package jalview.ext.ensembl;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.AlignmentUtils;
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 java.lang.reflect.Method;
import java.net.MalformedURLException;
import java.net.URL;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
: "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()
+ public void getGenomicRangesFromFeatures()
{
- 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()
+ 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"));
}
- /**
- * 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()
+ public void testIsGeneIdentifier()
{
- 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]);
+ 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"));
}
}
\ No newline at end of file