uniprot.clj

; Amaturish Clojure version of uniprot mapping function by @sjcockell
; Improved a bit by David Nolen
; http://blog.fuzzierlogic.com/archives/339
; http://gist.github.com/329730
(ns uniprot
  (:use [clojure.contrib.duck-streams])
  (:require [clojure.contrib.str-utils2 :as s])
  (:import java.net.URLEncoder))

(defn- url-encode [param] (URLEncoder/encode param))

(defn- map-to-query [amap] 
  (s/join "&" (map (fn [[k v]] (str (url-encode (name k)) "=" (url-encode v))) amap)))

(defn uniprot-mapping
  [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' )