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Clojure API for Ensembl data access via JEnsembl
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README.md

bio.ensembl

An experimental Clojure API wrapping the excellent Java Ensembl library JEnsembl, http://jensembl.sourceforge.net/.

This is alpha software: it is incomplete and the API is subject to change.

Please drop me a line if you would like to help with this effort or have suggestions for how the API should shape up.

Usage

(use 'org.bioclojure.bio.ensembl.core)

(def ensreg (registry :ensembldb))

(with-registry ensreg
  (list-species)
  (chromosome "human" "20")
  (gene "human" "ENSG00000153551"))

Alternatively, set the registry for your session:

(set-registry! ensreg)

(list-species)

(list-species :binomial)

(chromosome "human" "20")

(list-chromosomes "human")

(genes-on-region "human" "20" 1 100000)

(genes-on-region (chromosome "human" "20") 1 100000)

License

Copyright (C) 2012 Ray Miller ray@1729.org.uk.

Distributed under the Eclipse Public License, the same as Clojure.

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