X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fensembl%2FEnsemblSeqProxyTest.java;h=2d3948f80c9ede67d10e93b2c3a64eda5574886f;hb=3ea56b3730e5115138af264f5b5408104ebd9c20;hp=3a6bdc62a292d7a18d2414b415064e3025d23425;hpb=8504d9c48d03acee51397e5fefa3df660ad0a6cc;p=jalview.git diff --git a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java index 3a6bdc6..2d3948f 100644 --- a/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java +++ b/test/jalview/ext/ensembl/EnsemblSeqProxyTest.java @@ -1,40 +1,120 @@ 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.SequenceFeature; import jalview.datamodel.SequenceI; -import jalview.ext.ensembl.SeqFetcher; -import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType; 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.util.Arrays; 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 SeqFetcherTest + +public class EnsemblSeqProxyTest { - @Test - public void testCheckEnsembl() + 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(alwaysRun = true) + public void setUp() { - SeqFetcher sf = new SeqFetcher(); - sf.setTestEnsemblStatus(true); - sf.setTesting(true); - Assert.assertTrue(sf.isEnsemblAvailable()); - sf.setTestEnsemblStatus(false); - Assert.assertFalse(sf.isEnsemblAvailable()); + SequenceOntologyFactory.setInstance(new SequenceOntologyLite()); } - @Test(suiteName = "live") - public void testLiveCheckEnsembl() + @AfterClass(alwaysRun = true) + public void tearDown() { - SeqFetcher sf = new SeqFetcher(); - boolean isAvailable = sf.isEnsemblAvailable(); - System.out.println("Ensembl is " - + (isAvailable ? "UP!" : "DOWN ******************* BAD!")); + SequenceOntologyFactory.setInstance(null); } @DataProvider(name = "ens_seqs") @@ -44,58 +124,12 @@ public class SeqFetcherTest return allSeqs; } - public static Object[][] allSeqs = new Object[][] - { - { - EnsemblSeqType.CDS, - "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" } }; - @Test(dataProvider = "ens_seqs", suiteName = "live") - public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq) + public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq) throws Exception { - SeqFetcher sf = new SeqFetcher(); - FileParse fp = sf.getSequenceReader(type, Arrays.asList(new String[] + FileParse fp = proxy.getSequenceReader(Arrays + .asList(new String[] { sq })); SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray(); FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE); @@ -118,6 +152,105 @@ public class SeqFetcherTest "Sequences differ for " + tr.getName() + "\n" + "Exp:" + tr.getSequenceAsString() + "\n" + "Got:" + rseq[0].getSequenceAsString()); + } } + + @Test(groups = "Functional") + public void getGenomicRangesFromFeatures() + { + + } + + @Test(groups = "Functional") + public void testIsTranscriptIdentifier() + { + EnsemblSeqProxy testee = new EnsemblGene(); + assertFalse(testee.isTranscriptIdentifier(null)); + assertFalse(testee.isTranscriptIdentifier("")); + assertFalse(testee.isTranscriptIdentifier("ENSG00000012345")); + assertTrue(testee.isTranscriptIdentifier("ENST00000012345")); + assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345")); + assertFalse(testee.isTranscriptIdentifier("enst00000012345")); + assertFalse(testee.isTranscriptIdentifier("ENST000000123456")); + assertFalse(testee.isTranscriptIdentifier("ENST0000001234")); + } + + @Test(groups = "Functional") + public void testIsGeneIdentifier() + { + EnsemblSeqProxy testee = new EnsemblGene(); + assertFalse(testee.isGeneIdentifier(null)); + assertFalse(testee.isGeneIdentifier("")); + assertFalse(testee.isGeneIdentifier("ENST00000012345")); + assertTrue(testee.isGeneIdentifier("ENSG00000012345")); + assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345")); + assertFalse(testee.isGeneIdentifier("ensg00000012345")); + assertFalse(testee.isGeneIdentifier("ENSG000000123456")); + assertFalse(testee.isGeneIdentifier("ENSG0000001234")); + } + + /** + * Test the method that appends a single allele's reverse complement to a + * string buffer + */ + @Test(groups = "Functional") + public void testReverseComplementAllele() + { + 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 testReverseComplementAlleles() + { + 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 testSortFeatures() + { + 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