Ensembl4J

REST and FTP utils for the ENSEMBL REST API at http://rest.ensembl.org/

Example

Retrieve gene location

GeneLocation location = EnsemblUtils.getInstance()
                                    .findSpecies("human")
                                    .findGene("BHMT")
                                    .getLocation();

Retrieve variant details

VariantConsequence consequence = EnsemblUtils.getInstance()
                                             .getHuman();
                                             .findVariantDetail("rs682985")
                                             .getConsequence();		

Example with local cache (folder /cache)

EnsemblUtils.getInstance()
            .usingLocalCache()
            .getHuman();

REST

Sequences sequence = EnsemblRESTUtils.getInstance()
                                     .getCodingDNASequence("ENSG00000145692");

FTP

EnsemblFTPUtils.load()
               .withLocalDirectoryCache()
               .variationVCFFiles()
               .current()
               .forSpecies(species)
               .forChromosomes()
               .flatMap(resource -> resource.asParsedVCF()                                                      
                                            .getRecords())

Maven Snapshots

<dependency>
  <groupId>org.omnaest.genomics</groupId>
  <artifactId>Ensembl4J</artifactId>
  <version>0.0.1-SNAPSHOT</version>
</dependency>

<repositories>
	<repository>
		<id>ossrh</id>
		<url>https://oss.sonatype.org/content/repositories/snapshots</url>
		<snapshots>
			<enabled>true</enabled>
		</snapshots>
	</repository>
</repositories>