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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.nbio.core.sequence.io;
import org.biojava.nbio.core.sequence.DNASequence;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.compound.DNACompoundSet;
import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
import org.biojava.nbio.core.sequence.io.util.ClasspathResource;
import org.biojava.nbio.core.sequence.loader.GenbankProxySequenceReader;
import org.junit.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.LinkedHashMap;
/**
*
* @author Scooter Willis <willishf at gmail dot com>
*/
public class GenbankCookbookTest {
private final static Logger logger = LoggerFactory.getLogger(GenbankCookbookTest.class);
public GenbankCookbookTest() {
}
@BeforeClass
public static void setUpClass() throws Exception {
}
@AfterClass
public static void tearDownClass() throws Exception {
}
@Before
public void setUp() {
}
@After
public void tearDown() {
}
/**
* Test of process method, of class GenbankReader.
*/
@Test
public void testProcess() throws Throwable {
/*
* Method 2: With the GenbankReaderHelper
*/
//Try with the GenbankReaderHelper
ClasspathResource dnaResource = new ClasspathResource("NM_000266.gb", true);
//File dnaFile = new File("src/test/resources/NM_000266.gb");
//File protFile = new File("src/test/resources/BondFeature.gb");
ClasspathResource protResource = new ClasspathResource("BondFeature.gb");
LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence(dnaResource.getInputStream());
for (DNASequence sequence : dnaSequences.values()) {
logger.info("DNA Sequence: {}", sequence.getSequenceAsString());
}
LinkedHashMap<String, ProteinSequence> protSequences = GenbankReaderHelper.readGenbankProteinSequence(protResource.getInputStream());
for (ProteinSequence sequence : protSequences.values()) {
logger.info("Protein Sequence: {}", sequence.getSequenceAsString());
}
/*
* Method 3: With the GenbankReader Object
*/
//Try reading with the GanbankReader
GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<DNASequence, NucleotideCompound>(
dnaResource.getInputStream(),
new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(),
new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())
);
dnaSequences = dnaReader.process();
logger.info("DNA Sequence: {}", dnaSequences);
GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<ProteinSequence, AminoAcidCompound>(
protResource.getInputStream(),
new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(),
new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())
);
protSequences = protReader.process();
logger.info("Protein Sequence: {}", protSequences);
}
}
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