+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.datamodel.features.SequenceFeatures;
+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.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
{
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
private static final Object[][] allSeqs = new Object[][] {
{
new EnsemblProtein(),
+ "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
+ "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
+ "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
- + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
+ + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
+ // ? insertion added in ENSP00000288602.11, not in P15056
+ + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
+ // end insertion
+ + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
+ "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
+ "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
+ "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
- @DataProvider(name = "queries")
- public Object[][] createQueryData(Method m)
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
{
- return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
+ SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @Test(dataProvider = "queries")
- public void testIsValidReference(String query) throws Exception
+ @AfterClass(alwaysRun = true)
+ public void tearDown()
{
- EnsemblSequenceFetcher esq = new EnsemblProtein();
- Assert.assertTrue(esq.isValidReference(query),
- "Expected reference string " + query
- + " to be valid for regex "
- + esq.getAccessionValidator().toString());
+ SequenceOntologyFactory.setInstance(null);
}
@DataProvider(name = "ens_seqs")
}
@Test(dataProvider = "ens_seqs", suiteName = "live")
- public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
- throws Exception
+ public void testGetSequenceRecords(EnsemblSeqProxy 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,
+ FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
+ SequenceI[] expected = trueRes.getSeqsAsArray();
+ AlignmentI retrieved = proxy.getSequenceRecords(sq);
+
+ Assert.assertEquals(retrieved.getHeight(), expected.length,
"Different number of sequences retrieved for query " + sq);
- Alignment ral = new Alignment(sqs);
- for (SequenceI tr : trueSqs)
+
+ for (SequenceI tr : expected)
{
SequenceI[] rseq;
Assert.assertNotNull(
- rseq = ral.findSequenceMatch(tr.getName()),
+ rseq = retrieved.findSequenceMatch(tr.getName()),
"Couldn't find sequences matching expected sequence "
+ tr.getName());
Assert.assertEquals(rseq.length, 1,
"Sequences differ for " + tr.getName() + "\n" + "Exp:"
+ tr.getSequenceAsString() + "\n" + "Got:"
+ rseq[0].getSequenceAsString());
-
}
}
- @Test(suiteName = "live")
- public void testLiveCheckEnsembl()
+ @Test(groups = "Functional")
+ public void getGenomicRangesFromFeatures()
{
- 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<String> 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 the method that appends a single allele's reverse complement to a
+ * string buffer
*/
@Test(groups = "Functional")
- public void testComputePeptideVariants()
+ public void testReverseComplementAllele()
{
- String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
-
- /*
- * AGT codes for S - this is not included in the variants returned
- */
- List<String> 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());
+ 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());
- /*
- * 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());
+ 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());
+ }
- /*
- * 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());
+ /**
+ * 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");
- /*
- * 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());
+ 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());
+ }
- /*
- * 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());
+ @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);
+ List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
+ sf2, sf3, sf4 });
- /*
- * 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());
+ // sort by start position ascending (forward strand)
+ // sf2 and sf3 tie and should not be reordered by sorting
+ SequenceFeatures.sortFeatures(sfs, true);
+ assertSame(sfs.get(0), sf2);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf1);
+ assertSame(sfs.get(3), sf4);
- /*
- * 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());
+ // sort by end position descending (reverse strand)
+ SequenceFeatures.sortFeatures(sfs, false);
+ assertSame(sfs.get(0), sf1);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf2);
+ assertSame(sfs.get(3), sf4);
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff