/** * Create a GAFRecord from a LocatedSequenceFeature. * * @param lsf the LocatedSequenceFeature * @return the GAFRecord or null */ public static GAFRecord makeGAFRecord(SequenceFeature lsf) { String chrom = null; int chromStart = -1; int chromEnd = -1; String name = null; int score = 0; String strand = "."; if (lsf instanceof Chromosome) { return null; } else { Chromosome chr = lsf.getChromosome(); if (chr == null) { return null; } if (lsf.getSymbol() == null) { if (lsf.getPrimaryIdentifier() == null) { name = "(Unknown)"; } else { name = lsf.getPrimaryIdentifier(); } } else { name = lsf.getSymbol(); } name = name.replaceAll(" ", "_"); // replace white space in name to under score Location chrLocation = lsf.getChromosomeLocation(); if (chrLocation == null) { return null; } chromStart = chrLocation.getStart().intValue() - 1; // Interbase Coordinate chromEnd = chrLocation.getEnd().intValue(); if (chrLocation.getStrand() != null) { if ("1".equals(chrLocation.getStrand())) { strand = "+"; } else if ("-1".equals(chrLocation.getStrand())) { strand = "-"; } } } return new GAFRecord(chrom, chromStart, chromEnd, name, score, strand); }
public void testCreateSpanningLocations() throws Exception { Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class)); exon1.setId(new Integer(107)); Exon exon2 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class)); exon2.setId(new Integer(108)); Exon exon3 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class)); exon3.setId(new Integer(109)); Location exon1OnChr = createLocation(getChromosome(), exon1, "1", 51, 100, Location.class); exon1OnChr.setId(new Integer(1010)); Location exon2OnChr = createLocation(getChromosome(), exon2, "1", 201, 250, Location.class); exon2OnChr.setId(new Integer(1011)); Location exon3OnChr = createLocation(getChromosome(), exon3, "1", 201, 400, Location.class); exon3OnChr.setId(new Integer(1012)); Transcript trans1 = (Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class)); trans1.setId(new Integer(201)); Transcript trans2 = (Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class)); trans2.setId(new Integer(202)); Location trans2OnChr = createLocation(getChromosome(), trans2, "1", 61, 300, Location.class); Gene gene = (Gene) DynamicUtil.createObject(Collections.singleton(Gene.class)); gene.setId(new Integer(301)); exon1.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1}))); exon2.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1}))); // the location of exon3 should be ignored by createSpanningLocations() because trans2 // already has a location exon3.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans2}))); trans1.setGene(gene); trans2.setGene(gene); Set<InterMineObject> toStore = new HashSet<InterMineObject>( Arrays.asList( new InterMineObject[] { getChromosome(), gene, trans1, trans2, exon1, exon2, exon3, exon1OnChr, exon2OnChr, trans2OnChr })); for (InterMineObject imo : toStore) { osw.store(imo); } CalculateLocations cl = new CalculateLocations(osw); cl.createSpanningLocations("Transcript", "Exon", "exons"); cl.createSpanningLocations("Gene", "Transcript", "transcripts"); ObjectStore os = osw.getObjectStore(); Transcript resTrans1 = (Transcript) os.getObjectById(new Integer(201)); Assert.assertEquals(1, resTrans1.getLocations().size()); Location resTrans1Location = (Location) resTrans1.getLocations().iterator().next(); Assert.assertEquals(51, resTrans1Location.getStart().intValue()); Assert.assertEquals(250, resTrans1Location.getEnd().intValue()); Transcript resTrans2 = (Transcript) os.getObjectById(new Integer(202)); Assert.assertEquals(1, resTrans2.getLocations().size()); Location resTrans2Location = (Location) resTrans2.getLocations().iterator().next(); Assert.assertEquals(61, resTrans2Location.getStart().intValue()); Assert.assertEquals(300, resTrans2Location.getEnd().intValue()); Gene resGene = (Gene) os.getObjectById(new Integer(301)); Assert.assertEquals(1, resGene.getLocations().size()); Location resGeneLocation = (Location) resGene.getLocations().iterator().next(); Assert.assertEquals(51, resGeneLocation.getStart().intValue()); Assert.assertEquals(300, resGeneLocation.getEnd().intValue()); }