tanglingfung/ensembl-rest-client

Java client for the Ensembl REST API.

ensembl-rest-client

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");