFiles(new String [] { "rna1.fasta",
"rna2.fasta" });
IndexTools.indexFasta("test", new File(location),
files, SeqIOConstants.RNA);
SequenceDBLite db = new FlatSequenceDB(location, "rna");
Sequence seq1 = db.getSequence("id1");
assertEquals("gauaucgauu", seq1.seqString());
Sequence seq2 = db.getSequence("id2");
assertEquals("ggcgcgcgcg", seq2.seqString());
Sequence seq3 = db.getSequence("id3");
assertEquals("uuuuucgauu", seq3.seqString());
Sequence seq4 = db.getSequence("id4");
assertEquals("gguucgcgcg", seq4.seqString());
}
public void testIndexFastaProtein() throws Exception
{
File [] files = getDBFiles(new String [] { "protein1.fasta",
"protein2.fasta" });
IndexTools.indexFasta("test", new File(location),
files, SeqIOConstants.AA);
SequenceDBLite db = new FlatSequenceDB(location, "protein");
Sequence seq1 = db.getSequence("id1");
assertEquals("MTTSRGGGGG", seq1.seqString());
Sequence seq2 = db.getSequence("id2");
assertEquals("VVLLLLDDTN", seq2.seqString());
Sequence seq3 = db.getSequence("id3");
assertEquals("MVVVLNNGGG", seq3.seqString());
Sequence seq4 = db.getSequence("id4");
assertEquals("NGGDEEFDTN", seq4.seqString());
}
public void testIndexEmblDNA() throws Exception
{
File [] files = getDBFiles(new String [] { "part1.embl",
"part2.embl" });
IndexTools.indexEmbl("test", new File(location),
files, SeqIOConstants.DNA);
SequenceDBLite db = new FlatSequenceDB(location, "embl");
Sequence seq1 = db.getSequence("A16SRRNA");
assertEquals(1497, seq1.length());
Sequence seq2 = db.getSequence("A16STM112");
assertEquals(1346, seq2.length());
Sequence seq3 = db.getSequence("A16STM146");
assertEquals(1352, seq3.length());
Sequence seq4 = db.getSequence("AY080928");
assertEquals(557, seq4.length());
Sequence seq5 = db.getSequence("AY080929");
assertEquals(556, seq5.length());
Sequence seq6 = db.getSequence("AY080930");
assertEquals(557, seq6.length());
}
public void testIndexGenbankDNA() throws Exception
{
File [] files = getDBFiles(new String [] { "part1.gb",
"part2.gb" });
IndexTools.indexGenbank("test", new File(location),
files, SeqIOConstants.DNA);
SequenceDBLite db = new FlatSequenceDB(location, "genbank");
Sequence seq1 = db.getSequence("A16SRRNA");
assertEquals(1497, seq1.length());
Sequence seq2 = db.getSequence("A16STM112");
assertEquals(1346, seq2.length());
Sequence seq3 = db.getSequence("A16STM146");
assertEquals(1352, seq3.length());
Sequence seq4 = db.getSequence("AY080928");
assertEquals(557, seq4.length());
Sequence seq5 = db.getSequence("AY080929");
assertEquals(556, seq5.length());
Sequence seq6 = db.getSequence("AY080930");
assertEquals(557, seq6.length());
}
public void testIndexSwissprot() throws Exception
{
File [] files = getDBFiles(new String [] { "part1.swiss",
"part2.swiss" });
IndexTools.indexSwissprot("test", new File(location), files);
SequenceDBLite db = new FlatSequenceDB(location, "swiss");
Sequence seq1 = db.getSequence("104K_THEPA");
assertEquals(924, seq1.length());
Sequence seq2 = db.getSequence("108_LYCES");
assertEquals(102, seq2.length());
Sequence seq3 = db.getSequence("10KD_VIGUN");
assertEquals(75, seq3.length());
Sequence seq4 = db.getSequence("110K_PLAKN");
assertEquals(296, seq4.length());
Sequence seq5 = db.getSequence("11S3_HELAN");
assertEquals(493, seq5.length());
Sequence seq6 = db.getSequence("11SB_CUCMA");
assertEquals(480, seq6.length());
}
private File [] getDBFiles(String [] fileNames) throws Exception
{
File [] files = new File [fileNames.length];
for (int i = 0; i < files.length; i++)
{
URL seqURL = getClass().getResource(fileNames[i]);
files[i] = new File(seqURL.getFile());
}
return files;
}
}
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