Java client for the Ensembl REST API.
###Hacking ensembl-rest-client
Install
- JDK 1.6 or later, http://openjdk.java.net/
- Apache Maven 3.0.5 or later, http://maven.apache.org/
To build
$ mvn install
To assemble example
$ cd example
$ mvn assembly:assembly
To run example
$ java -jar target/ensembl-rest-client-example-1.1-SNAPSHOT-jar-with-dependencies.jar
features, 7:140424943-140425943
rs185077298 C T 7 140424949 140424949 1
rs188275729 G A 7 140424968 140424968 1
rs180985059 C G 7 140424979 140424979 1
rs55702309 A T 7 140425000 140425000 1
rs139404728 A G 7 140425101 140425101 1
rs184694572 A G 7 140425102 140425102 1
rs145149263 AAG - 7 140425282 140425284 1
rs189717101 A G 7 140425377 140425377 1
rs181357222 A G 7 140425385 140425385 1
rs144129600 G A 7 140425388 140425388 1
rs186773220 A G 7 140425423 140425423 1
rs188964443 G C 7 140425441 140425441 1
rs34603310 A - 7 140425500 140425500 1
rs78422198 AA - 7 140425500 140425501 1
rs78068602 A C 7 140425511 140425511 1
rs80171608 C A 7 140425514 140425514 1
rs75839948 G C 7 140425720 140425720 1
lookup, ENSG00000157764
ENSG00000157764 homo_sapiens Gene core 7 140424943 140624564 -1
id search, COSM476
COSM476 7 140453136 140453136 1 ENSG00000157764 ENST00000288602 A/T missense_variant
COSM476 7 140453136 140453136 1 ENSG00000157764 ENST00000479537 A/T missense_variant
COSM476 7 140453136 140453136 1 ENSG00000157764 ENST00000479537 A/T NMD_transcript_variant
COSM476 7 140453136 140453136 1 ENSG00000157764 ENST00000496384 A/T missense_variant
COSM476 7 140453136 140453136 1 ENSG00000157764 ENST00000497784 A/T NMD_transcript_variant
COSM476 7 140453136 140453136 1 ENSG00000157764 ENST00000497784 A/T 3_prime_UTR_variant
region search, 9:22125503-22125502:1
null 9 22125503 22125502 1 ENSG00000240498 ENST00000585267 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000580576 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000428597 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000584816 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000584020 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000577551 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000584637 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000581051 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000582072 -/C downstream_gene_variant
null 9 22125503 22125502 1 ENSG00000240498 ENST00000422420 -/C downstream_gene_variant
###Using ensembl-rest-client
Add the following dependency declaration to your pom.xml
<dependency>
<groupId>com.github.heuermh.ensemblrestclient</groupId>
<artifactId>ensembl-rest-client</artifactId>
<version>1.1-SNAPSHOT</version>
</dependency>E.g.
// create an injector
Injector injector = Guice.createInjector(new EnsemblRestClientModule());
// feature service
FeatureService featureService = injector.getInstance(FeatureService.class);
Variation rs185077298 = featureService.variationFeature("human", "rs185077298");
List<Variation> chr7 = featureService.variationFeatures("human", "7:140424943-140425943");
// lookup service
LookupService lookupService = injector.getInstance(LookupService.class);
Lookup ensg00000157764 = lookupService.lookup("human", "ENSG00000157764");
// variation service
VariationService variationService = injector.getInstance(VariationService.class);
VariationConsequences cosm476 = variationService.consequences("human", "COSM476");
VariationConsequences chr9 = variationService.consequences("human", "9:22125503-22125502:1", "C");