package jalview.ext.ensembl; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; import jalview.io.FastaFile; import jalview.io.FileParse; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyLite; import java.lang.reflect.Method; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; public class EnsemblSeqProxyTest { private static final Object[][] allSeqs = new Object[][] { { new EnsemblProtein(), "CCDS5863.1", ">CCDS5863.1\n" + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n" + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n" + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n" + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n" + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n" + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n" + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n" + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n" + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n" + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n" + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n" + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n" + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" }, { new EnsemblCdna(), "CCDS5863.1", ">CCDS5863.1\n" + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n" + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n" + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n" + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n" + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n" + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n" + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n" + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n" + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n" + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n" + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n" + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n" + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n" + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n" + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n" + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n" + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n" + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n" + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n" + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n" + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n" + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n" + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n" + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n" + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n" + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n" + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n" + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n" + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n" + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n" + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n" + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n" + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n" + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n" + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n" + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n" + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n" + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n" + "GGTGCGTTTCCTGTCCACTGA\n" }, { new EnsemblProtein(), "ENSP00000288602", ">ENSP00000288602\n" + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n" + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n" + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n" + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n" + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n" + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n" + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n" + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n" + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n" + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n" + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n" + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n" + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } }; @BeforeClass public void setUp() { SequenceOntologyFactory.setInstance(new SequenceOntologyLite()); } @AfterClass public void tearDown() { SequenceOntologyFactory.setInstance(null); } @DataProvider(name = "ens_seqs") public Object[][] createData(Method m) { System.out.println(m.getName()); return allSeqs; } @Test(dataProvider = "ens_seqs", suiteName = "live") public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq) throws Exception { FileParse fp = proxy.getSequenceReader(Arrays .asList(new String[] { sq })); SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray(); FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE); SequenceI[] trueSqs = trueRes.getSeqsAsArray(); Assert.assertEquals(sqs.length, trueSqs.length, "Different number of sequences retrieved for query " + sq); Alignment ral = new Alignment(sqs); for (SequenceI tr : trueSqs) { SequenceI[] rseq; Assert.assertNotNull( rseq = ral.findSequenceMatch(tr.getName()), "Couldn't find sequences matching expected sequence " + tr.getName()); Assert.assertEquals(rseq.length, 1, "Expected only one sequence for sequence ID " + tr.getName()); Assert.assertEquals( rseq[0].getSequenceAsString(), tr.getSequenceAsString(), "Sequences differ for " + tr.getName() + "\n" + "Exp:" + tr.getSequenceAsString() + "\n" + "Got:" + rseq[0].getSequenceAsString()); } } @Test(suiteName = "live") public void testLiveCheckEnsembl() { EnsemblRestClient sf = new EnsemblRestClient() { @Override public String getDbName() { // TODO Auto-generated method stub return null; } @Override public AlignmentI getSequenceRecords(String queries) throws Exception { // TODO Auto-generated method stub return null; } @Override protected URL getUrl(List ids) throws MalformedURLException { // TODO Auto-generated method stub return null; } @Override protected boolean useGetRequest() { // TODO Auto-generated method stub return false; } @Override protected String getRequestMimeType(boolean b) { // TODO Auto-generated method stub return null; } @Override protected String getResponseMimeType() { // TODO Auto-generated method stub return null; } }; boolean isAvailable = sf.isEnsemblAvailable(); System.out.println("Ensembl is " + (isAvailable ? "UP!" : "DOWN or unreachable ******************* BAD!")); } /** * Tests for the method that computes all peptide variants given codon * variants */ @Test(groups = "Functional") public void testComputePeptideVariants() { String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } }; /* * AGT codes for S - this is not included in the variants returned */ List variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S"); assertEquals("[]", variants.toString()); // S is reported if it differs from the current value (A): variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A"); assertEquals("[S]", variants.toString()); /* * synonymous variant is not reported */ codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } }; // AGC and AGT both code for S variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s"); assertEquals("[]", variants.toString()); /* * equivalent variants are only reported once */ codonVariants = new String[][] { { "C" }, { "T" }, { "A", "C", "G", "T" } }; // CTA CTC CTG CTT all code for L variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S"); assertEquals("[L]", variants.toString()); /* * vary codons 1 and 2; variant products are sorted and non-redundant */ codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } }; // aga ata cga cta code for R, I, R, L variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S"); assertEquals("[I, L, R]", variants.toString()); /* * vary codons 2 and 3 */ codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } }; // aga agc ata atc code for R, S, I, I variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S"); assertEquals("[I, R]", variants.toString()); /* * vary codons 1 and 3 */ codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } }; // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S"); assertEquals("[K, N, Y, STOP]", variants.toString()); /* * vary codons 1, 2 and 3 */ codonVariants = new String[][] { { "a", "t" }, { "G", "C" }, { "t", "g" } }; // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S"); assertEquals("[C, R, T, W]", variants.toString()); } /** * Tests for the method that maps the subset of a dna sequence that has CDS * (or subtype) feature. */ @Test(groups = "Functional") public void testGetCdsRanges() { EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter(); SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt"); dnaSeq.createDatasetSequence(); SequenceI ds = dnaSeq.getDatasetSequence(); // CDS for dna 3-6 SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null); ds.addSequenceFeature(sf); // exon feature should be ignored here sf = new SequenceFeature("exon", "", 7, 9, 0f, null); ds.addSequenceFeature(sf); // CDS for dna 10-12 sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null); ds.addSequenceFeature(sf); List ranges = new ArrayList(); int mappedLength = testee.getCdsRanges(dnaSeq, ranges); assertEquals(6, mappedLength); assertEquals(2, ranges.size()); assertEquals(4, ranges.get(0)[0]); assertEquals(6, ranges.get(0)[1]); assertEquals(10, ranges.get(1)[0]); assertEquals(12, ranges.get(1)[1]); } @Test(groups = "Functional") public void getGenomicRangesFromFeatures() { } /** * Tests for the method that maps the subset of a dna sequence that has CDS * (or subtype) feature - case where the start codon is incomplete. */ @Test(groups = "Functional") public void testGetCdsRanges_fivePrimeIncomplete() { EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter(); SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt"); dnaSeq.createDatasetSequence(); SequenceI ds = dnaSeq.getDatasetSequence(); // CDS for dna 5-6 (incomplete codon), 7-9 SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null); sf.setPhase("2"); // skip 2 bases to start of next codon ds.addSequenceFeature(sf); // CDS for dna 13-15 sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null); ds.addSequenceFeature(sf); List ranges = new ArrayList(); int mappedLength = testee.getCdsRanges(dnaSeq, ranges); /* * check the mapping starts with the first complete codon */ assertEquals(6, mappedLength); assertEquals(2, ranges.size()); assertEquals(7, ranges.get(0)[0]); assertEquals(9, ranges.get(0)[1]); assertEquals(13, ranges.get(1)[0]); assertEquals(15, ranges.get(1)[1]); } @Test(groups = "Functional") public void testIsTranscriptIdentifier() { assertFalse(EnsemblSeqProxy.isTranscriptIdentifier(null)); assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("")); assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENSG00000012345")); assertTrue(EnsemblSeqProxy.isTranscriptIdentifier("ENST00000012345")); assertTrue(EnsemblSeqProxy.isTranscriptIdentifier("ENSMUST00000012345")); assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("enst00000012345")); assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENST000000123456")); assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENST0000001234")); } @Test(groups = "Functional") public void testIsGeneIdentifier() { assertFalse(EnsemblSeqProxy.isGeneIdentifier(null)); assertFalse(EnsemblSeqProxy.isGeneIdentifier("")); assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENST00000012345")); assertTrue(EnsemblSeqProxy.isGeneIdentifier("ENSG00000012345")); assertTrue(EnsemblSeqProxy.isGeneIdentifier("ENSMUSG00000012345")); assertFalse(EnsemblSeqProxy.isGeneIdentifier("ensg00000012345")); assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENSG000000123456")); assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENSG0000001234")); } }