/** * 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.seq.io; import java.io.BufferedReader; import java.io.ByteArrayOutputStream; import java.io.IOException; import java.io.InputStream; import java.io.InputStreamReader; import junit.framework.Test; import junit.framework.TestCase; import junit.framework.TestSuite; import org.biojava.bio.BioException; import org.biojava.bio.seq.Sequence; import org.biojava.bio.seq.SequenceIterator; import org.biojava.bio.symbol.SymbolList; /** * JUnit test for SeqIOTools objects * @author David Huen * @since 1.3 */ public class SeqIOToolsTest extends TestCase { public SeqIOToolsTest(String name) { super(name); } private boolean compareSymbolLists(SymbolList sl0, SymbolList sl1) { // compare lengths if (sl0.length() != sl1.length()) return false; // compare symbols for (int i=1; i <= sl0.length(); i++) { if (sl0.symbolAt(i) != sl1.symbolAt(i)) return false; } return true; } public void testDNAReadersAndWriters() { /******* test readFastaDNA *********/ // get access to the test file InputStream inputS = this.getClass().getResourceAsStream("/files/AY069118.fa"); assertNotNull(inputS); // get SequenceIterator SequenceIterator seqI = SeqIOTools.readFastaDNA( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence fastaDNASeq = null; try { fastaDNASeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(fastaDNASeq); // is its length correct? assertEquals("Fasta sequence AY069118.fa had incorrect length", fastaDNASeq.length(), 1502); ByteArrayOutputStream baos = new ByteArrayOutputStream(); try { SeqIOTools.writeFasta(baos, fastaDNASeq); } catch (IOException ex) { fail(ex.getMessage()); } /******* test readGenbank **********/ // get access to the test file inputS = this.getClass().getResourceAsStream("/files/AY069118.gb"); assertNotNull(inputS); // get SequenceIterator seqI = SeqIOTools.readGenbank( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence genbankDNASeq = null; try { genbankDNASeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(genbankDNASeq); // is its length correct? assertEquals("Genbank sequence AY069118.gb had incorrect length", genbankDNASeq.length(), 1502); // compare with fasta reference assertTrue(compareSymbolLists(fastaDNASeq, genbankDNASeq)); baos = new ByteArrayOutputStream(); try { SeqIOTools.writeFasta(baos, genbankDNASeq); } catch (IOException ex) { fail(ex.getMessage()); } /******* test readGenbankXml ***********/ // get access to the test file inputS = this.getClass().getResourceAsStream("/files/AY069118-gb.xml"); assertNotNull(inputS); // get SequenceIterator seqI = SeqIOTools.readGenbankXml( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence genbankXmlDNASeq = null; try { genbankXmlDNASeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(genbankXmlDNASeq); // is its length correct? assertEquals("GenbankXml sequence AY069118-gb.xml had incorrect length", genbankXmlDNASeq.length(), 1502); // compare with fasta reference assertTrue(compareSymbolLists(fastaDNASeq, genbankXmlDNASeq)); baos = new ByteArrayOutputStream(); try { SeqIOTools.writeFasta(baos, genbankXmlDNASeq); } catch (IOException ex) { fail(ex.getMessage()); } /******* test readEmblNucleotide **********/ // get access to the test file inputS = this.getClass().getResourceAsStream("/files/AY069118.em"); assertNotNull(inputS); // get SequenceIterator seqI = SeqIOTools.readEmblNucleotide( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence emblDNASeq = null; try { emblDNASeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(emblDNASeq); // is its length correct? assertEquals("Genbank sequence AY069118.em had incorrect length", emblDNASeq.length(), 1502); // compare with fasta reference assertTrue(compareSymbolLists(fastaDNASeq, emblDNASeq)); baos = new ByteArrayOutputStream(); try { SeqIOTools.writeFasta(baos, emblDNASeq); } catch (IOException ex) { fail(ex.getMessage()); } } public void testProteinReadersAndWriters() { /******* test readFastaProtein *********/ // get access to the test file InputStream inputS = this.getClass().getResourceAsStream("/files/AAL039263.fa"); assertNotNull(inputS); // get SequenceIterator SequenceIterator seqI = SeqIOTools.readFastaProtein( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence fastaProteinSeq = null; try { fastaProteinSeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(fastaProteinSeq); // is its length correct? assertEquals("Fasta sequence AAL39263.fa had incorrect length", fastaProteinSeq.length(), 370); ByteArrayOutputStream baos = new ByteArrayOutputStream(); try { SeqIOTools.writeFasta(baos, fastaProteinSeq); } catch (IOException ex) { fail(ex.getMessage()); } /******* test readGenpept **********/ // get access to the test file inputS = this.getClass().getResourceAsStream("/files/AAL039263.gb"); assertNotNull(inputS); // get SequenceIterator seqI = SeqIOTools.readGenpept( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence genbankProteinSeq = null; try { genbankProteinSeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(genbankProteinSeq); // is its length correct? assertEquals("Genbank sequence AAL39263.gb had incorrect length", genbankProteinSeq.length(), 370); // compare with fasta reference assertTrue(compareSymbolLists(fastaProteinSeq, genbankProteinSeq)); baos = new ByteArrayOutputStream(); try { SeqIOTools.writeGenpept(baos, genbankProteinSeq); } catch (Exception ex) { fail(ex.getMessage()); } /******* test readSwissProt **********/ // get access to the test file System.out.println("Testing SP read"); System.out.println("Testing SP read"); inputS = this.getClass().getResourceAsStream("/files/AAC4_HUMAN.sp"); assertNotNull(inputS); // get SequenceIterator seqI = SeqIOTools.readSwissprot( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence swissProteinSeq = null; try { swissProteinSeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(swissProteinSeq); // is its length correct? assertEquals("SwissProt sequence AAC4_HUMAN.sp had incorrect length", swissProteinSeq.length(), 911); baos = new ByteArrayOutputStream(); try { SeqIOTools.writeSwissprot(baos, swissProteinSeq); } catch (Exception ex) { fail(ex.getMessage()); } } public void testBigDNA() { /****** read big sequence as fasta ***********/ // get access to the test file InputStream inputS = this.getClass().getResourceAsStream("/files/NC_004432.fa"); assertNotNull(inputS); // get SequenceIterator SequenceIterator seqI = SeqIOTools.readFastaDNA( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence bigFastaDNASeq = null; try { bigFastaDNASeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(bigFastaDNASeq); // is its length correct? assertEquals("Fasta sequence NC_004432.fa had incorrect length", bigFastaDNASeq.length(), 1358633); /****** read big sequence as genbank ***********/ // get access to the test file inputS = this.getClass().getResourceAsStream("/files/NC_004432.gb"); assertNotNull(inputS); // get SequenceIterator seqI = SeqIOTools.readGenbank( new BufferedReader(new InputStreamReader(inputS))); // get sequence assertTrue(seqI.hasNext()); Sequence bigGenbankDNASeq = null; try { bigGenbankDNASeq = seqI.nextSequence(); } catch (BioException be) {} assertNotNull(bigGenbankDNASeq); // is its length correct? assertEquals("Genbank sequence NC_004432.gb had incorrect length", bigGenbankDNASeq.length(), 1358633); // compare with fasta reference assertTrue(compareSymbolLists(bigFastaDNASeq, bigGenbankDNASeq)); } public void testIdentifyFormat() { // Test formats which may be in any alphabet String [] formats = new String [] { "raw", "fasta", "nbrf", "ig", "embl", "genbank", "refseq", "gcg", "gff", "clustal", "msf" }; int [] formatIds = new int [] { SeqIOConstants.RAW, SeqIOConstants.FASTA, SeqIOConstants.NBRF, SeqIOConstants.IG, SeqIOConstants.EMBL, SeqIOConstants.GENBANK, SeqIOConstants.REFSEQ, SeqIOConstants.GCG, SeqIOConstants.GFF, AlignIOConstants.CLUSTAL, AlignIOConstants.MSF }; String [] alphas = new String [] { "dna", "rna", "aa", "protein" }; int [] alphaIds = new int [] { SeqIOConstants.DNA, SeqIOConstants.RNA, SeqIOConstants.AA, SeqIOConstants.AA }; for (int i = 0; i < formats.length; i++) { for (int j = 0; j < alphas.length; j++) { assertEquals((formatIds[i] | alphaIds[j]), SeqIOTools.identifyFormat(formats[i], alphas[j])); } } // Test formats which throw exceptions unless in a specific // alphabet assertEquals(SeqIOConstants.SWISSPROT, SeqIOTools.identifyFormat("swissprot", "protein")); assertEquals(SeqIOConstants.SWISSPROT, SeqIOTools.identifyFormat("swissprot", "aa")); assertEquals(SeqIOConstants.SWISSPROT, SeqIOTools.identifyFormat("swiss", "protein")); assertEquals(SeqIOConstants.SWISSPROT, SeqIOTools.identifyFormat("swiss", "aa")); assertEquals(SeqIOConstants.GENPEPT, SeqIOTools.identifyFormat("genpept", "protein")); assertEquals(SeqIOConstants.GENPEPT, SeqIOTools.identifyFormat("genpept", "aa")); assertEquals(SeqIOConstants.PDB, SeqIOTools.identifyFormat("pdb", "protein")); assertEquals(SeqIOConstants.PDB, SeqIOTools.identifyFormat("pdb", "aa")); assertEquals(SeqIOConstants.PHRED, SeqIOTools.identifyFormat("phred", "dna")); } // creates a suite public static Test suite() { TestSuite suite = new TestSuite(SeqIOToolsTest.class); return suite; } // harness for tests public static void main(String [] args) { junit.textui.TestRunner.run(suite()); } }