uniprot.clj

; Amaturish Clojure version of uniprot mapping function by @sjcockell
; http://blog.fuzzierlogic.com/archives/339
; http://gist.github.com/329730
(ns uniprot
  (:use    clojure.contrib.duck-streams)
  (:import java.net.URLEncoder))

(defn- url-encode
  "Passes a String through java.net.URLEncoder.encode"
  [ param ] (URLEncoder/encode param))

(defn- map-to-query
  "Convert a map to a query string"
  [ a-map ]
  (let [ key-set (keys a-map) ]
    (reduce
      (fn [ accum curr-key ]
        (let [ key (if (keyword? curr-key) (name curr-key) curr-key) val (curr-key a-map) ]
          (str accum (url-encode key) "=" (url-encode val) (if (= curr-key (last key-set)) "" "&"))))
      "" key-set)))

(defn uniprot-mapping
  "Call the uniprot webservice and convert the given ID between the given Uniprot types"
  [ from to query ]
  (slurp* (str "http://www.uniprot.org/mapping?" (map-to-query { :from from :to to :query query :format "tab" }))))

(println (uniprot-mapping "ENSEMBL_ID" "ACC" "ENSG00000141510"))

uniprot.groovy

// Groovy version of uniprot mapping function by @sjcockell
// http://blog.fuzzierlogic.com/archives/339
// http://gist.github.com/329730

import java.net.URLEncoder as U

def uniprot_mapping( fromtype, totype, identifier ) {
  base   = 'http://www.uniprot.org'
  tool   = 'mapping'
  params = [ from   : fromtype,
             to     : totype,
             format : 'tab',
             query  : identifier ]
  params = params.collect { "${U.encode(it.key)}=${U.encode(it.value)}" }.join( '&' )
  new URL( "$base/$tool?$params" ).text
}

// For mapping example types, see:
// http://www.uniprot.org/faq/28#id_mapping_examples

println uniprot_mapping( 'ENSEMBL_ID', 'ACC', 'ENSG00000141510' )