package jalview.ext.ensembl;
+import static org.testng.AssertJUnit.assertEquals;
+
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
import jalview.io.AppletFormatAdapter;
import jalview.io.FastaFile;
import jalview.io.FileParse;
-import jalview.util.DBRefUtils;
+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
{
- @Test
- public void testCheckEnsembl()
- {
- SeqFetcher sf = new SeqFetcher();
- sf.setTestEnsemblStatus(true);
- sf.setTesting(true);
- Assert.assertTrue(sf.isEnsemblAvailable());
- sf.setTestEnsemblStatus(false);
- Assert.assertFalse(sf.isEnsemblAvailable());
- }
-
- @Test(suiteName = "live")
- public void testLiveCheckEnsembl()
- {
- SeqFetcher sf = new SeqFetcher();
- boolean isAvailable = sf.isEnsemblAvailable();
- System.out.println("Ensembl is "
- + (isAvailable ? "UP!" : "DOWN ******************* BAD!"));
- }
-
- @DataProvider(name = "ens_seqs")
- public Object[][] createData(Method m)
- {
- System.out.println(m.getName());
- return allSeqs;
- }
-
- public static Object[][] allSeqs = new Object[][]
- {
+ private static final Object[][] allSeqs = new Object[][] {
{
- EnsemblSeqType.PROTEIN,
+ new EnsemblProtein(),
"CCDS5863.1",
">CCDS5863.1\n"
+ "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
{
- EnsemblSeqType.TRANSCRIPT,
+ new EnsemblCdna(),
"CCDS5863.1",
">CCDS5863.1\n"
+ "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
+ "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
+ "GGTGCGTTTCCTGTCCACTGA\n" },
{
- EnsemblSeqType.PROTEIN,
+ new EnsemblProtein(),
"ENSP00000288602",
">ENSP00000288602\n"
+ "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
+ "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
+ @BeforeClass
+ public void setUp()
+ {
+ SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+ }
+
+ @AfterClass
+ public void tearDown()
+ {
+ SequenceOntologyFactory.setInstance(null);
+ }
+
+ @DataProvider(name = "queries")
+ public Object[][] createQueryData(Method m)
+ {
+ return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
+ }
+
+ @Test(dataProvider = "queries")
+ public void testIsValidReference(String query) throws Exception
+ {
+ EnsemblSequenceFetcher esq = new EnsemblProtein();
+ Assert.assertTrue(esq.isValidReference(query),
+ "Expected reference string " + query
+ + " to be valid for regex "
+ + esq.getAccessionValidator().toString());
+ }
+
+ @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(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);
"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<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(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<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());
+
+ /*
+ * 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<int[]> ranges = new ArrayList<int[]>();
+ 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);
+ ds.addSequenceFeature(sf);
+ // CDS for dna 13-15
+ sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = new ArrayList<int[]>();
+ 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]);
+ }
}
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git://source.jalview.org / jalview.git / blobdiff