Examples with Taxon ubic.gemma.model.genome.Taxon used on opensource projects

Example 16 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class GoldenPathQueryTest method setUp.

@Override
protected void setUp() throws Exception {
    super.setUp();
    Taxon t = Taxon.Factory.newInstance();
    t.setCommonName("human");
    t.setIsGenesUsable(true);
    t.setIsSpecies(true);
    try {
        String databaseHost = Settings.getString("gemma.testdb.host");
        String databaseUser = Settings.getString("gemma.testdb.user");
        String databasePassword = Settings.getString("gemma.testdb.password");
        queryer = new GoldenPathQuery(Settings.getString("gemma.goldenpath.db.human"), databaseHost, databaseUser, databasePassword);
        this.hasDb = true;
    } catch (Exception e) {
        this.hasDb = false;
    }
}

Example 17 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class SimpleExpressionDataLoaderServiceTest method testLoad.

@Test
public final void testLoad() throws Exception {
    Taxon taxon = this.getTaxon("mouse");
    SimpleExpressionExperimentMetaData metaData = new SimpleExpressionExperimentMetaData();
    ArrayDesign ad = ArrayDesign.Factory.newInstance();
    ad.setShortName(RandomStringUtils.randomAlphabetic(5));
    ad.setName(RandomStringUtils.randomAlphabetic(5));
    ad.setPrimaryTaxon(taxon);
    ad.setTechnologyType(TechnologyType.ONECOLOR);
    Collection<ArrayDesign> ads = new HashSet<>();
    ads.add(ad);
    metaData.setArrayDesigns(ads);
    metaData.setTaxon(taxon);
    metaData.setShortName(RandomStringUtils.randomAlphabetic(5));
    metaData.setName(RandomStringUtils.randomAlphabetic(5));
    metaData.setDescription("Simple expression data loader service test - load");
    metaData.setQuantitationTypeName("testing");
    metaData.setGeneralType(GeneralType.QUANTITATIVE);
    metaData.setScale(ScaleType.LOG2);
    metaData.setType(StandardQuantitationType.AMOUNT);
    metaData.setIsRatio(true);
    try (InputStream data = this.getClass().getResourceAsStream("/data/testdata.txt")) {
        ee = service.create(metaData, data);
    }
    ee = eeService.thaw(ee);
    assertNotNull(ee);
    assertEquals(30, ee.getRawExpressionDataVectors().size());
    assertEquals(12, ee.getBioAssays().size());
}

Example 18 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class StringBiomartProteinConverterTest method setUp.

@Before
public void setUp() {
    String fileNameBiomartmouse = "/data/loader/protein/biomart/biomartmmusculusShort.txt";
    URL fileNameBiomartmouseURL = this.getClass().getResource(fileNameBiomartmouse);
    File taxonBiomartFile = new File(fileNameBiomartmouseURL.getFile());
    Taxon taxon = Taxon.Factory.newInstance();
    taxon.setIsGenesUsable(true);
    taxon.setNcbiId(10090);
    taxon.setScientificName("Mus musculus");
    taxon.setIsSpecies(true);
    taxa.add(taxon);
    try {
        BiomartEnsemblNcbiObjectGenerator biomartEnsemblNcbiObjectGenerator = new BiomartEnsemblNcbiObjectGenerator();
        biomartEnsemblNcbiObjectGenerator.setBioMartFileName(taxonBiomartFile);
        Map<String, Ensembl2NcbiValueObject> map = biomartEnsemblNcbiObjectGenerator.generate(taxa);
        stringBiomartProteinConverter = new StringProteinProteinInteractionConverter(map);
    } catch (Exception e) {
        e.printStackTrace();
        fail();
    }
    stringProteinProteinInteractionOne = new StringProteinProteinInteraction("ENSMUSP00000111623", "ENSMUSP00000100396");
    StringProteinProteinInteraction stringProteinProteinInteractionTwo = new StringProteinProteinInteraction("ENSMUSP00000100395", "ENSMUSP00000100396");
    StringProteinProteinInteraction stringProteinProteinInteractionThree = new StringProteinProteinInteraction("ENSMUSP00000100407", "ENSMUSP00000100395");
    // add them to array
    stringProteinProteinInteractions.add(stringProteinProteinInteractionOne);
    stringProteinProteinInteractions.add(stringProteinProteinInteractionTwo);
    stringProteinProteinInteractions.add(stringProteinProteinInteractionThree);
}

Example 19 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class DatabaseViewGeneratorImpl method generateDatasetView.

private void generateDatasetView(Integer limit, Collection<ExpressionExperiment> experiments) throws IOException {
    DatabaseViewGeneratorImpl.log.info("Generating dataset summary view");
    /*
         * Get handle to output file
         */
    File file = this.getViewFile(DatabaseViewGeneratorImpl.DATASET_SUMMARY_VIEW_BASENAME);
    DatabaseViewGeneratorImpl.log.info("Writing to " + file);
    try (Writer writer = new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(file)))) {
        writer.write("GemmaDsId\tSource\tSourceAccession\tShortName\tName\tDescription\ttaxon\tManufacturer\n");
        /*
             * Print out their names etc.
             */
        int i = 0;
        for (ExpressionExperiment ee : experiments) {
            ee = expressionExperimentService.thawLite(ee);
            DatabaseViewGeneratorImpl.log.info("Processing: " + ee.getShortName());
            String acc = "";
            String source = "";
            if (ee.getAccession() != null && ee.getAccession().getAccession() != null) {
                acc = ee.getAccession().getAccession();
                source = ee.getAccession().getExternalDatabase().getName();
            }
            Long gemmaId = ee.getId();
            String shortName = ee.getShortName();
            String name = ee.getName();
            String description = ee.getDescription();
            description = StringUtils.replaceChars(description, '\t', ' ');
            description = StringUtils.replaceChars(description, '\n', ' ');
            description = StringUtils.replaceChars(description, '\r', ' ');
            Taxon taxon = expressionExperimentService.getTaxon(ee);
            if (taxon == null)
                continue;
            Collection<ArrayDesign> ads = expressionExperimentService.getArrayDesignsUsed(ee);
            StringBuilder manufacturers = new StringBuilder();
            // TODO could cache the arrayDesigns to make faster, thawing ad is time consuming
            for (ArrayDesign ad : ads) {
                ad = arrayDesignService.thawLite(ad);
                if (ad.getDesignProvider() == null) {
                    DatabaseViewGeneratorImpl.log.debug("Array Design: " + ad.getShortName() + " has no design provoider assoicated with it. Skipping");
                    continue;
                }
                manufacturers.append(ad.getDesignProvider().getName()).append(",");
            }
            writer.write(String.format("%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", gemmaId, source, acc, shortName, name, description, taxon.getCommonName(), StringUtils.removeEnd(manufacturers.toString(), ",")));
            if (limit != null && (limit > 0 && ++i > limit))
                break;
        }
    }
}

Example 20 with Taxon

use of ubic.gemma.model.genome.Taxon in project Gemma by PavlidisLab.

the class RepeatScan method repeatScan.

/**
 * Run repeatmasker on the sequences. The sequence will be updated with the masked (lower-case) sequences and the
 * fraction of masked bases will be filled in.
 *
 * @param sequences sequences
 * @return sequences that had repeats.
 */
public Collection<BioSequence> repeatScan(Collection<BioSequence> sequences) {
    try {
        if (sequences.size() == 0) {
            RepeatScan.log.warn("No sequences to test");
            return sequences;
        }
        File querySequenceFile = File.createTempFile("repmask", ".fa");
        SequenceWriter.writeSequencesToFile(sequences, querySequenceFile);
        Taxon taxon = sequences.iterator().next().getTaxon();
        this.execRepeatMasker(querySequenceFile, taxon);
        final String outputSequencePath = querySequenceFile.getParent() + File.separatorChar + querySequenceFile.getName() + ".masked";
        // final String outputScorePath = querySequenceFile.getParent() + File.separatorChar
        // + querySequenceFile.getName() + ".masked";
        File output = new File(outputSequencePath);
        if (!output.exists()) {
            this.handleNoOutputCondition(querySequenceFile, outputSequencePath);
            return new HashSet<>();
        }
        return this.processRepeatMaskerOutput(sequences, outputSequencePath);
    } catch (IOException e) {
        throw new RuntimeException(e);
    }
}