Fetching Data Files With BioGroovy

It’s often useful to fetch data from a web service and cache it in your local directory. This cuts down on the amount of traffic between your machine and the web service you’re invoking, and it makes unit testing your code easier. In this example, we’ll fetch data for 3 genes and write it out as XML files.

 import org.biogroovy.io.eutils.EntrezGeneSlurper;
 import org.biogroovy.models.Gene;
 @Grab(group='org.biogroovy', module='biogroovy', version='1.1')

 EntrezGeneSlurper slurper = new EntrezGeneSlurper();
 File dir = new File(System.getProperty('user.home'), 'biogroovy_test_files');
 slurper.fetchAsFile(dir, "675,1034,133")

 // double check that the files were written out
 dir.list().each{println it}

About aspenbio

I write software for scientists. I'm interested in Java/Groovy/Grails, the Semantic Web and Cancer Biology.
This entry was posted in Bioinformatics, Informatics and tagged . Bookmark the permalink.

2 Responses to Fetching Data Files With BioGroovy

  1. Paolo says:

    Is BioGroovy available on GitHub?

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