Fetching Gene Cartoon With BioGroovy

EntrezGene provides a gene cartoon which shows the coding regions and untranslated regions for a gene. This informative cartoon shows the mRNA and the resulting protein for a particular gene. In this BioGroovy example, I’ll show you how to fetch the cartoon.

Suppose in this case, that we have a list of EntrezGene IDs and we want to fetch
the cartoon for each ID.

def list = [123, 456, 789]
list.each(){
def eUrl = “http://www.ncbi.nlm.nih.gov/entrez/sutils/geneprod.fcgi?geneid=${it}”;
println “Fetching ${it}”

def file = new FileOutputStream(new File(“/Users/markfortner/Documents/pancreatic_cancer/data/${it}.gif”));
def out = new BufferedOutputStream(file)
out << new URL(eUrl).openStream()
out.close()
}

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About Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
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