X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxyTest.java;h=77f6b8bebd7e32801555bea5b1ee4f577af3825e;hb=b342c421914723ac1b3403280cb8bc346011326e;hp=7ef8dd79cc899be0bd999dbf01b6c29bed00d4bd;hpb=e24933a537e0f640c75d4685c468615872bc77fc;p=jalview.git diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java index 7ef8dd7..77f6b8b 100644 --- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java +++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java @@ -1,26 +1,42 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.ext.ensembl; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; +import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; 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.gui.JvOptionPane; +import jalview.io.DataSourceType; 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; @@ -28,9 +44,16 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; - public class EnsemblSeqProxyTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + private static final Object[][] allSeqs = new Object[][] { { new EnsemblProtein(), @@ -110,13 +133,13 @@ public class EnsemblSeqProxyTest + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n" + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } }; - @BeforeClass + @BeforeClass(alwaysRun = true) public void setUp() { SequenceOntologyFactory.setInstance(new SequenceOntologyLite()); } - @AfterClass + @AfterClass(alwaysRun = true) public void tearDown() { SequenceOntologyFactory.setInstance(null); @@ -130,14 +153,13 @@ public class EnsemblSeqProxyTest } @Test(dataProvider = "ens_seqs", suiteName = "live") - public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq) - throws Exception + public void testGetOneSeqs(EnsemblRestClient proxy, String sq, + String fastasq) throws Exception { FileParse fp = proxy.getSequenceReader(Arrays - .asList(new String[] - { sq })); + .asList(new String[] { sq })); SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray(); - FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE); + FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE); SequenceI[] trueSqs = trueRes.getSeqsAsArray(); Assert.assertEquals(sqs.length, trueSqs.length, "Different number of sequences retrieved for query " + sq); @@ -157,167 +179,8 @@ public class EnsemblSeqProxyTest "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") @@ -327,63 +190,66 @@ public class EnsemblSeqProxyTest } /** - * 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 the method that appends a single allele's reverse complement to a + * string buffer */ @Test(groups = "Functional") - public void testGetCdsRanges_fivePrimeIncomplete() + public void testReverseComplementAllele() { - 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]); + StringBuilder sb = new StringBuilder(); + EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C + EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c + EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G + EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A + EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T + assertEquals("C,c,G,A,T", sb.toString()); + + sb = new StringBuilder(); + EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC- + EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation"); + EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation"); + assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString()); } + /** + * Test the method that computes the reverse complement of the alleles in a + * sequence_variant feature + */ @Test(groups = "Functional") - public void testIsTranscriptIdentifier() + public void testReverseComplementAlleles() { - 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")); + String alleles = "C,G,-TAC,HGMD_MUTATION,gac"; + SequenceFeature sf = new SequenceFeature("sequence_variant", alleles, + 1, 2, 0f, null); + sf.setValue("alleles", alleles); + sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c"); + + EnsemblSeqProxy.reverseComplementAlleles(sf); + String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc"; + // verify description is updated with reverse complement + assertEquals(revcomp, sf.getDescription()); + // verify alleles attribute is updated with reverse complement + assertEquals(revcomp, sf.getValue("alleles")); + // verify attributes string is updated with reverse complement + assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes()); } @Test(groups = "Functional") - public void testIsGeneIdentifier() + public void testSortFeatures() { - 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")); + SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null); + SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null); + SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null); + SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null); + SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 }; + + // sort by start position ascending (forward strand) + // sf2 and sf3 tie and should not be reordered by sorting + EnsemblSeqProxy.sortFeatures(sfs, true); + assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs); + + // sort by end position descending (reverse strand) + EnsemblSeqProxy.sortFeatures(sfs, false); + assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs); } -} \ No newline at end of file +}